1WUN

Human Factor Viia-Tissue Factor Complexed with ethylsulfonamide-D-Trp-Gln-p-aminobenzamidine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure-based design of P3 moieties in the peptide mimetic factor VIIa inhibitor

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Yoshihashi, K., Kitazawa, T., Suzuki, T., 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) Biochem Biophys Res Commun 327: 589-596

  • DOI: 10.1016/j.bbrc.2004.12.042
  • Primary Citation of Related Structures:  
    1WUN, 1WV7

  • PubMed Abstract: 

    • Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is seen as a promising target for developing new anticoagulant drugs. Structure-based designs of the P3 moiety in the peptide mimetic factor VIIa inhibitor successfully lead to novel inhibitors with selectivity for FVIIa/TF and extrinsic coagulation the same as or even higher than those of previously reported peptide mimetic factor VIIa inhibitors ...

    Selective factor VIIa-tissue factor complex (FVIIa/TF) inhibition is seen as a promising target for developing new anticoagulant drugs. Structure-based designs of the P3 moiety in the peptide mimetic factor VIIa inhibitor successfully lead to novel inhibitors with selectivity for FVIIa/TF and extrinsic coagulation the same as or even higher than those of previously reported peptide mimetic factor VIIa inhibitors. X-ray crystal structure analysis reveals that one of the novel inhibitors shows improved selectivity by forming interactions between the inhibitor and FVIIa as expected. Another of the novel inhibitors achieves improved selectivity through an unexpected hydrogen bond with Gln217, with a unique bent conformation in FVIIa/TF accompanied by conformational changes of the inhibitor and the protein.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIA [auth L]152Homo sapiensMutation(s): 10 
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIB [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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tissue factorC [auth T]218Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13726
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5B
Query on P5B
Download Ideal Coordinates CCD File 
O [auth H]N-(ETHYLSULFONYL)TRYPTOPHYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}GLUTAMAMIDE
C26 H33 N7 O5 S
FJGWLOKDOKYXMU-FCHUYYIVSA-N		 Ligand Interaction
BGC
Query on BGC
Download Ideal Coordinates CCD File 
D [auth L]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N		 Ligand Interaction
FUC
Query on FUC
Download Ideal Coordinates CCD File 
E [auth L]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
F [auth L],
G [auth L],
H [auth L],
I [auth L],
J [auth L],
F [auth L],
G [auth L],
H [auth L],
I [auth L],
J [auth L],
K [auth L],
L,
M [auth L],
N [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU		A [auth L]L-PEPTIDE LINKINGC6 H9 N O6GLU
Binding Affinity Annotations 
IDSourceBinding Affinity
P5B Binding MOAD:  1WUN IC50: 62 (nM) from 1 assay(s)
PDBBind:  1WUN IC50: 62 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.29α = 90
b = 82.53β = 90
c = 123.53γ = 90
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-08
    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: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary