1O0D

Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

D-Phe-Pro-Arg type thrombin inhibitors: unexpected selectivity by modification of the P1 moiety

Lange, U.E.Bauke, D.Hornberger, W.Mack, H.Seitz, W.Hoeffken, H.W.

(2003) Bioorg Med Chem Lett 13: 2029-2033

  • DOI: https://doi.org/10.1016/s0960-894x(03)00347-0
  • Primary Citation of Related Structures:  
    1NZQ, 1O0D

  • PubMed Abstract: 

    Synthesis of thrombin inhibitors and their binding mode to thrombin is described. Modification of the P1 moiety leads to an increased selectivity versus trypsin. The observed selectivity is discussed in view of their thrombin-inhibitor complex X-ray structures.


  • Organizational Affiliation

    BASF AG, D-67056, Ludwigshafen, Germany. wolfgang.hoeffken@basf-ag.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]36Homo 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
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chainB [auth H]259Homo 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
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Decapeptide Hirudin AnalogueC [auth D]11N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
163
Query on 163

Download Ideal Coordinates CCD File 
D [auth H](2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID
C23 H32 N6 O4
AXMHAIYMRMPDQD-QGZVFWFLSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
ALC
Query on ALC
C [auth D]L-PEPTIDE LINKINGC9 H17 N O2ALA
HYP
Query on HYP
C [auth D]L-PEPTIDE LINKINGC5 H9 N O3PRO
SMF
Query on SMF
C [auth D]L-PEPTIDE LINKINGC10 H13 N O5 SPHE
Binding Affinity Annotations 
IDSourceBinding Affinity
163 PDBBind:  1O0D IC50: 6.2 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.88α = 90
b = 71.96β = 101.06
c = 73.52γ = 90
Software Package:
Software NamePurpose
SMARTdata collection
X-GENdata reduction
CNSrefinement
SMARTdata reduction
X-GENdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-10-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    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: 2012-12-12
    Changes: Other
  • Version 1.4: 2016-05-25
    Changes: Source and taxonomy
  • Version 1.5: 2017-10-11
    Changes: Advisory, Refinement description
  • Version 1.6: 2018-04-04
    Changes: Data collection