1JWT

CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH A NOVEL BICYCLIC LACTAM INHIBITOR

• PDB DOI:  https://doi.org/10.2210/pdb1JWT/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2001-09-05 Released: 2002-02-27 
• Deposition Author(s): Levesque, S., St-Denis, Y., Bachand, B., Preville, P., Leblond, L., Winocour, P.D., Edmunds, J.J., Rubin, J.R., Siddiqui, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.301 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 

Literature

Novel bicyclic lactam inhibitors of thrombin: potency and selectivity optimization through P1 residues.

Levesque, S., St-Denis, Y., Bachand, B., Preville, P., Leblond, L., Winocour, P.D., Edmunds, J.J., Rubin, J.R., Siddiqui, M.A.

(2001) Bioorg Med Chem Lett 11: 3161-3164

• PubMed: 11720865 
• DOI: https://doi.org/10.1016/s0960-894x(01)00661-8
• Primary Citation of Related Structures:  
  1JWT


• PubMed Abstract: 
  

Peptidomimetic inhibitors of thrombin lacking the important Ser195-carbonyl interaction have been prepared. The binding energy lost after the removal of the activated carbonyl was recaptured through a series of modifications of the P1 residues of the bicyclic lactam inhibitors. Selected substituted compounds displayed useful pharmacological profiles both in vitro and in vivo.

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Organizational Affiliation: 

Shire BioChem Inc., 275 Armand-Frappier Blvd., Laval, H7V 4A7, Québec, Canada. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 35.62 kDa 
• Atom Count: 2,463 
• Modelled Residue Count: 299 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	305	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BLI	B [auth A]	4-OXO-2-PHENYLMETHANESULFONYL-OCTAHYDRO-PYRROLO[1,2-A]PYRAZINE-6-CARBOXYLIC ACID [1-(N-HYDROXYCARBAMIMIDOYL)-PIPERIDIN-4-YLMETHYL]-AMIDE C22 H32 N6 O5 S DHTSUHWLPAEEQB-OALUTQOASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BLI	Binding MOAD:  1JWT	Ki: 14 (nM) from 1 assay(s)
	PDBBind:  1JWT	Ki: 14 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.301 
• R-Value Work: 0.182 
• R-Value Observed: 0.182 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.54	α = 90
b = 72.18	β = 100.99
c = 73.41	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
AUTOMAR	data reduction
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-27 
Deposition Author(s): Levesque, S., St-Denis, Y., Bachand, B., Preville, P., Leblond, L., Winocour, P.D., Edmunds, J.J., Rubin, J.R., Siddiqui, M.A.

Revision History  

• Version 1.0: 2002-02-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description