3C1K

Crystal structure of thrombin in complex with inhibitor 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure-based design of novel groups for use in the P1 position of thrombin inhibitor scaffolds. Part 2: N-acetamidoimidazoles.

Isaacs, R.C.Solinsky, M.G.Cutrona, K.J.Newton, C.L.Naylor-Olsen, A.M.McMasters, D.R.Krueger, J.A.Lewis, S.D.Lucas, B.J.Kuo, L.C.Yan, Y.Lynch, J.J.Lyle, E.A.

(2008) Bioorg Med Chem Lett 18: 2062-2066

  • DOI: 10.1016/j.bmcl.2008.01.098
  • Primary Citation of Related Structures:  
    3C1K

  • PubMed Abstract: 
  • Guided by X-ray crystallography of thrombin-inhibitor complexes and molecular modeling, alkylation of the N1 nitrogen of the imidazole P1 ligand of the pyridinoneacetamide thrombin inhibitor 1 with various acetamide moieties furnished inhibitors with significantly improved thrombin potency, trypsin selectivity, functional in vitro anticoagulant potency and in vivo antithrombotic efficacy ...

    Guided by X-ray crystallography of thrombin-inhibitor complexes and molecular modeling, alkylation of the N1 nitrogen of the imidazole P1 ligand of the pyridinoneacetamide thrombin inhibitor 1 with various acetamide moieties furnished inhibitors with significantly improved thrombin potency, trypsin selectivity, functional in vitro anticoagulant potency and in vivo antithrombotic efficacy. In the pyrazinoneacetamide series, oral bioavailability was also improved.


    Organizational Affiliation

    Department of Medicinal Chemistry, Merck Research Laboratories, West Point, PA 19486, USA. richard_isaacs@merck.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProthrombinA287Homo sapiensMutation(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
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Protein Feature View
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HirugenB11Hirudo medicinalisMutation(s): 0 
UniProt
Find proteins for P28511 (Hirudo medicinalis)
Explore P28511 
Go to UniProtKB:  P28511
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28511
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T15
Query on T15

Download Ideal Coordinates CCD File 
C [auth A]2-{3-[(benzylsulfonyl)amino]-6-methyl-2-oxopyridin-1(2H)-yl}-N-({1-[2-(tert-butylamino)-2-oxoethyl]-4-methyl-1H-imidazol-5-yl}methyl)acetamide
C26 H34 N6 O5 S
JIBFIIUWYBXSQB-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
B L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
T15 Binding MOAD:  3C1K Ki: 0.36 (nM) from 1 assay(s)
PDBBind:  3C1K Ki: 0.36 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.839α = 90
b = 72.279β = 101.19
c = 73.195γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2008-01-23 
  • Released Date: 2008-03-18 
  • Deposition Author(s): Yan, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2013-03-13
    Changes: Other