1WSS

Human Factor Viia-Tissue Factor in Complex with peptide-mimetic inhibitor that has two charged groups in P2 and P4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.218 

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This is version 1.4 of the entry. See complete history


Literature

Structure of human factor VIIa/tissue factor in complex with a peptide-mimetic inhibitor: high selectivity against thrombin by introducing two charged groups in P2 and P4.

Kadono, S.Sakamoto, A.Kikuchi, Y.Oh-Eda, M.Yabuta, N.Koga, T.Hattori, K.Shiraishi, T.Haramura, M.Kodama, H.Ono, Y.Esaki, T.Sato, H.Watanabe, Y.Itoh, S.Ohta, M.Kozono, T.

(2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 169-173

  • DOI: 10.1107/S1744309105000047
  • Primary Citation of Related Structures:  
    1WSS

  • PubMed Abstract: 
  • The crystal structure of human factor VIIa/soluble tissue factor (FVIIa/sTF) in complex with a highly selective peptide-mimetic FVIIa inhibitor which shows 1670-fold selectivity against thrombin inhibition has been solved at 2.6 A resolution. The inhibitor is bound to FVIIa/sTF at the S1, S2 and S3 sites and at the additional S1 subsite ...

    The crystal structure of human factor VIIa/soluble tissue factor (FVIIa/sTF) in complex with a highly selective peptide-mimetic FVIIa inhibitor which shows 1670-fold selectivity against thrombin inhibition has been solved at 2.6 A resolution. The inhibitor is bound to FVIIa/sTF at the S1, S2 and S3 sites and at the additional S1 subsite. Two charged groups, the amidino group in P2 and the carboxylate group in P4, form ionic interactions with Asp60 and Lys192 of FVIIa, respectively. Structural comparisons between factor VIIa and thrombin show that thrombin has oppositely charged residues, Lys60F and Glu192, in the S2 site and the S1 subsites, respectively. These data suggest that the utilization of the differences of charge distribution in the S2 site and the S1 subsites between FVIIa and thrombin is critical for achieving high selectivity against thrombin inhibition. These results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF.


    Organizational Affiliation

    Fuji Gotemba Research Laboratories, Chugai Pharmaceutical Co. Ltd, 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. kadonosuj@chugai-pharm.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VII L152Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VII H254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
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 factor T218Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
NIH Common Fund Data Resources
PHAROS:  P13726
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
LL-PEPTIDE LINKINGC6 H9 N O6GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3CBIC50 :  17   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.56α = 90
b = 82.3β = 90
c = 123.52γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-07-23
    Changes: Structure summary
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary