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235,183 Structures from the PDB

1,068,577 Computed Structure Models (CSM)

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QUERY: BIRD Class = "Thrombin inhibitor"

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Search Summary

This query matches 85 Structures.

Refinements

Structure Determination Methodology

experimental (85)

Scientific Name of Source Organism

	Homo sapiens (73)
	Hirudo medicinalis (63)
	Bos taurus (12)
	synthetic construct (8)
	Theonella sp. (1)
	unidentified (1)

Taxonomy

	Eukaryota (85)
	Eukaryota (eukaryotes) (9)
	other sequences (8)
	unclassified sequences (1)

Experimental Method

	X-RAY DIFFRACTION (85)
	NEUTRON DIFFRACTION (1)

Polymer Entity Type

Protein (85)

Refinement Resolution (Å)

	1.0 - 1.5 (17)
	1.5 - 2.0 (51)
	2.0 - 2.5 (17)
	2.5 - 3.0 (1)

Release Date

	1990 - 1994 (3)
	1995 - 1999 (5)
	2000 - 2004 (2)
	2005 - 2009 (41)
	2010 - 2014 (30)
	2015 - 2019 (3)
	2020 - 2024 (1)

Enzyme Classification Name

Hydrolases (85)

Symmetry Type

	Asymmetric (85)
	Cyclic (1)

SCOP Classification

	All beta proteins (27)
	Small proteins (5)

AllSelected

1 to 25 of 85 Structures

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1A46 \| pdb_00001a46	Download File View File

THROMBIN COMPLEXED WITH HIRUGEN AND A BETA-STRAND MIMETIC INHIBITOR

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.12 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00K, NA

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1A4W \| pdb_00001a4w	Download File View File

CRYSTAL STRUCTURES OF THROMBIN WITH THIAZOLE-CONTAINING INHIBITORS: PROBES OF THE S1' BINDING SITE

Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

(1996) Biophys J 71: 2830-2839

Released	1998-04-29
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	NA, QWE

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1A5G \| pdb_00001a5g	Download File View File

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

St Charles, R., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.06 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00L, NA

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1A61 \| pdb_00001a61	Download File View File

THROMBIN COMPLEXED WITH A BETA-MIMETIC THIAZOLE-CONTAINING INHIBITOR

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A., Kahn, M.

(1999) J Med Chem 42: 1376-1383

Released	1998-06-17
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein)
Unique Ligands	00N, NA

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1DOJ \| pdb_00001doj	Download File View File

Crystal structure of human alpha-thrombin*RWJ-51438 complex at 1.7 A

Recacha, R., Costanzo, M.J., Maryanoff, B.E., Carson, M., DeLucas, L., Chattopadhyay, D.

(2000) Acta Crystallogr D Biol Crystallogr 56: 1395-1400

Released	2000-11-03
Method	X-RAY DIFFRACTION 1.7 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (protein) HIRUGEN (protein)
Unique Ligands	1Z0, NA, NAG

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1EB1 \| pdb_00001eb1	Download File View File

Complex structure of human thrombin with N-methyl-arginine inhibitor

Friedrich, R., Steinmetzer, T., Bode, W.

(2002) J Mol Biology 316: 869

Released	2002-01-28
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	3-CYCLOHEXYL-D-ALANYL-L-PROLYL-N~2~-METHYL-L-ARGININE (protein) PEPTIDE INHIBITOR (protein) THROMBIN HEAVY CHAIN (protein) THROMBIN LIGHT CHAIN (protein)

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1TBZ \| pdb_00001tbz	Download File View File

HUMAN THROMBIN WITH ACTIVE SITE N-METHYL-D PHENYLALANYL-N-[5-(AMINOIMINOMETHYL)AMINO]-1-{{BENZOTHIAZOLYL)CARBONYL] BUTYL]-L-PROLINAMIDE TRIFLUROACETATE AND EXOSITE-HIRUGEN

Matthews, J.H., Krishnan, R., Costanzo, M.J., Maryanoff, B.E., Tulinsky, A.

(1996) Biophys J 71: 2830-2839

Released	1998-05-27
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (protein) HIRUGEN (protein)
Unique Ligands	00Q, NA

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1TMB \| pdb_00001tmb	Download File View File

MOLECULAR BASIS FOR THE INHIBITION OF HUMAN ALPHA-THROMBIN BY THE MACROCYCLIC PEPTIDE CYCLOTHEONAMIDE A

Qiu, X., Padmanabhan, K.P., Maryanoff, B.E., Tulinsky, A.

(1993) Proc Natl Acad Sci U S A 90: 8048-8052

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.3 Å
Organisms	Hirudo medicinalis Homo sapiens Theonella sp.
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) HIRUGEN (protein) cyclotheonamide A (protein)

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1TMT \| pdb_00001tmt	Download File View File

CHANGES IN INTERACTIONS IN COMPLEXES OF HIRUDIN DERIVATIVES AND HUMAN ALPHA-THROMBIN DUE TO DIFFERENT CRYSTAL FORMS

Priestle, J.P., Gruetter, M.G.

(1993) Protein Sci 2: 1630-1642

Released	1994-09-30
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) CGP 50,856 INHIBITOR, cleaved C-terminal hirudin fragment (protein) CGP 50,856 INHIBITOR, cleaved N-terminal tripeptide fragment, d-Phe-Pro-Arg (protein)
Unique Ligands	NAG

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2FEQ \| pdb_00002feq	Download File View File

orally active thrombin inhibitors

Mack, H., Baucke, D., Hornberger, W., Lange, U.E.W., Hoeffken, H.W.

(2006) Bioorg Med Chem Lett 16: 2641-2647

Released	2006-08-08
Method	X-RAY DIFFRACTION 2.44 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Decapeptide Hirudin Analogue (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	34P

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2FES \| pdb_00002fes	Download File View File

Orally active thrombin inhibitors

Hoeffken, H.W.

(2006) Bioorg Med Chem Lett 16: 2641-2647

Released	2006-05-09
Method	X-RAY DIFFRACTION 2.42 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Decapeptide Hirudin Analogue (protein) Thrombin heavy chain (protein) Thrombin light chain (protein)
Unique Ligands	3SP

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2HGT \| pdb_00002hgt	Download File View File

STRUCTURE OF THE HIRUGEN AND HIRULOG 1 COMPLEXES OF ALPHA-THROMBIN

Tulinsky, A., Carperos, V.

(1991) J Mol Biology 221: 1379-1393

Released	1994-01-31
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	ALPHA-THROMBIN (LARGE SUBUNIT) (protein) ALPHA-THROMBIN (SMALL SUBUNIT) (protein) Hirulog (protein)

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2WPH \| pdb_00002wph	Download File View File

factor IXa superactive triple mutant

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

Released	2009-12-22
Method	X-RAY DIFFRACTION 1.5 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	COAGULATION FACTOR IXA HEAVY CHAIN (protein) COAGULATION FACTOR IXA LIGHT CHAIN (protein) D-PHE-PRO-ARG-CHLOROMETHYL KETONE (protein)
Unique Ligands	1PE, CA

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2WPI \| pdb_00002wpi	Download File View File

factor IXa superactive double mutant

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

Released	2009-12-22
Method	X-RAY DIFFRACTION 1.99 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	COAGULATION FACTOR IXA HEAVY CHAIN (protein) COAGULATION FACTOR IXA LIGHT CHAIN (protein) D-PHE-PRO-ARG-CHLOROMETHYL KETONE (protein)
Unique Ligands	CA

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2WPJ \| pdb_00002wpj	Download File View File

factor IXa superactive triple mutant, NaCl-soaked

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

Released	2009-12-22
Method	X-RAY DIFFRACTION 1.6 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	COAGULATION FACTOR IXA HEAVY CHAIN (protein) COAGULATION FACTOR IXA LIGHT CHAIN (protein) D-PHE-PRO-ARG-CHLOROMETHYL KETONE (protein)
Unique Ligands	CA

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2WPK \| pdb_00002wpk	Download File View File

factor IXa superactive triple mutant, ethylene glycol-soaked

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

Released	2009-12-22
Method	X-RAY DIFFRACTION 2.21 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	COAGULATION FACTOR IXA HEAVY CHAIN (protein) COAGULATION FACTOR IXA LIGHT CHAIN (protein) D-PHE-PRO-ARG-CHLOROMETHYL KETONE (protein)
Unique Ligands	CA, EDO

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2WPL \| pdb_00002wpl	Download File View File

factor IXa superactive triple mutant, EDTA-soaked

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

Released	2009-12-22
Method	X-RAY DIFFRACTION 1.82 Å
Organisms	Homo sapiens synthetic construct
Macromolecule	COAGULATION FACTOR IXA HEAVY CHAIN (protein) COAGULATION FACTOR IXA LIGHT CHAIN (protein) D-PHE-PRO-ARG-CHLOROMETHYL KETONE (protein)

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2ZC9 \| pdb_00002zc9	Download File View File

Thrombin in complex with Inhibitor

Baum, B., Heine, A., Klebe, G.

(2009) J Mol Biology 391: 552-564

Released	2008-10-28
Method	X-RAY DIFFRACTION 1.58 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Hirudin variant-1 (protein) Thrombin Heavy Chain (protein) Thrombin Light Chain (protein)
Unique Ligands	22U, NA

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2ZDA \| pdb_00002zda	Download File View File

Exploring Thrombin S1 pocket

Baum, B., Heine, A., Klebe, G.

(2009) J Mol Biology 391: 552-564

Released	2008-10-28
Method	X-RAY DIFFRACTION 1.73 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Hirudin variant-1 (protein) Thrombin Heavy Chain (protein) Thrombin Light Chain (protein)
Unique Ligands	32U, NA, PO4

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2ZDK \| pdb_00002zdk	Download File View File

Exploring Trypsin S3 Pocket

Baum, B., Brandt, T., Heine, A., Klebe, G.

(2011) J Mol Biology 405: 1170-1187

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.67 Å
Organisms	Bos taurus
Macromolecule	Cationic trypsin (protein)
Unique Ligands	50U, CA, DMS, GOL, SO4

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2ZDL \| pdb_00002zdl	Download File View File

Exploring trypsin S3 pocket

Baum, B., Brandt, T., Heine, A., Klebe, G.

(2011) J Mol Biology 405: 1170-1187

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.8 Å
Organisms	Bos taurus
Macromolecule	Cationic trypsin (protein)
Unique Ligands	45U, CA, GOL, SO4

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2ZDM \| pdb_00002zdm	Download File View File

Exploring trypsin S3 pocket

Baum, B., Brandt, T., Heine, A., Klebe, G.

(2011) J Mol Biology 405: 1170-1187

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.93 Å
Organisms	Bos taurus
Macromolecule	Cationic trypsin (protein)
Unique Ligands	46U, CA, GOL

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2ZDN \| pdb_00002zdn	Download File View File

Exploring trypsin S3 pocket

Baum, B., Brandt, T., Heine, A., Klebe, G.

(2011) J Mol Biology 405: 1170-1187

Released	2008-10-14
Method	X-RAY DIFFRACTION 1.98 Å
Organisms	Bos taurus
Macromolecule	Cationic trypsin (protein)
Unique Ligands	49U, CA, GOL

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2ZDV \| pdb_00002zdv	Download File View File

Exploring Thrombin S1 pocket

Baum, B., Heine, A., Klebe, G.

To be published

Released	2008-10-28
Method	X-RAY DIFFRACTION 1.72 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Hirudin variant-1 (protein) Thrombin Heavy Chain (protein) Thrombin Light Chain (protein)
Unique Ligands	37U, NA, PO4

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2ZF0 \| pdb_00002zf0	Download File View File

Exploring Thrombin S1 Pocket

Baum, B., Heine, A., Klebe, G.

To be published

Released	2008-11-04
Method	X-RAY DIFFRACTION 2.2 Å
Organisms	Hirudo medicinalis Homo sapiens
Macromolecule	Hirudin variant-1 (protein) Thrombin Heavy Chain (protein) Thrombin Light Chain (protein)
Unique Ligands	51U, NA

1 to 25 of 85 Structures

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Structure Determination Methodology

Scientific Name of Source Organism

Taxonomy

Experimental Method

Polymer Entity Type

Refinement Resolution (Å)

Release Date

Enzyme Classification Name

Symmetry Type

SCOP Classification

1A46 | pdb_00001a46

1A4W | pdb_00001a4w

1A5G | pdb_00001a5g

1A61 | pdb_00001a61

1DOJ | pdb_00001doj

1EB1 | pdb_00001eb1

1TBZ | pdb_00001tbz

1TMB | pdb_00001tmb

1TMT | pdb_00001tmt

2FEQ | pdb_00002feq

2FES | pdb_00002fes

2HGT | pdb_00002hgt

2WPH | pdb_00002wph

2WPI | pdb_00002wpi

2WPJ | pdb_00002wpj

2WPK | pdb_00002wpk

2WPL | pdb_00002wpl

2ZC9 | pdb_00002zc9

2ZDA | pdb_00002zda

2ZDK | pdb_00002zdk

2ZDL | pdb_00002zdl

2ZDM | pdb_00002zdm

2ZDN | pdb_00002zdn

2ZDV | pdb_00002zdv

2ZF0 | pdb_00002zf0