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- PDB-7mbo: FACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE I... -

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Basic information

Entry
Database: PDB / ID: 7mbo
TitleFACTOR XIA (PICHIA PASTORIS; C500S [C122S]) IN COMPLEX WITH THE INHIBITOR Milvexian (BMS-986177), IUPAC NAME:(6R,10S)-10-{4-[5-chloro-2-(4-chloro-1H-1,2,3-triazol-1-yl)phenyl]-6- oxopyrimidin-1(6H)-yl}-1-(difluoromethyl)-6-methyl-1,4,7,8,9,10-hexahydro-15,11- (metheno)pyrazolo[4,3-b][1,7]diazacyclotetradecin-5(6H)-one
ComponentsCoagulation factor XIa light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / COAGULATION FACTOR / SYNTETHIC INHIBITOR / BLOOD / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Milvexian / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.924 Å
AuthorsSheriff, S.
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Discovery of Milvexian, a High-Affinity, Orally Bioavailable Inhibitor of Factor XIa in Clinical Studies for Antithrombotic Therapy.
Authors: Dilger, A.K. / Pabbisetty, K.B. / Corte, J.R. / De Lucca, I. / Fang, T. / Yang, W. / Pinto, D.J.P. / Wang, Y. / Zhu, Y. / Mathur, A. / Li, J. / Hou, X. / Smith, D. / Sun, D. / Zhang, H. / ...Authors: Dilger, A.K. / Pabbisetty, K.B. / Corte, J.R. / De Lucca, I. / Fang, T. / Yang, W. / Pinto, D.J.P. / Wang, Y. / Zhu, Y. / Mathur, A. / Li, J. / Hou, X. / Smith, D. / Sun, D. / Zhang, H. / Krishnananthan, S. / Wu, D.R. / Myers Jr., J.E. / Sheriff, S. / Rossi, K.A. / Chacko, S. / Zheng, J.J. / Galella, M.A. / Ziemba, T. / Dierks, E.A. / Bozarth, J.M. / Wu, Y. / Crain, E. / Wong, P.C. / Luettgen, J.M. / Wexler, R.R. / Ewing, W.R.
#1: Journal: J. Med. Chem. / Year: 2014
Title: Tetrahydroquinoline derivatives as potent and selective factor XIa inhibitors.
Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. ...Authors: Quan, M.L. / Wong, P.C. / Wang, C. / Woerner, F. / Smallheer, J.M. / Barbera, F.A. / Bozarth, J.M. / Brown, R.L. / Harpel, M.R. / Luettgen, J.M. / Morin, P.E. / Peterson, T. / Ramamurthy, V. / Rendina, A.R. / Rossi, K.A. / Watson, C.A. / Wei, A. / Zhang, G. / Seiffert, D. / Wexler, R.R.
#2: Journal: J. Med. Chem. / Year: 2014
Title: Phenylimidazoles as potent and selective inhibitors of coagulation factor XIa with in vivo antithrombotic activity.
Authors: Hangeland, J.J. / Friends, T.J. / Rossi, K.A. / Smallheer, J.M. / Wang, C. / Sun, Z. / Corte, J.R. / Fang, T. / Wong, P.C. / Rendina, A.R. / Barbera, F.A. / Bozarth, J.M. / Luettgen, J.M. / ...Authors: Hangeland, J.J. / Friends, T.J. / Rossi, K.A. / Smallheer, J.M. / Wang, C. / Sun, Z. / Corte, J.R. / Fang, T. / Wong, P.C. / Rendina, A.R. / Barbera, F.A. / Bozarth, J.M. / Luettgen, J.M. / Watson, C.A. / Zhang, G. / Wei, A. / Ramamurthy, V. / Morin, P.E. / Bisacchi, G.S. / Subramaniam, S. / Arunachalam, P. / Mathur, A. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L.
#3: Journal: Bioorg. Med. Chem. Lett. / Year: 2015
Title: Pyridine and pyridinone-based factor XIa inhibitors.
Authors: Corte, J.R. / Fang, T. / Hangeland, J.J. / Friends, T.J. / Rendina, A.R. / Luettgen, J.M. / Bozarth, J.M. / Barbera, F.A. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Morin, P.E. / Seiffert, D. ...Authors: Corte, J.R. / Fang, T. / Hangeland, J.J. / Friends, T.J. / Rendina, A.R. / Luettgen, J.M. / Bozarth, J.M. / Barbera, F.A. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Morin, P.E. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L.
#4: Journal: Bioorg. Med. Chem. Lett. / Year: 2015
Title: Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
Authors: Pinto, D.J. / Smallheer, J.M. / Corte, J.R. / Austin, E.J. / Wang, C. / Fang, T. / Smith II, L.M. / Rossi, K.A. / Rendina, A.R. / Bozarth, J.M. / Zhang, G. / Wei, A. / Ramamurthy, V. / ...Authors: Pinto, D.J. / Smallheer, J.M. / Corte, J.R. / Austin, E.J. / Wang, C. / Fang, T. / Smith II, L.M. / Rossi, K.A. / Rendina, A.R. / Bozarth, J.M. / Zhang, G. / Wei, A. / Ramamurthy, V. / Sheriff, S. / Myers Jr., J.E. / Morin, P.E. / Luettgen, J.M. / Seiffert, D.A. / Quan, M.L. / Wexler, R.R.
#5: Journal: ACS Med Chem Lett / Year: 2015
Title: Discovery of a Potent Parenterally Administered Factor XIa Inhibitor with Hydroxyquinolin-2(1H)-one as the P2' Moiety.
Authors: Hu, Z. / Wong, P.C. / Gilligan, P.J. / Han, W. / Pabbisetty, K.B. / Bozarth, J.M. / Crain, E.J. / Harper, T. / Luettgen, J.M. / Myers Jr., J.E. / Ramamurthy, V. / Rossi, K.A. / Sheriff, S. / ...Authors: Hu, Z. / Wong, P.C. / Gilligan, P.J. / Han, W. / Pabbisetty, K.B. / Bozarth, J.M. / Crain, E.J. / Harper, T. / Luettgen, J.M. / Myers Jr., J.E. / Ramamurthy, V. / Rossi, K.A. / Sheriff, S. / Watson, C.A. / Wei, A. / Zheng, J.J. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L.
#6: Journal: Bioorg. Med. Chem. Lett. / Year: 2016
Title: Novel phenylalanine derived diamides as Factor XIa inhibitors.
Authors: Smith II, L.M. / Orwat, M.J. / Hu, Z. / Han, W. / Wang, C. / Rossi, K.A. / Gilligan, P.J. / Pabbisetty, K.B. / Osuna, H. / Corte, J.R. / Rendina, A.R. / Luettgen, J.M. / Wong, P.C. / ...Authors: Smith II, L.M. / Orwat, M.J. / Hu, Z. / Han, W. / Wang, C. / Rossi, K.A. / Gilligan, P.J. / Pabbisetty, K.B. / Osuna, H. / Corte, J.R. / Rendina, A.R. / Luettgen, J.M. / Wong, P.C. / Narayanan, R. / Harper, T.W. / Bozarth, J.M. / Crain, E.J. / Wei, A. / Ramamurthy, V. / Morin, P.E. / Xin, B. / Zheng, J. / Seiffert, D.A. / Quan, M.L. / Lam, P.Y.S. / Wexler, R.R. / Pinto, D.J.P.
#7: Journal: Bioorg. Med. Chem. / Year: 2016
Title: Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group.
Authors: Corte, J.R. / Fang, T. / Pinto, D.J. / Orwat, M.J. / Rendina, A.R. / Luettgen, J.M. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Myers Jr., J.E. / Sheriff, S. / Narayanan, R. / Harper, T.W. / ...Authors: Corte, J.R. / Fang, T. / Pinto, D.J. / Orwat, M.J. / Rendina, A.R. / Luettgen, J.M. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Myers Jr., J.E. / Sheriff, S. / Narayanan, R. / Harper, T.W. / Zheng, J.J. / Li, Y.X. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L.
#8: Journal: J. Med. Chem. / Year: 2017
Title: Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker.
Authors: Corte, J.R. / Fang, T. / Osuna, H. / Pinto, D.J. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. / Luettgen, J.M. / Seiffert, D. ...Authors: Corte, J.R. / Fang, T. / Osuna, H. / Pinto, D.J. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. / Luettgen, J.M. / Seiffert, D.A. / Decicco, C.P. / Wexler, R.R. / Quan, M.L.
#9: Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency.
Authors: Corte, J.R. / Yang, W. / Fang, T. / Wang, Y. / Osuna, H. / Lai, A. / Ewing, W.R. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. ...Authors: Corte, J.R. / Yang, W. / Fang, T. / Wang, Y. / Osuna, H. / Lai, A. / Ewing, W.R. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. / Luettgen, J.M. / Seiffert, D.A. / Quan, M.L. / Wexler, R.R. / Lam, P.Y.S.
#10: Journal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: Macrocyclic factor XIa inhibitors.
Authors: Wang, C. / Corte, J.R. / Rossi, K.A. / Bozarth, J.M. / Wu, Y. / Sheriff, S. / Myers Jr., J.E. / Luettgen, J.M. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L.
#11: Journal: J. Med. Chem. / Year: 2017
Title: Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).
Authors: Pinto, D.J.P. / Orwat, M.J. / Smith II, L.M. / Quan, M.L. / Lam, P.Y.S. / Rossi, K.A. / Apedo, A. / Bozarth, J.M. / Wu, Y. / Zheng, J.J. / Xin, B. / Toussaint, N. / Stetsko, P. / ...Authors: Pinto, D.J.P. / Orwat, M.J. / Smith II, L.M. / Quan, M.L. / Lam, P.Y.S. / Rossi, K.A. / Apedo, A. / Bozarth, J.M. / Wu, Y. / Zheng, J.J. / Xin, B. / Toussaint, N. / Stetsko, P. / Gudmundsson, O. / Maxwell, B. / Crain, E.J. / Wong, P.C. / Lou, Z. / Harper, T.W. / Chacko, S.A. / Myers Jr., J.E. / Sheriff, S. / Zhang, H. / Hou, X. / Mathur, A. / Seiffert, D.A. / Wexler, R.R. / Luettgen, J.M. / Ewing, W.R.
#12: Journal: Bioorg. Med. Chem. Lett. / Year: 2019
Title: Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.
Authors: Clark, C.G. / Rossi, K.A. / Corte, J.R. / Fang, T. / Smallheer, J.M. / De Lucca, I. / Nirschl, D.S. / Orwat, M.J. / Pinto, D.J.P. / Hu, Z. / Wang, Y. / Yang, W. / Jeon, Y. / Ewing, W.R. / ...Authors: Clark, C.G. / Rossi, K.A. / Corte, J.R. / Fang, T. / Smallheer, J.M. / De Lucca, I. / Nirschl, D.S. / Orwat, M.J. / Pinto, D.J.P. / Hu, Z. / Wang, Y. / Yang, W. / Jeon, Y. / Ewing, W.R. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Bozarth, J.M. / Wu, Y. / Rendina, A. / Harper, T. / Zheng, J. / Xin, B. / Xiang, Q. / Leuttgen, J.M. / Seiffert, D.A. / Wexler, R.R. / Lam, P.Y.S.
#13: Journal: J. Med. Chem. / Year: 2019
Title: Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.
Authors: Corte, J.R. / Pinto, D.J.P. / Fang, T. / Osuna, H. / Yang, W. / Wang, Y. / Lai, A. / Clark, C.G. / Sun, J.-H. / Rampulla, R. / Mathur, A. / Kaspady, M. / Neithnadka, P.R. / Li, Y.-X.C. / ...Authors: Corte, J.R. / Pinto, D.J.P. / Fang, T. / Osuna, H. / Yang, W. / Wang, Y. / Lai, A. / Clark, C.G. / Sun, J.-H. / Rampulla, R. / Mathur, A. / Kaspady, M. / Neithnadka, P.R. / Li, Y.-X.C. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Harper, T.W. / Huang, C. / Zheng, J.J. / Bozarth, J.M. / Wu, Y. / Wong, P.C. / Crain, E.J. / Seiffert, D.A. / Luettgen, J.M. / Lam, P.Y. / Wexler, R.R. / Ewing, W.R.
#14: Journal: Bioorg. Med. Chem. Lett. / Year: 2020
Title: Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa.
Authors: Fang, T. / Corte, J.R. / Gilligan, P.J. / Jeon, Y. / Osuna, H. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. / Luettgen, J.M. ...Authors: Fang, T. / Corte, J.R. / Gilligan, P.J. / Jeon, Y. / Osuna, H. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Harper, T.W. / Bozarth, J.M. / Wu, Y. / Luettgen, J.M. / Seiffert, D.A. / Wexler, R.R. / Lam, P.Y.S.
#15: Journal: J. Med. Chem. / Year: 2020
Title: Discovery of a High Affinity, Orally Bioavailable Macrocyclic FXIa Inhibitor with Antithrombotic Activity in Preclinical Species
Authors: Yang, W. / Wang, Y. / Lai, A. / Clark, C.G. / Corte, J.R. / Fang, T. / Gilligan, P.J. / Jeon, Y. / Pabbisetty, K.B. / Rampulla, R.A. / Mathur, A. / Kaspady, M. / Neithnadka, P.R. / Arumugam, ...Authors: Yang, W. / Wang, Y. / Lai, A. / Clark, C.G. / Corte, J.R. / Fang, T. / Gilligan, P.J. / Jeon, Y. / Pabbisetty, K.B. / Rampulla, R.A. / Mathur, A. / Kaspady, M. / Neithnadka, P.R. / Arumugam, A. / Raju, S. / Rossi, K.A. / Myers Jr., J.E. / Sheriff, S. / Lou, Z. / Zheng, J.J. / Chacko, S.A. / Huang, C.S. / Bozarth, J.M. / Wu, Y. / Crain, E.J. / Wong, P.C. / Seiffert, D.A. / Luettgen, J.M. / Lam, P.Y.S. / Wexler, R.R. / Ewing, W.R.
History
DepositionApr 1, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 29, 2021Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half_anomalous / _reflns.pdbx_absDiff_over_sigma_anomalous ..._reflns.pdbx_CC_half_anomalous / _reflns.pdbx_absDiff_over_sigma_anomalous / _reflns.pdbx_aniso_diffraction_limit_1 / _reflns.pdbx_aniso_diffraction_limit_2 / _reflns.pdbx_aniso_diffraction_limit_3 / _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[1] / _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[2] / _reflns.pdbx_aniso_diffraction_limit_axis_1_ortho[3] / _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[1] / _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[2] / _reflns.pdbx_aniso_diffraction_limit_axis_2_ortho[3] / _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[1] / _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[2] / _reflns.pdbx_aniso_diffraction_limit_axis_3_ortho[3] / _reflns.pdbx_percent_possible_anomalous / _reflns.pdbx_percent_possible_ellipsoidal / _reflns.pdbx_percent_possible_ellipsoidal_anomalous / _reflns.pdbx_percent_possible_spherical / _reflns.pdbx_percent_possible_spherical_anomalous / _reflns.pdbx_redundancy_anomalous / _reflns_shell.pdbx_CC_half_anomalous / _reflns_shell.pdbx_absDiff_over_sigma_anomalous / _reflns_shell.pdbx_percent_possible_anomalous / _reflns_shell.pdbx_percent_possible_ellipsoidal / _reflns_shell.pdbx_percent_possible_ellipsoidal_anomalous / _reflns_shell.pdbx_percent_possible_spherical / _reflns_shell.pdbx_percent_possible_spherical_anomalous / _reflns_shell.pdbx_redundancy_anomalous
Revision 1.3Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.4Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XIa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7043
Polymers26,8561
Non-polymers8482
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.025, 69.588, 85.127
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XIa light chain / FXI / Plasma thromboplastin antecedent / PTA


Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: C500S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Komagataella pastoris (fungus) / References: UniProt: P03951, coagulation factor XIa
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-YXG / Milvexian / BMS-986177 / (6R,10S)-10-{4-[5-chloro-2-(4-chloro-1H-1,2,3-triazol-1-yl)phenyl]-6-oxopyrimidin-1(6H)-yl}-1-(difluoromethyl)-6-methyl-1,4,7,8,9,10-hexahydro-15,11-(metheno)pyrazolo[4,3-b][1,7]diazacyclotetradecin-5(6H)-one


Mass: 626.444 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H23Cl2F2N9O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: anticoagulant, inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 MM MES, pH 6.5, 20% (W/V) PEG 6000, 10 MM CALCIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.924→53.874 Å / Num. obs: 132503 / % possible obs: 90.1 % / Redundancy: 6.19 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways through the data processing procedure (rejection of overloaded or too partial reflections, outlier/misfit rejection during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.999 / CC1/2 anomalous: -0.186 / Rmerge(I) obs: 0.0436 / Rpim(I) all: 0.0185 / Rrim(I) all: 0.0475 / AbsDiff over sigma anomalous: 0.734 / Aniso diffraction limit 1: 0.997 Å / Aniso diffraction limit 2: 0.944 Å / Aniso diffraction limit 3: 0.924 Å / Aniso diffraction limit axis 1 ortho1: 1 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: 0 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 1 / Net I/σ(I): 18.23 / Num. measured all: 820542 / % possible anomalous: 88.1 / % possible ellipsoidal: 90.1 / % possible ellipsoidal anomalous: 88.1 / % possible spherical: 83.5 / % possible spherical anomalous: 81 / Redundancy anomalous: 3.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
2.699-53.8746.080.035146.734031140311662566250.999-0.1910.0150.03830.78297.397.697.397.697.33.3797.6
2.134-2.6996.630.034745.274390443904662566250.999-0.180.01430.03760.78199.599.499.599.499.53.5199.4
1.86-2.1346.210.03740.174112241122662566250.999-0.1470.01590.04030.82899.499.299.499.299.43.2799.2
1.686-1.866.50.042135.464308143081662566250.999-0.1080.01770.04580.79598.398.498.398.498.33.498.4
1.563-1.6866.840.048631.54532445324662566250.999-0.1140.01990.05250.80598.198.498.198.498.13.5798.4
1.468-1.5636.650.056226.514404744047662566250.998-0.1060.02330.06090.77696.997.296.997.296.93.4797.2
1.392-1.4686.460.066222.394280242802662666260.997-0.0590.0280.0720.77297.397.597.397.597.33.3697.5
1.33-1.3926.680.079119.074423144231662466240.997-0.060.03270.08570.76995.996.595.996.595.93.4796.5
1.277-1.336.790.090616.924500645006662666260.995-0.0390.03710.09810.73794.896.194.896.194.83.5496.1
1.231-1.2776.590.101514.94363243632662566250.994-0.030.04220.11010.72594.695.994.695.994.63.4395.9
1.191-1.2316.430.115512.994263842638662666260.993-0.0180.04880.12560.7294.695.494.695.494.63.3495.4
1.156-1.1916.560.130711.854349043490662566250.992-0.0440.05470.14190.72793.894.693.894.693.83.3994.6
1.124-1.1566.730.149510.434455444554662566250.989-0.0390.06150.16190.70692.693.592.693.592.63.4893.5
1.095-1.1246.550.18028.544338643386662566250.984-0.0110.07540.19570.791.492.491.492.491.43.492.4
1.068-1.0956.30.23696.414173341733662366230.97-0.0360.10120.25810.69490.491.390.491.390.43.2691.3
1.044-1.0686.450.30025.14271942719662666260.957-0.0520.12630.32620.66989.290.489.290.489.23.3490.4
1.021-1.0446.470.3744.124290542905662866280.933-0.0620.15690.40640.67487.488.987.488.987.43.3688.9
1-1.0215.430.455133594435944662566250.874-0.0410.20990.50320.6738286.48286.4822.986.4
0.975-14.410.59942.022921829218662466240.751-0.0330.3040.67670.6864.774.564.768.159.12.4974.5
0.924-0.9753.090.73991.32049520495662566250.581-0.0350.45740.87570.66936.342.936.328.622.41.8442.9

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
AMoREphasing
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SOR

3sor


Resolution: 0.924→53.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.022 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.022 / SU Rfree Blow DPI: 0.022 / SU Rfree Cruickshank DPI: 0.021
RfactorNum. reflection% reflectionSelection details
Rfree0.1683 6441 -RANDOM
Rwork0.1616 ---
obs0.1619 132503 83.4 %-
Displacement parametersBiso mean: 12.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.1017 Å20 Å20 Å2
2--0.0049 Å20 Å2
3---0.0968 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 0.924→53.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 57 290 2207
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083845HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.066933HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1141SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes666HARMONIC5
X-RAY DIFFRACTIONt_it3782HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion256SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3452SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion5.63
X-RAY DIFFRACTIONt_other_torsion12.41
LS refinement shellResolution: 0.924→0.95 Å
RfactorNum. reflection% reflection
Rfree0.2536 126 -
Rwork0.2495 --
obs--89.04 %

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