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.

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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 

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 
• 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.

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Organizational Affiliation: 

BioChem Pharma Inc., Laval, Québec, Canada. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA THROMBIN	A	287	Homo sapiens	Mutation(s): 0  Gene Names: F2 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

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
110	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

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

Entry History 

Deposition Data

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

Revision History  

• 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