1TA2

Crystal structure of thrombin in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1021/jm9801713
  • Primary Citation of Related Structures:  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, ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
thrombin
A
287Homo sapiensGene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hirudin
B
11Hirudo medicinalisN/A
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
176
Query on 176

Download SDF File 
Download CCD File 
A
1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE-3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE
C27 H27 Cl2 N3 O2
VTUWWZYFAXSACB-UKILVPOCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
176Ki: 3 nM (100) BINDINGDB
176Ki: 3 nM BINDINGMOAD
176Ki: 3 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.810α = 90.00
b = 72.360β = 100.90
c = 72.960γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2004-06-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description