1G37

CRYSTAL STRUCTURE OF HUMAN ALPHA-THROMBIN COMPLEXED WITH BCH-10556 AND EXOSITE-DIRECTED PEPTIDE

PDB DOI: https://doi.org/10.2210/pdb1G37/pdb

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

Deposited: 2000-10-23 Released: 2001-04-21
Deposition Author(s): Bachand, B., Tarazi, M., St-Denis, Y., Edmunds, J.J., Winocour, P.D., Leblond, L., Siddiqui, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Potent and selective bicyclic lactam inhibitors of thrombin. Part 4: transition state inhibitors.

Bachand, B., Tarazi, M., St-Denis, Y., Edmunds, J.J., Winocour, P.D., Leblond, L., Siddiqui, M.A.

(2001) Bioorg Med Chem Lett 11: 287-290

PubMed: 11212093 Search on PubMed
DOI: https://doi.org/10.1016/s0960-894x(00)00636-3
Primary Citation of Related Structures:
1G37

PubMed Abstract:
Bicyclic piperazinone based thrombin inhibitors of general structure 2 were prepared and evaluated in vitro and in vivo. These inhibitors, having in common an electrophilic basic trans-cyclohexylamine P1 residue, displayed high thrombin affinity, high selectivity against trypsin and good in vivo efficacy in the rat arterial thrombosis model.

Organizational Affiliation

BioChem Pharma Inc., Laval, Québec, Canada. bachandb@biochempharma.com

Macromolecule Content

Total Structure Weight: 34.72 kDa
Atom Count: 2,444
Modelled Residue Count: 286
Deposited Residue Count: 296
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	A	287	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
THROMBIN NONAPEPTIDE INHIBITOR	B	9	N/A	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
110 Query on 110 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	3-(4-AMINO-CYCLOHEXYL)-2-HYDROXY-3-[(4-OXO-2-PHENYLMETHANESULFONYL-1,2,3,4-TETRAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBONYL)-AMINO]-PROPIONIC ACID BUTYL ESTER C₂₈ H₃₈ N₄ O₇ S RFAVPVOPIIHJKP-KCXKOMAXSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
110	PDBBind: 1G37	IC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.45	α = 90
b = 72.03	β = 100.71
c = 73.15	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2001-04-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2001-04-21
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: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description