1G30

THROMBIN INHIBITOR COMPLEX

PDB DOI: https://doi.org/10.2210/pdb1G30/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, Hirudo medicinalis
Mutation(s): No

Deposited: 2000-10-23 Released: 2001-10-23
Deposition Author(s): Nar, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.

Nar, H., Bauer, M., Schmid, A., Stassen, J.M., Wienen, W., Priepke, H.W., Kauffmann, I.K., Ries, U.J., Hauel, N.H.

(2001) Structure 9: 29-38

PubMed: 11342132 Search on PubMed
DOI: https://doi.org/10.1016/s0969-2126(00)00551-7
Primary Citation of Related Structures:
1G2L, 1G2M, 1G30, 1G32, 1G36, 1OYQ

PubMed Abstract:
A major current focus of pharmaceutical research is the development of selective inhibitors of the blood coagulation enzymes thrombin or factor Xa to be used as orally bioavailable anticoagulant drugs in thromboembolic disorders and in the prevention of venous and arterial thrombosis. Simultaneous direct inhibition of thrombin and factor Xa by synthetic proteinase inhibitors as a novel approach to antithrombotic therapy could result in potent anticoagulants with improved pharmacological properties.

Organizational Affiliation

Department of Medicinal Chemistry, Boehringer Ingelheim Pharma KG, 88397 Biberach an der Riss, Germany. herbert.nar@bc.boehringer-ingelheim.com

Macromolecule Content

Total Structure Weight: 35.89 kDa
Atom Count: 2,591
Modelled Residue Count: 289
Deposited Residue Count: 306
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTHROMBIN	A	36	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTHROMBIN	B	259	Homo sapiens	Mutation(s): 0 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734 Go to UniProtKB: P00734
PHAROS: P00734 GTEx: ENSG00000180210
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00734
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HIRUDIN IIB	C	11	Hirudo medicinalis	Mutation(s): 0
UniProt
Find proteins for P28504 (Hirudo medicinalis) Explore P28504 Go to UniProtKB: P28504
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28504
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T87 Query on T87 Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B]	D [auth B]	[(1-{2[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-1-METHYL-1H-BENZOIMIDAZOL-5-YL}-CYCLOPROPYL)-PYRIDIN-2-YL-METHYLENEAMINOOXY]-ACETIC ACID ETHYL ESTER C₂₉ H₃₁ N₇ O₃ RNOYCNIZOAIUSV-LSWMGQQCSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TYS Query on TYS	C	L-PEPTIDE LINKING	C₉ H₁₁ N O₆ S		TYR

Binding Affinity Annotations
ID	Source	Binding Affinity
T87	PDBBind: 1G30	Ki: 140 (nM) from 1 assay(s)
	BindingDB: 1G30	Ki: 140 (nM) from 1 assay(s)
	Binding MOAD: 1G30	Ki: 140 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.264
R-Value Work: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.3	α = 90
b = 70.9	β = 100.3
c = 72.8	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
CNX	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2001-10-23

Deposition Author(s):

Nar, H.

Revision History (Full details and data files)

Version 1.0: 2001-10-23
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2012-12-12
Changes: Other
Version 1.4: 2013-03-13
Changes: Other
Version 1.5: 2018-10-03
Changes: Advisory, Data collection