2PW8
 
 | | Crystal structure of sulfo-hirudin complexed to thrombin | | Descriptor: | Hirudin variant-1, NICKEL (II) ION, SODIUM ION, ... | | Authors: | Liu, C.C, Brustad, E, Liu, W, Schultz, P.G. | | Deposit date: | 2007-05-10 | | Release date: | 2007-08-21 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | Crystal structure of a biosynthetic sulfo-hirudin complexed to thrombin.
J.Am.Chem.Soc., 129, 2007
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3P6Z
 | | Structural basis of thrombin mediated factor V activation: essential role of the hirudin-like sequence Glu666-Glu672 for processing at the heavy chain-B domain junction | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | | Authors: | Corral-Rodriguez, M.A, Bock, P.E, Hernandez-Carvajal, E, Gutierrez-Gallego, R, Fuentes-Prior, P. | | Deposit date: | 2010-10-11 | | Release date: | 2011-06-15 | | Last modified: | 2024-03-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural basis of thrombin-mediated factor V activation: the Glu666-Glu672 sequence is critical for processing at the heavy chain-B domain junction.
Blood, 117, 2011
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2R2M
 | | 2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors | | Descriptor: | Hirudin-3A, N-[2-({[amino(imino)methyl]amino}oxy)ethyl]-2-{6-chloro-3-[(2,2-difluoro-2-phenylethyl)amino]-2-fluorophenyl}acetamide, Thrombin heavy chain, ... | | Authors: | Spurlino, J. | | Deposit date: | 2007-08-27 | | Release date: | 2008-08-26 | | Last modified: | 2011-07-13 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | 2-(2-Chloro-6-Fluorophenyl)Acetamides as Potent Thrombin Inhibitors
Bioorg.Med.Chem.Lett., 17, 2007
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6EO9
 | | Crystal structure of thrombin in complex with a novel glucose-conjugated potent inhibitor | | Descriptor: | DIMETHYL SULFOXIDE, Hirudin variant-2, N-(2-{[5-(5-chlorothiophen-2-yl)-1,2-oxazol-3-yl]methoxy}-6-{3-[(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)oxy]propoxy}phenyl)-1-(propan-2-yl)piperidine-4-carboxamide, ... | | Authors: | Belviso, B.D, Caliandro, R, Aresta, B.M, De Candia, M, Altomare, C.D. | | Deposit date: | 2017-10-09 | | Release date: | 2017-12-13 | | Last modified: | 2019-10-16 | | Method: | X-RAY DIFFRACTION (1.84 Å) | | Cite: | How a beta-D-glucoside side chain enhances binding affinity to thrombin of inhibitors bearing 2-chlorothiophene as P1 moiety: crystallography, fragment deconstruction study, and evaluation of antithrombotic properties.
J. Med. Chem., 57, 2014
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6GBW
 | | Thrombin in complex with MI2100 ((S)-N-(2-(aminomethyl)-5-chlorobenzyl)-1-((benzylsulfonyl)-L-arginyl)pyrrolidine-2-carboxamide) | | Descriptor: | (2~{S})-~{N}-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2~{S})-5-carbamimidamido-2-[(phenylmethyl)sulfonylamino]pentanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G. | | Deposit date: | 2018-04-16 | | Release date: | 2019-04-24 | | Last modified: | 2024-01-17 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | Strategies for Late-Stage Optimization: Profiling Thermodynamics by Preorganization and Salt Bridge Shielding.
J.Med.Chem., 62, 2019
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3HAT
 | | ACTIVE SITE MIMETIC INHIBITION OF THROMBIN | | Descriptor: | FPAM (FIBRINOPEPTIDE A MIMIC), Hirudin variant-2, Thrombin heavy chain, ... | | Authors: | Tulinsky, A, Mathews, I.I. | | Deposit date: | 1994-10-16 | | Release date: | 1995-02-27 | | Last modified: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Active-site mimetic inhibition of thrombin.
Acta Crystallogr.,Sect.D, 51, 1995
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3HTC
 | | THE STRUCTURE OF A COMPLEX OF RECOMBINANT HIRUDIN AND HUMAN ALPHA-THROMBIN | | Descriptor: | ALPHA-THROMBIN (LARGE SUBUNIT), ALPHA-THROMBIN (SMALL SUBUNIT), HIRUDIN VARIANT 2 | | Authors: | Tulinsky, A, Rydel, T.J, Ravichandran, K.G, Huber, R, Bode, W. | | Deposit date: | 1993-06-11 | | Release date: | 1994-01-31 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | The structure of a complex of recombinant hirudin and human alpha-thrombin.
Science, 249, 1990
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2HWL
 | | Crystal structure of thrombin in complex with fibrinogen gamma' peptide | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Fibrinogen gamma' peptide, Prothrombin, ... | | Authors: | Pineda, A.O, Chen, Z.W, Marino, F, Mathews, F.S, Mosesson, M.W, Di Cera, E. | | Deposit date: | 2006-08-01 | | Release date: | 2006-09-19 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Crystal structure of thrombin in complex with fibrinogen gamma' peptide.
Biophys.Chem., 125, 2007
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2JH5
 | | Human Thrombin Hirugen Inhibitor complex | | Descriptor: | 2-(5-CHLORO-2-THIENYL)-N-{(3S)-1-[(1S)-1-METHYL-2-MORPHOLIN-4-YL-2-OXOETHYL]-2-OXOPYRROLIDIN-3-YL}ETHENESULFONAMIDE, CALCIUM ION, HIRUDIN IIIA, ... | | Authors: | Senger, S, Chan, C, Convery, M.A, Hubbard, J.A, Young, R.J, Shah, G.P, Watson, N.S. | | Deposit date: | 2007-02-20 | | Release date: | 2007-05-08 | | Last modified: | 2017-06-28 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Sulfonamide-Related Conformational Effects and Their Importance in Structure-Based Design.
Bioorg.Med.Chem.Lett., 17, 2007
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3UTU
 | | High affinity inhibitor of human thrombin | | Descriptor: | (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2S)-2-[(3-chloro-4-methoxybenzene)sulfonamido]-3-{[(4-cyanophenyl)methyl]carbamoyl}propanoyl]pyrrolidine-2-carboxamide, Hirudin variant-1, SODIUM ION, ... | | Authors: | Baum, B, Steinmetzer, T, Heine, A, Klebe, G. | | Deposit date: | 2011-11-26 | | Release date: | 2012-08-29 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Beyond heparinization: design of highly potent thrombin inhibitors suitable for surface coupling
Chemmedchem, 7, 2012
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3UWJ
 | | Human Thrombin In Complex With MI353 | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin variant-2, N-(benzylsulfonyl)-D-leucyl-N-(4-carbamimidoylbenzyl)-L-prolinamide, ... | | Authors: | Biela, A, Heine, A, Klebe, G. | | Deposit date: | 2011-12-02 | | Release date: | 2012-12-12 | | Last modified: | 2023-12-06 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect
J.Med.Chem., 55, 2012
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4AYV
 | | Human thrombin - inhibitor complex | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN-3A', SODIUM ION, ... | | Authors: | Banner, D.W, D'Arcy, A, Winkler, F.K, Hilpert, K. | | Deposit date: | 2012-06-22 | | Release date: | 2012-08-15 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
J.Med.Chem., 37, 1994
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4AX9
 | | Human thrombin complexed with Napsagatran, RO0466240 | | Descriptor: | 2-[[(2S)-4-[[(3S)-1-carbamimidoylpiperidin-3-yl]methylamino]-2-(naphthalen-2-ylsulfonylamino)-4-oxidanylidene-butanoyl] -cyclopropyl-amino]ethanoic acid, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-1, ... | | Authors: | Banner, D.W, D'Arcy, A, Winkler, F.K, Hilpert, K, Spinelli, S, Cambillau, C. | | Deposit date: | 2012-06-11 | | Release date: | 2012-06-20 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
J.Med.Chem., 37, 1994
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4AZ2
 | | Human thrombin - inhibitor complex | | Descriptor: | (R)-N-((S)-1-CARBAMIMIDOYL-PIPERIDIN-3-YLMETHYL)-2-(NAPHTHALENE-2-SULFONYLAMINO)-3-PHENYL-PROPIONAMIDE, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN-3A', ... | | Authors: | Banner, D.W, D'Arcy, A, Winkler, F.K, Hilpert, K. | | Deposit date: | 2012-06-22 | | Release date: | 2012-08-15 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors.
J.Med.Chem., 37, 1994
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4BAM
 | | Thrombin in complex with inhibitor | | Descriptor: | (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(dimethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-1, ... | | Authors: | Xue, Y, Musil, D. | | Deposit date: | 2012-09-14 | | Release date: | 2013-01-16 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.88 Å) | | Cite: | Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
Biochemistry, 52, 2013
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4BAH
 | | Thrombin in complex with inhibitor | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-1, SODIUM ION, ... | | Authors: | Xue, Y, Musil, D. | | Deposit date: | 2012-09-14 | | Release date: | 2013-01-16 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.94 Å) | | Cite: | Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
Biochemistry, 52, 2013
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4BAQ
 | | Thrombin in complex with inhibitor | | Descriptor: | (2S)-N-[(4-carbamimidoylphenyl)methyl]-1-[(2R)-2-cyclohexyl-2-[[2-(ethylamino)-2-oxidanylidene-ethyl]amino]ethanoyl]azetidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-1, ... | | Authors: | Xue, Y, Musil, D. | | Deposit date: | 2012-09-14 | | Release date: | 2013-01-16 | | Last modified: | 2020-07-29 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Identification of Structure-Kinetic and Structure-Thermodynamic Relationships for Thrombin Inhibitors.
Biochemistry, 52, 2013
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3EGK
 | | KNOBLE Inhibitor | | Descriptor: | Hirudin variant-1, SODIUM ION, Thrombin heavy chain, ... | | Authors: | Baum, B, Heine, A, Klebe, G, Muenzel, M. | | Deposit date: | 2008-09-10 | | Release date: | 2008-09-30 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | KNOBLE: a knowledge-based approach for the design and synthesis of readily accessible small-molecule chemical probes to test protein binding
Angew.Chem.Int.Ed.Engl., 46, 2007
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3EQ0
 | | Thrombin Inhibitor | | Descriptor: | (2S)-N-[[2-(aminomethyl)-5-chloro-phenyl]methyl]-1-[(2R)-5-carbamimidamido-2-(phenylmethylsulfonylamino)pentanoyl]pyrrolidine-2-carboxamide, Hirudin variant-1, SODIUM ION, ... | | Authors: | Baum, B, Heine, A, Klebe, G, Steinmetzer, T. | | Deposit date: | 2008-09-30 | | Release date: | 2009-08-18 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.53 Å) | | Cite: | Thrombin Inhibition
To be Published
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3F68
 | | Thrombin Inhibition | | Descriptor: | Hirudin variant-2, N-acetyl-3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide, Prothrombin, ... | | Authors: | Baum, B, Heine, A, Klebe, G. | | Deposit date: | 2008-11-05 | | Release date: | 2009-10-20 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin.
J.Mol.Biol., 391, 2009
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6Y02
 | | Thrombin in complex with 13k | | Descriptor: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylfuran-2-yl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Abazi, N. | | Deposit date: | 2020-02-06 | | Release date: | 2021-02-17 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Thrombin in complex with 13k
To be published
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6Y9H
 | | Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2) | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2), DIMETHYL SULFOXIDE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Abazi, N. | | Deposit date: | 2020-03-09 | | Release date: | 2021-03-31 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.48 Å) | | Cite: | Thrombin in complex with D-Phe-Pro-m-Trifluoromethylbenzylamide derivative (phe2)
To be published
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6YB6
 | | Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c) | | Descriptor: | 2-(aminomethyl)-5-chloranyl-benzene-1,4-diol, 2-acetamido-2-deoxy-beta-D-glucopyranose, D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Abazi, N. | | Deposit date: | 2020-03-16 | | Release date: | 2021-03-31 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Thrombin in complex with D-Phe-Pro-3-chloro-1,3-dihydroxybenzylamide derivative (13c)
To be published
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3DUX
 | | Understanding Thrombin Inhibition | | Descriptor: | 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | | Authors: | Baum, B, Heine, A, Klebe, G. | | Deposit date: | 2008-07-18 | | Release date: | 2009-06-23 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
J.Mol.Biol., 391, 2009
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6YHG
 | | Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a) | | Descriptor: | 1-(3-methoxyphenyl)methanamine, 2-acetamido-2-deoxy-beta-D-glucopyranose, D-PHENYLALANINE, ... | | Authors: | Sandner, A, Heine, A, Klebe, G, Collins, C. | | Deposit date: | 2020-03-29 | | Release date: | 2021-04-07 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.33 Å) | | Cite: | Thrombin in complex with D-Phe-Pro-m-methoxybenzylamide derivative (16a)
To be published
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