2PGB
 
 | | Inhibitor-free human thrombin mutant C191A-C220A | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Prothrombin, SULFATE ION | | 著者 | Bush-Pelc, L.A, Marino, F, Chen, Z, Pineda, A.O, Mathews, F.S, Di Cera, E. | | 登録日 | 2007-04-09 | | 公開日 | 2007-07-17 | | 最終更新日 | 2023-08-30 | | 実験手法 | X-RAY DIFFRACTION (1.54 Å) | | 主引用文献 | Important role of the cys-191 cys-220 disulfide bond in thrombin function and allostery
J.Biol.Chem., 282, 2007
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1SHH
 | | Slow form of Thrombin Bound with PPACK | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, thrombin | | 著者 | Pineda, A.O, Carrell, C.J, Bush, L.A, Prasad, S, Caccia, S, Chen, Z.W, Mathews, F.S, Di Cera, E. | | 登録日 | 2004-02-25 | | 公開日 | 2004-06-08 | | 最終更新日 | 2024-03-13 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Molecular dissection of na+ binding to thrombin.
J.Biol.Chem., 279, 2004
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3SI3
 | | Human Thrombin In Complex With UBTHR103 | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, D-phenylalanyl-N-(pyridin-2-ylmethyl)-L-prolinamide, GLYCEROL, ... | | 著者 | Biela, A, Heine, A, Klebe, G. | | 登録日 | 2011-06-17 | | 公開日 | 2012-06-20 | | 最終更新日 | 2023-12-06 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
J.Mol.Biol., 418, 2012
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3GIC
 | | Structure of thrombin mutant delta(146-149e) in the free form | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, Thrombin heavy chain, Thrombin light chain | | 著者 | Bah, A, Carrell, C.J, Chen, Z, Gandhi, P.S, Di Cera, E. | | 登録日 | 2009-03-05 | | 公開日 | 2009-06-02 | | 最終更新日 | 2023-09-06 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Stabilization of the E* form turns thrombin into an anticoagulant.
J.Biol.Chem., 284, 2009
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4UFF
 | | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl- propanamide | | 分子名称: | (2R)-2-(benzylsulfonylamino)-N-(2-((4-carbamimidoylphenyl)methylamino)-2-oxo-ethyl)-N-methyl-3-phenyl-propanamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-2, ... | | 著者 | Ruehmann, E, Heine, A, Klebe, G. | | 登録日 | 2015-03-16 | | 公開日 | 2016-01-27 | | 最終更新日 | 2023-12-20 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
Chemmedchem, 11, 2016
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3UTU
 | | High affinity inhibitor of human thrombin | | 分子名称: | (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, ... | | 著者 | Baum, B, Steinmetzer, T, Heine, A, Klebe, G. | | 登録日 | 2011-11-26 | | 公開日 | 2012-08-29 | | 最終更新日 | 2023-12-06 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Beyond heparinization: design of highly potent thrombin inhibitors suitable for surface coupling
Chemmedchem, 7, 2012
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3U69
 | | Unliganded wild-type human thrombin | | 分子名称: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... | | 著者 | Figueiredo, A.C, Clement, C.C, Philipp, M, Barbosa Pereira, P.J. | | 登録日 | 2011-10-12 | | 公開日 | 2012-04-11 | | 最終更新日 | 2023-09-13 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Rational design and characterization of d-phe-pro-d-arg-derived direct thrombin inhibitors.
Plos One, 7, 2012
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3BEI
 | | Crystal structure of the slow form of thrombin in a self_inhibited conformation | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Prothrombin | | 著者 | Gandhi, P.S, Chen, Z, Mathews, F.S, Di Cera, E. | | 登録日 | 2007-11-19 | | 公開日 | 2007-12-25 | | 最終更新日 | 2023-08-30 | | 実験手法 | X-RAY DIFFRACTION (1.55 Å) | | 主引用文献 | Structural identification of the pathway of long-range communication in an allosteric enzyme.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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6HSX
 | | Thrombin in Complex with a D-Phe-Pro-diaminopyridine derivative | | 分子名称: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[[2,6-bis(azanyl)pyridin-4-yl]methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | 著者 | Ngo, K, Heine, A, Klebe, G. | | 登録日 | 2018-10-02 | | 公開日 | 2019-10-23 | | 最終更新日 | 2024-01-24 | | 実験手法 | X-RAY DIFFRACTION (1.56 Å) | | 主引用文献 | Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins?
J.Med.Chem., 63, 2020
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6T57
 | | Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative | | 分子名称: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(1-carbamimidoylpiperidin-4-yl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | 著者 | Ngo, K, Abazi, N, Heine, A, Klebe, G. | | 登録日 | 2019-10-15 | | 公開日 | 2020-11-18 | | 最終更新日 | 2024-01-24 | | 実験手法 | X-RAY DIFFRACTION (1.57 Å) | | 主引用文献 | Thrombin in Complex with a D-Phe-Pro-N-amidinopiperidine Derivative
To Be Published
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6T54
 | | Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative | | 分子名称: | (2~{S})-1-[(2~{R})-2-azanyl-3-phenyl-propanoyl]-~{N}-[(5-bromanylthiophen-2-yl)methyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, DIMETHYL SULFOXIDE, ... | | 著者 | Ngo, K, Abazi, N, Heine, A, Klebe, G. | | 登録日 | 2019-10-15 | | 公開日 | 2020-11-18 | | 最終更新日 | 2024-01-31 | | 実験手法 | X-RAY DIFFRACTION (1.57 Å) | | 主引用文献 | Thrombin in Complex with a D-Phe-Pro-2-bromothiophene Derivative
To Be Published
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1O2G
 | | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating Binding of Active Site-Directed Serine Protease Inhibitors | | 分子名称: | 3-{5-[AMINO(IMINIO)METHYL]-1H-INDOL-2-YL}-1,1'-BIPHENYL-2-OLATE, ACETYL HIRUDIN, SODIUM ION, ... | | 著者 | Katz, B.A, Elrod, K, Verner, E, Mackman, R.L, Luong, C, Shrader, W, Sendzik, M, Spencer, J.R, Sprengeler, P.A, Kolesnikov, A, Tai, W.F, Hui, H, Breitenbucher, G, Allen, D, Janc, J. | | 登録日 | 2003-03-06 | | 公開日 | 2003-05-13 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | Elaborate Manifold of Short Hydrogen Bond Arrays Mediating
Binding of Active Site-Directed Serine Protease Inhibitors
J.Mol.Biol., 329, 2003
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6Z8V
 | | X-ray structure of the complex between human alpha thrombin and a thrombin binding aptamer variant (TBA-3L), which contains 1-beta-D-lactopyranosyl residue in the side chain of Thy3 at N3. | | 分子名称: | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, POTASSIUM ION, Prothrombin, ... | | 著者 | Troisi, R, Timofeev, E.N, Sica, F. | | 登録日 | 2020-06-02 | | 公開日 | 2021-01-27 | | 最終更新日 | 2024-01-24 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | Expanding the recognition interface of the thrombin-binding aptamer HD1 through modification of residues T3 and T12.
Mol Ther Nucleic Acids, 23, 2021
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2ZC9
 | | Thrombin in complex with Inhibitor | | 分子名称: | D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | | 著者 | Baum, B, Heine, A, Klebe, G. | | 登録日 | 2007-11-06 | | 公開日 | 2008-10-28 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
J.Mol.Biol., 391, 2009
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3RMM
 | | Human Thrombin in complex with MI332 | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, Hirudin variant-2, ... | | 著者 | Biela, A, Heine, A, Klebe, G. | | 登録日 | 2011-04-21 | | 公開日 | 2012-04-25 | | 最終更新日 | 2023-12-06 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | 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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3U9A
 | | Human Thrombin In Complex With MI330 | | 分子名称: | (2S)-N-[[2-(aminomethyl)-5-chloranyl-phenyl]methyl]-1-[(2S)-2-[(3-chloranyl-4-methoxy-phenyl)sulfonylamino]-4-[(4-cyanophenyl)methylamino]-4-oxidanylidene-butanoyl]pyrrolidine-2-carboxamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... | | 著者 | Biela, A, Heine, A, Klebe, G. | | 登録日 | 2011-10-18 | | 公開日 | 2012-10-24 | | 最終更新日 | 2023-12-06 | | 実験手法 | X-RAY DIFFRACTION (1.58 Å) | | 主引用文献 | Thrombin Inhibition
To be Published
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4UFE
 | | Thrombin in complex with (2R)-2-(benzylsulfonylamino)-N-(2-((4- carbamimidoylphenyl)methylamino)-2-oxo-butyl)-3-phenyl-propanamide | | 分子名称: | (2R)-N-[(2S)-1-[(4-carbamimidoylphenyl)methylamino]-1-oxidanylidene-propan-2-yl]-3-phenyl-2-[(phenylmethyl)sulfonylamino]propanamide, 2-acetamido-2-deoxy-beta-D-glucopyranose, HIRUDIN VARIANT-2, ... | | 著者 | Ruehmann, E, Heine, A, Klebe, G. | | 登録日 | 2015-03-16 | | 公開日 | 2016-01-27 | | 最終更新日 | 2023-12-20 | | 実験手法 | X-RAY DIFFRACTION (1.593 Å) | | 主引用文献 | Boosting Affinity by Correct Ligand Preorganization for the S2 Pocket of Thrombin: A Study by Isothermal Titration Calorimetry, Molecular Dynamics, and High-Resolution Crystal Structures.
Chemmedchem, 11, 2016
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3DUX
 | | Understanding Thrombin Inhibition | | 分子名称: | 3-cyclohexyl-D-alanyl-N-(3-chlorobenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | | 著者 | Baum, B, Heine, A, Klebe, G. | | 登録日 | 2008-07-18 | | 公開日 | 2009-06-23 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Think twice: understanding the high potency of bis(phenyl)methane inhibitors of thrombin
J.Mol.Biol., 391, 2009
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1AHT
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2ZGB
 | | Thrombin Inhibition | | 分子名称: | D-leucyl-N-(3-chlorobenzyl)-L-prolinamide, Hirudin variant-1, SODIUM ION, ... | | 著者 | Baum, B, Heine, A, Klebe, G. | | 登録日 | 2008-01-21 | | 公開日 | 2008-12-16 | | 最終更新日 | 2023-11-15 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Non-additivity of functional group contributions in protein-ligand binding: a comprehensive study by crystallography and isothermal titration calorimetry.
J.Mol.Biol., 397, 2010
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4CH2
 | | Low-salt crystal structure of a thrombin-GpIbalpha peptide complex | | 分子名称: | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide, GLYCEROL, PLATELET GLYCOPROTEIN IB ALPHA CHAIN, ... | | 著者 | Lechtenberg, B.C, Freund, S.M.V, Huntington, J.A. | | 登録日 | 2013-11-28 | | 公開日 | 2013-12-11 | | 最終更新日 | 2023-12-20 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Gpibalpha Interacts Exclusively with Exosite II of Thrombin
J.Mol.Biol., 426, 2014
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3B9F
 | | 1.6 A structure of the PCI-thrombin-heparin complex | | 分子名称: | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose, GLYCEROL, Plasma serine protease inhibitor, ... | | 著者 | Li, W, Adams, T.E, Huntington, J.A. | | 登録日 | 2007-11-05 | | 公開日 | 2008-04-22 | | 最終更新日 | 2023-11-01 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Molecular basis of thrombin recognition by protein C inhibitor revealed by the 1.6-A structure of the heparin-bridged complex.
Proc.Natl.Acad.Sci.Usa, 105, 2008
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3JZ1
 | | Crystal structure of human thrombin mutant N143P in E:Na+ form | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, NITRATE ION, ... | | 著者 | Niu, W, Chen, Z, Bush-Pelc, L.A, Bah, A, Gandhi, P.S, Di Cera, E. | | 登録日 | 2009-09-22 | | 公開日 | 2009-10-20 | | 最終更新日 | 2023-09-06 | | 実験手法 | X-RAY DIFFRACTION (1.6 Å) | | 主引用文献 | Mutant N143P reveals how Na+ activates thrombin
J.Biol.Chem., 284, 2009
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3VXF
 | | X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 | | 分子名称: | 2-acetamido-2-deoxy-beta-D-glucopyranose, BIVALIRUDIN, Thrombin heavy chain, ... | | 著者 | Yamada, T, Kurihara, K, Masumi, K, Tamada, T, Tomoyori, K, Ohnishi, Y, Tanaka, I, Kuroki, R, Niimura, N. | | 登録日 | 2012-09-12 | | 公開日 | 2013-09-04 | | 最終更新日 | 2020-07-29 | | 実験手法 | NEUTRON DIFFRACTION (1.602 Å), X-RAY DIFFRACTION | | 主引用文献 | 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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2BDY
 | | thrombin in complex with inhibitor | | 分子名称: | Hirudin IIIB', N-(4-CARBAMIMIDOYL-BENZYL)-2-[2-HYDROXY-6-METHYL-3-(NAPHTHALENE-1-SULFONYLAMINO)-PHENYL]-ACETAMIDE, SODIUM ION, ... | | 著者 | Xue, Y. | | 登録日 | 2005-10-21 | | 公開日 | 2006-10-24 | | 最終更新日 | 2017-10-18 | | 実験手法 | X-RAY DIFFRACTION (1.61 Å) | | 主引用文献 | Phenolic P2/P3 core motif as thrombin inhibitors--design, synthesis, and X-ray co-crystal structure.
Bioorg.Med.Chem.Lett., 16, 2006
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