1G30

THROMBIN INHIBITOR COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.

Nar, H.Bauer, M.Schmid, A.Stassen, J.M.Wienen, W.Priepke, H.W.Kauffmann, I.K.Ries, U.J.Hauel, N.H.

(2001) Structure 9: 29-38

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A major current focus of pharmaceutical research is the development of selective inhibitors of the blood coagulation enzymes thrombin or factor Xa to be used as orally bioavailable anticoagulant drugs in thromboembolic disorders and in the prevention ...

    A major current focus of pharmaceutical research is the development of selective inhibitors of the blood coagulation enzymes thrombin or factor Xa to be used as orally bioavailable anticoagulant drugs in thromboembolic disorders and in the prevention of venous and arterial thrombosis. Simultaneous direct inhibition of thrombin and factor Xa by synthetic proteinase inhibitors as a novel approach to antithrombotic therapy could result in potent anticoagulants with improved pharmacological properties.


    Organizational Affiliation

    Department of Medicinal Chemistry, Boehringer Ingelheim Pharma KG, 88397 Biberach an der Riss, Germany. herbert.nar@bc.boehringer-ingelheim.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTHROMBIN
A
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
PROTHROMBIN
B
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
HIRUDIN IIB
C
11Hirudo medicinalisMutation(s): 0 
Find proteins for P28506 (Hirudo medicinalis)
Go to UniProtKB:  P28506
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
T87
Query on T87

Download SDF File 
Download CCD File 
B
[(1-{2[(4-CARBAMIMIDOYL-PHENYLAMINO)-METHYL]-1-METHYL-1H-BENZOIMIDAZOL-5-YL}-CYCLOPROPYL)-PYRIDIN-2-YL-METHYLENEAMINOOXY]-ACETIC ACID ETHYL ESTER
C29 H31 N7 O3
RNOYCNIZOAIUSV-LSWMGQQCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
C
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
T87Ki: 140 nM (100) BINDINGDB
T87Ki: 140 nM BINDINGMOAD
T87Ki: 140 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.210 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 69.300α = 90.00
b = 70.900β = 100.30
c = 72.800γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing
CNXrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2000-10-23 
  • Released Date: 2001-10-23 
  • Deposition Author(s): Nar, H.

Revision History 

  • Version 1.0: 2001-10-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    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: 2013-03-13
    Type: Other