1W0Y

tf7a_3771 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of Selective Phenylglycine Amide Tissue Factor/Factor Viia Inhibitors

Groebke-Zbinden, K.Banner, D.W.Ackermann, J.D'Arcy, A.Kirchhofer, D.Ji, Y.-H.Tschopp, T.B.Wallbaum, S.Weber, L.

(2005) Bioorg Med Chem Lett 15: 817

  • DOI: 10.1016/j.bmcl.2004.10.092
  • Primary Citation of Related Structures:  
    1W0Y, 1W2K

  • PubMed Abstract: 
  • Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling ...

    Proof of concept experiments have shown that tissue factor/factor VIIa inhibitors have antithrombotic activity without enhancing bleeding propensity. Starting from lead compounds generated by a biased combinatorial approach, phenylglycine amide tissue factor/factor VIIa inhibitors with low nanomolar affinity and good selectivity against other serine proteases of the coagulation cascade were designed, using the guidance of X-ray structural analysis and molecular modelling.


    Related Citations: 
    • The Crystal Structure of the Complex of Blood Coagulation Factor Viia with Soluble Tissue Factor
      Banner, D.W., D'Arcy, A., Chene, C., Winkler, F.K., Guha, A., Konigsberg, W.H., Nemerson, Y., Kirchhofer, D.
      (1996) Nature 380: 41

    Organizational Affiliation

    F. Hoffmann-La Roche Ltd, CH-4070 Basel, Switzerland. katrin.groebke_zbinden@roche.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BLOOD COAGULATION FACTOR VIIAA [auth H]254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
BLOOD COAGULATION FACTOR VIIAB [auth L]142Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TISSUE FACTORC [auth T]210Homo sapiensMutation(s): 0 
Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
PHAROS:  P13726
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
771
Query on 771

Download Ideal Coordinates CCD File 
D [auth H]4-(4-BENZYLOXY-2-METHANESULFONYLAMINO-5-METHOXY-BENZYLAMINO)-BENZAMIDINE
C23 H26 N4 O4 S
CRFICMUDNBIMKL-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download Ideal Coordinates CCD File 
P [auth L]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

Download Ideal Coordinates CCD File 
G [auth L]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
F [auth H]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth H] , H [auth L] , I [auth L] , J [auth L] , K [auth L] , L , M [auth L] , N [auth L] , 
E [auth H],  H [auth L],  I [auth L],  J [auth L],  K [auth L],  L,  M [auth L],  N [auth L],  O [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
B [auth L]L-PEPTIDE LINKINGC6 H9 N O6GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
771Ki:  380   nM  BindingDB
771Ki:  380   nM  Binding MOAD
771Ki :  380   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.338α = 90
b = 82.378β = 90
c = 123.963γ = 90
Software Package:
Software NamePurpose
CNXrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary