1TA6

Crystal structure of thrombin in complex with compound 14b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 

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
  • Structures With Same Primary Citation

  • 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 sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Hirudin
B
11Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Go to UniProtKB:  P28504
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
177
Query on 177

Download CCD File 
A
1-[2-AMINO-2-CYCLOHEXYL-ACETYL]-PYRROLIDINE-3-CARBOXYLIC ACID 5-CHLORO-2-(2-ETHYLCARBAMOYL-ETHOXY)-BENZYLAMIDE
C24 H35 Cl N4 O4
BMHVHOJXEQTIEA-SIKLNZKXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
BL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
177Ki :  0.7400000095367432   nM  PDBBind
177Ki:  0.7400000095367432   nM  Binding MOAD
177Ki:  0.7400000095367432   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Work: 0.186 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.4α = 90
b = 72.14β = 101
c = 73.52γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • 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