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

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データベース: PDB / ID: 7mbo
タイトルFACTOR 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
要素Coagulation factor XIa light chain
キーワードHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / COAGULATION FACTOR / SYNTETHIC INHIBITOR / BLOOD / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
機能・相同性
機能・相同性情報


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
類似検索 - 分子機能
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
類似検索 - ドメイン・相同性
Milvexian / Coagulation factor XI
類似検索 - 構成要素
生物種Homo sapiens (ヒト)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 0.924 Å
データ登録者Sheriff, S.
引用
ジャーナル: J.Med.Chem. / 年: 2022
タイトル: Discovery of Milvexian, a High-Affinity, Orally Bioavailable Inhibitor of Factor XIa in Clinical Studies for Antithrombotic Therapy.
著者: 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. / ...著者: 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: ジャーナル: J. Med. Chem. / 年: 2014
タイトル: Tetrahydroquinoline derivatives as potent and selective factor XIa inhibitors.
著者: 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. ...著者: 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: ジャーナル: J. Med. Chem. / 年: 2014
タイトル: Phenylimidazoles as potent and selective inhibitors of coagulation factor XIa with in vivo antithrombotic activity.
著者: 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. / ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2015
タイトル: Pyridine and pyridinone-based factor XIa inhibitors.
著者: 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. ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2015
タイトル: Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties.
著者: 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. / ...著者: 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: ジャーナル: ACS Med Chem Lett / 年: 2015
タイトル: Discovery of a Potent Parenterally Administered Factor XIa Inhibitor with Hydroxyquinolin-2(1H)-one as the P2' Moiety.
著者: 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. / ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2016
タイトル: Novel phenylalanine derived diamides as Factor XIa inhibitors.
著者: 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. / ...著者: 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: ジャーナル: Bioorg. Med. Chem. / 年: 2016
タイトル: Orally bioavailable pyridine and pyrimidine-based Factor XIa inhibitors: Discovery of the methyl N-phenyl carbamate P2 prime group.
著者: 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. / ...著者: 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: ジャーナル: J. Med. Chem. / 年: 2017
タイトル: Structure-Based Design of Macrocyclic Factor XIa Inhibitors: Discovery of the Macrocyclic Amide Linker.
著者: 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. ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2017
タイトル: Macrocyclic inhibitors of Factor XIa: Discovery of alkyl-substituted macrocyclic amide linkers with improved potency.
著者: 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. ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2017
タイトル: Macrocyclic factor XIa inhibitors.
著者: 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: ジャーナル: J. Med. Chem. / 年: 2017
タイトル: Discovery of a Parenteral Small Molecule Coagulation Factor XIa Inhibitor Clinical Candidate (BMS-962212).
著者: 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, ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2019
タイトル: Structure based design of macrocyclic factor XIa inhibitors: Discovery of cyclic P1 linker moieties with improved oral bioavailability.
著者: 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. / ...著者: 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: ジャーナル: J. Med. Chem. / 年: 2019
タイトル: Potent, Orally Bioavailable and Efficacious Macrocyclic Inhibitors of Factor XIa. Discovery of Pyridine-Based Macrocycles Possessing Phenylazole Carboxamide P1 Groups.
著者: 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. / ...著者: 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: ジャーナル: Bioorg. Med. Chem. Lett. / 年: 2020
タイトル: Orally bioavailable amine-linked macrocyclic inhibitors of factor XIa.
著者: 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. / ...著者: 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: ジャーナル: J. Med. Chem. / 年: 2020
タイトル: Discovery of a High Affinity, Orally Bioavailable Macrocyclic FXIa Inhibitor with Antithrombotic Activity in Preclinical Species
著者: 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, ...著者: 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.
履歴
登録2021年4月1日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年9月15日Provider: repository / タイプ: Initial release
改定 1.12021年9月22日Group: Database references / カテゴリ: 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
改定 1.22021年9月29日Group: Data collection / カテゴリ: 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
改定 1.32022年2月23日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.42023年10月18日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Coagulation factor XIa light chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)27,7043
ポリマ－26,8561
非ポリマー8482
水5,224290
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
タイプ名称対称操作数
identity operation1_555x,y,z1
手法PISA
単位格子
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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要素

#1: タンパク質 Coagulation factor XIa light chain / FXI / Plasma thromboplastin antecedent / PTA


分子量: 26856.496 Da / 分子数: 1 / 変異: C500S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: F11 / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: P03951, coagulation factor XIa
#2: 糖 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 / N-アセチル-β-D-グルコサミン


タイプ: D-saccharide, beta linking / 分子量: 221.208 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C8H15NO6
識別子タイププログラム
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: 化合物 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


分子量: 626.444 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C28H23Cl2F2N9O2 / タイプ: SUBJECT OF INVESTIGATION / コメント: 抗凝固剤, 阻害剤*YM
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 290 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.15 Å3/Da / 溶媒含有率: 42.84 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5
詳細: 100 MM MES, pH 6.5, 20% (W/V) PEG 6000, 10 MM CALCIUM ACETATE

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 17-ID / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年10月5日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 1 Å / 相対比: 1
反射解像度: 0.924→53.874 Å / Num. obs: 132503 / % possible obs: 90.1 % / 冗長度: 6.19 %
詳細: 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 ...詳細: 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
反射 シェル
解像度 (Å)冗長度 (%)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

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解析

ソフトウェア
名称バージョン分類
BUSTER2.11.7精密化
PDB_EXTRACT3.27データ抽出
XDSデータ削減
Aimlessデータスケーリング
AMoRE位相決定
STARANISOデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 3SOR

3sor


解像度: 0.924→53.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.957 / SU R Cruickshank DPI: 0.022 / 交差検証法: THROUGHOUT / SU R Blow DPI: 0.022 / SU Rfree Blow DPI: 0.022 / SU Rfree Cruickshank DPI: 0.021
Rfactor反射数%反射Selection details
Rfree0.1683 6441 -RANDOM
Rwork0.1616 ---
obs0.1619 132503 83.4 %-
原子変位パラメータBiso 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
精密化ステップサイクル: LAST / 解像度: 0.924→53.88 Å
タンパク質核酸リガンド溶媒全体
原子数1860 0 57 290 2207
拘束条件
Refine-IDタイプDev ideal数Restraint 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精密化 シェル解像度: 0.924→0.95 Å
Rfactor反射数%反射
Rfree0.2536 126 -
Rwork0.2495 --
obs--89.04 %

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