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

  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene 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
Thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Decapeptide Hirudin Analogue
D
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
163
Query on 163

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000480
Query on PRD_000480
DHIRUDIN ANALOGUEOligopeptide / Anticoagulant, Antithrombotic

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
163IC50: 6.2 nM BINDINGMOAD
163IC50: 6.2 nM PDBBIND
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 = 70.880α = 90.00
b = 71.960β = 101.06
c = 73.520γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
X-GENdata scaling
X-GENdata reduction
SMARTdata collection
SMARTdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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