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- PDB-5exm: FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5exm | ||||||
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Title | FACTOR XIA IN COMPLEX WITH THE INHIBITOR methyl ~{N}-[4-[2-[(1~{S})-1-[[4-(aminomethyl)cyclohexyl]carbonylamino]-2-phenyl-ethyl]pyridin-4-yl]phenyl]carbamate | ||||||
![]() | Coagulation factor XIa light chain | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Wei, A. | ||||||
![]() | ![]() 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.P. / Orwat, M.J. / Han, W. / Rendina, A.R. / Luettgen, J.M. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Myers Jr., J.E. / Sheriff, S. / Narayanan, R. / ...Authors: Corte, J.R. / Fang, T. / Pinto, D.J.P. / Orwat, M.J. / Han, W. / Rendina, A.R. / Luettgen, J.M. / Rossi, K.A. / Wei, A. / Ramamurthy, V. / Myers Jr., J.E. / Sheriff, S. / Narayanan, R. / Harper, T. / Zheng, J.J. / Li, Y.-X. / Seiffert, D.A. / Wexler, R.R. / Quan, M.L. #1: ![]() 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: ![]() 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: ![]() 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: ![]() Title: Structure-based design of inhibitors of coagulation factor XIa with novel P1 moieties Authors: Pinto, D.J.P. / Smallheer, J.M. / Corte, J.R. / Austin, E.J.D. / 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.P. / Smallheer, J.M. / Corte, J.R. / Austin, E.J.D. / 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: ![]() 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: ![]() 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. / Bozarth, J.M. / Crain, E.J. / Wei, A. / Ramamurthy, V. / Morin, P.E. / Seiffert, D.A. / Quan, M.L. / Lam, P.Y.S. / Wexler, R.R. / Pinto, D.J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 71.6 KB | Display | ![]() |
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PDB format | ![]() | 50.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 706.8 KB | Display | ![]() |
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Full document | ![]() | 707.1 KB | Display | |
Data in XML | ![]() | 13.2 KB | Display | |
Data in CIF | ![]() | 19.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5exlC ![]() 5exnC ![]() 4ty7S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Antibody | Mass: 27600.342 Da / Num. of mol.: 1 / Fragment: COAGULATION FACTOR XI, HEAVY CHAIN / Mutation: N113G,T115G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Chemical | ChemComp-5ST / | ||||
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100 MM SODIUM ACETATE, PH 4.6, 26%(w/v) MEPEG2000, 200 MM AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 92 / Detector: CCD / Date: Jul 19, 2005 / Details: MICROMAX CONFOCAL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 23326 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 28.95 Å2 / Rsym value: 0.087 / Net I/σ(I): 32.2 |
Reflection shell | Resolution: 2.09→2.16 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 6.5 / Rejects: 0 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4TY7 Resolution: 2.09→28.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.143
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Displacement parameters | Biso max: 122.44 Å2 / Biso mean: 28.56 Å2 / Biso min: 12.63 Å2
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Refine analyze | Luzzati coordinate error obs: 0.238 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.09→28.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.18 Å / Total num. of bins used: 12
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