4O03
| Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Prothrombin | Authors: | Pozzi, N, Chen, Z, Shropshire, D.B, Pelc, L.A, Di Cera, E. | Deposit date: | 2013-12-13 | Release date: | 2014-05-21 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (3.38 Å) | Cite: | The linker connecting the two kringles plays a key role in prothrombin activation. Proc.Natl.Acad.Sci.USA, 111, 2014
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2GP9
| Crystal structure of the slow form of thrombin in a self-inhibited conformation | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Prothrombin | Authors: | Pineda, A, Chen, Z, Mathews, F.S, Di Cera, E. | Deposit date: | 2006-04-17 | Release date: | 2006-09-12 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (1.87 Å) | Cite: | Crystal structure of thrombin in a self-inhibited conformation. J.Biol.Chem., 281, 2006
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4H6T
| Crystal structure of prethrombin-2 mutant E14eA/D14lA/E18A/S195A | Descriptor: | PHOSPHATE ION, Prothrombin | Authors: | Pozzi, N, Chen, Z, Zapata, F, Pelc, L.A, Di Cera, E. | Deposit date: | 2012-09-19 | Release date: | 2013-03-13 | Last modified: | 2023-09-20 | Method: | X-RAY DIFFRACTION (2.4 Å) | Cite: | Autoactivation of thrombin precursors. J.Biol.Chem., 288, 2013
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3RLW
| Human Thrombin in complex with MI328 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-20 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.69 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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3RMO
| Human Thrombin in complex with MI004 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.4 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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3RM0
| Human Thrombin in complex with MI354 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-20 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.34 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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3RMM
| Human Thrombin in complex with MI332 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.58 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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3RM2
| Human Thrombin in complex with MI003 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-20 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.23 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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3RML
| Human Thrombin in complex with MI331 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.53 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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3RLY
| Human Thrombin in complex with MI329 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-20 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.51 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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3RMN
| Human Thrombin in complex with MI341 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | Authors: | Biela, A, Heine, A, Klebe, G. | Deposit date: | 2011-04-21 | Release date: | 2012-04-25 | Last modified: | 2023-12-06 | Method: | X-RAY DIFFRACTION (1.78 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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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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2FES
| Orally active thrombin inhibitors | Descriptor: | Decapeptide Hirudin Analogue, N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({5-[(E)-AMINO(IMINO)METHYL]THIEN-2-YL}METHYL)-L-PROLINAMIDE, Thrombin heavy chain, ... | Authors: | Hoeffken, H.W. | Deposit date: | 2005-12-16 | Release date: | 2006-05-09 | Last modified: | 2023-08-30 | Method: | X-RAY DIFFRACTION (2.42 Å) | Cite: | Orally active thrombin inhibitors. Part 1: optimization of the P1-moiety. Bioorg.Med.Chem.Lett., 16, 2006
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3U69
| Unliganded wild-type human thrombin | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Figueiredo, A.C, Clement, C.C, Philipp, M, Barbosa Pereira, P.J. | Deposit date: | 2011-10-12 | Release date: | 2012-04-11 | Last modified: | 2023-09-13 | Method: | X-RAY DIFFRACTION (1.55 Å) | Cite: | Rational design and characterization of d-phe-pro-d-arg-derived direct thrombin inhibitors. Plos One, 7, 2012
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3U8O
| Human thrombin complexed with D-Phe-Pro-D-Arg-D-Thr | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | Authors: | Figueiredo, A.C, Clement, C.C, Philipp, M, Pereira, P.J.B. | Deposit date: | 2011-10-17 | Release date: | 2012-05-23 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.28 Å) | Cite: | Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors. Plos One, 7, 2012
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3U8R
| Human thrombin complexed with D-Phe-Pro-D-Arg-Ile | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | Authors: | Figueiredo, A.C, Clement, C.C, Philipp, M, Pereira, P.J.B. | Deposit date: | 2011-10-17 | Release date: | 2012-05-23 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.47 Å) | Cite: | Rational design and characterization of D-Phe-Pro-D-Arg-derived direct thrombin inhibitors. Plos One, 7, 2012
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1H8I
| X-ray crystal structure of human alpha-thrombin with a tripeptide phosphonate inhibitor. | Descriptor: | HIRUDIN I, N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-[(1S)-4-methoxy-1-phosphonobutyl]-L-prolinamide, THROMBIN | Authors: | Skordalakes, E, Dodson, G.G, Green, D, Deadman, J. | Deposit date: | 2001-02-08 | Release date: | 2001-03-02 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.75 Å) | Cite: | Inhibition of Human Alpha-Thrombin by a Phosphonate Tripeptide Proceeds Via a Metastable Pentacoordinated Phosphorus Intermediate J.Mol.Biol., 311, 2001
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1H8D
| X-ray structure of the human alpha-thrombin complex with a tripeptide phosphonate inhibitor. | Descriptor: | HIRUDIN I, N-[(benzyloxy)carbonyl]-beta-phenyl-D-phenylalanyl-N-{(1S,3E)-1-[dihydroxy(diphenoxy)-lambda~5~-phosphanyl]-4-methoxybut-3-en-1-yl}-L-prolinamide, THROMBIN | Authors: | Skordalakes, E, Dodson, G.G, Green, D, Deadman, J. | Deposit date: | 2001-02-01 | Release date: | 2001-02-26 | Last modified: | 2023-12-13 | Method: | X-RAY DIFFRACTION (1.4 Å) | Cite: | Inhibition of Human Alpha-Thrombin by a Phosphonate Tripeptide Proceeds Via a Metastable Pentacoordinated Phosphorus Intermediate J.Mol.Biol., 311, 2001
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3S69
| Crystal structure of saxthrombin | Descriptor: | CALCIUM ION, Thrombin-like enzyme defibrase | Authors: | Huang, K, Zhao, W, Teng, M, Niu, L. | Deposit date: | 2011-05-25 | Release date: | 2012-05-23 | Method: | X-RAY DIFFRACTION (1.43 Å) | Cite: | Structure of saxthrombin, a thrombin-like enzyme from Gloydius saxatilis. Acta Crystallogr.,Sect.F, 67, 2011
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3TU7
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3VXE
| Human alpha-thrombin-Bivalirudin complex at PD5.0 | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BIVALIRUDIN, Thrombin heavy chain, ... | Authors: | Yamada, T, Kurihara, K, Masumi, K, Tamada, T, Tomoyori, K, Ohnishi, Y, Tanaka, I, Kuroki, R, Niimura, N. | Deposit date: | 2012-09-12 | Release date: | 2013-09-04 | Last modified: | 2023-11-08 | Method: | X-RAY DIFFRACTION (1.25 Å) | Cite: | Neutron and X-ray crystallographic analysis of the human alpha-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex Biochim.Biophys.Acta, 1834, 2013
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3C1K
| Crystal structure of thrombin in complex with inhibitor 15 | Descriptor: | 2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide, Hirugen, Prothrombin | Authors: | Yan, Y. | Deposit date: | 2008-01-23 | Release date: | 2008-03-18 | Last modified: | 2013-03-13 | Method: | X-RAY DIFFRACTION (1.84 Å) | Cite: | Structure-based design of novel groups for use in the P1 position of thrombin inhibitor scaffolds. Part 2: N-acetamidoimidazoles. Bioorg.Med.Chem.Lett., 18, 2008
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3DA9
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3U8T
| Human thrombin complexed with D-Phe-Pro-D-Arg-Cys | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, CHLORIDE ION, ... | Authors: | Figueiredo, A.C, Clement, C.C, Philipp, M, Pereira, P.J.B. | Deposit date: | 2011-10-17 | Release date: | 2012-04-11 | Last modified: | 2020-07-29 | Method: | X-RAY DIFFRACTION (1.861 Å) | Cite: | Rational design and characterization of d-phe-pro-d-arg-derived direct thrombin inhibitors. Plos One, 7, 2012
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6ZUG
| Crystal Structure of Thrombin in complex with compound10 | Descriptor: | 2-[(3-chlorophenyl)methylamino]-7-methoxy-~{N}-[[(3~{S})-oxolan-3-yl]methyl]-~{N}-propyl-1,3-benzoxazole-5-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, Hirudin-2, ... | Authors: | Schafer, M. | Deposit date: | 2020-07-22 | Release date: | 2020-08-26 | Last modified: | 2024-05-01 | Method: | X-RAY DIFFRACTION (1.8 Å) | Cite: | Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics. J.Med.Chem., 63, 2020
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