1TA2 | pdb_00001ta2

Crystal structure of thrombin in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work: 
    0.150 (Depositor) 
  • R-Value Observed: 
    0.151 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1TA2

This is version 1.4 of the entry. See complete history

Literature

Design and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position

Tucker, T.J.Brady, S.F.Lumma, W.C.Lewis, S.D.Gardel, S.J.Naylor-Olsen, A.M.Yan, Y.Sisko, J.T.Stauffer, K.J.Lucas, B.Y.Lynch, J.J.Cook, J.J.Stranieri, M.T.Holahan, M.A.Lyle, E.A.Baskin, E.P.Chen, I.-W.Dancheck, K.B.Krueger, J.A.Cooper, C.M.Vacca, J.P.

(1998) J Med Chem 41: 3210-3219

  • DOI: https://doi.org/10.1021/jm9801713
  • Primary Citation Related Structures: 
    1TA2, 1TA6

  • PubMed Abstract: 

    As part of an ongoing effort to prepare therapeutically useful orally active thrombin inhibitors, we have synthesized a series of compounds that utilize nonbasic groups in the P1 position. The work is based on our previously reported lead structure, compound 1, which was discovered via a resin-based approach to varying P1. By minimizing the size and lipophilicity of the P3 group and by incorporating hydrogen-bonding groups on the N-terminus or on the 2-position of the P1 aromatic ring, we have prepared a number of derivatives in this series that exhibit subnanomolar enzyme potency combined with good in vivo antithrombotic and bioavailability profiles. The oxyacetic amide compound 14b exhibited the best overall profile of in vitro and in vivo activity, and crystallographic studies indicate a unique mode of binding in the thrombin active site.


  • Organizational Affiliation
    • Departments of Medicinal Chemistry, Biological Chemistry, Pharmacology, Drug Metabolism, and Molecular Design and Diversity, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.

Macromolecule Content 

  • Total Structure Weight: 34.95 kDa 
  • Atom Count: 2,510 
  • Modeled Residue Count: 287 
  • Deposited Residue Count: 298 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
thrombin287Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Hirudin11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28504
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
176

Query on 176



Download:Ideal Coordinates CCD File
C [auth A]1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE-3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE
C27 H27 Cl2 N3 O2
VTUWWZYFAXSACB-UKILVPOCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
176 BindingDB:  1TA2 Ki: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Work:  0.150 (Depositor) 
  • R-Value Observed: 0.151 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.81α = 90
b = 72.36β = 100.9
c = 72.96γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary