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: 2.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 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 61: 169-173

  • DOI: 10.1107/S1744309105000047

  • 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 inh ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII
L
152Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII
H
254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tissue factor
T
218Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Go to Gene View: F3
Go to UniProtKB:  P13726
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3CB
Query on 3CB

Download SDF File 
Download CCD File 
H
N-[(3-CARBOXYBENZYL)SULFONYL]ISOLEUCYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}-5-IMINOORNITHINAMIDE
3-({1-[3-CARBAMIMIDOYL-1-(4-CARBAMIMIDOYL-BENZYLCARBAMOYL)-PROPYLCARBAMOYL]-2-METHYL-BUTYLSULFAMOYL}-METHYL)-BENZOIC ACID
C27 H37 N7 O6 S
UBGNMISWPGURDN-XORNHQRDSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
H, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

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Download CCD File 
L
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
L
L-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: 2.6 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.560α = 90.00
b = 82.300β = 90.00
c = 123.520γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
CNXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-10
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2014-07-23
    Type: Structure summary