2ZP0

Human factor viia-tissue factor complexed with benzylsulfonamide-D-ile-gln-P-aminobenzamidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Peptide Mimetic Factor VIIa Inhibitor: Importance of Hydrophilic Pocket in S2 Site to Improve Selectivity aganist Thrombin

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

(2005) Lett Drug Des Discov 2: 177-181


Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VII light chainA [auth L]152Homo 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
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VII heavy chainB [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: 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PI0 (Subject of Investigation/LOI)
Query on PI0

Download Ideal Coordinates CCD File 
O [auth H](2S)-N-[(4-carbamimidoylphenyl)methyl]-2-[[(2R,3R)-3-methyl-2-(phenylmethylsulfonylamino)pentanoyl]amino]pentanediamide
C26 H36 N6 O5 S
RKXCEYZSZWJMTQ-FRGLQRNOSA-N
 Ligand Interaction
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
D [auth L]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC (Subject of Investigation/LOI)
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] , K [auth L] , L , M [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
PI0 PDBBind:  2ZP0 IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.37α = 90
b = 81.99β = 90
c = 123.31γ = 90
Software Package:
Software NamePurpose
CNXrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary