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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Shire BioChem Inc., 275 Armand-Frappier Blvd., Laval, H7V 4A7, Québec, Canada. slevesque@ca.shire.com

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BLI Query on BLI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
BLI	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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-02-27

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary