1DVA

Crystal Structure of the Complex Between the Peptide Exosite Inhibitor E-76 and Coagulation Factor VIIA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Peptide exosite inhibitors of factor VIIa as anticoagulants.

Dennis, M.S., Eigenbrot, C., Skelton, N.J., Ultsch, M.H., Santell, L., Dwyer, M.A., O'Connell, M.P., Lazarus, R.A.

(2000) Nature 404: 465-470

  • DOI: 10.1038/35006574
  • Primary Citation of Related Structures:  
    1DVA

  • PubMed Abstract: 

    • Potent anticoagulants have been derived by targeting the tissue factor-factor VIIa complex with naive peptide libraries displayed on M13 phage. The peptides specifically block the activation of factor X with a median inhibitory concentration of 1 nM and selectively inhibit tissue-factor-dependent clotting ...

    Potent anticoagulants have been derived by targeting the tissue factor-factor VIIa complex with naive peptide libraries displayed on M13 phage. The peptides specifically block the activation of factor X with a median inhibitory concentration of 1 nM and selectively inhibit tissue-factor-dependent clotting. The peptides do not bind to the active site of factor VIIa; rather, they work by binding to an exosite on the factor VIIa protease domain, and non-competitively inhibit activation of factor X and amidolytic activity. One such peptide (E-76) has a well defined structure in solution determined by NMR spectroscopy that is similar to the X-ray crystal structure when complexed with factor VIIa. These structural and functional studies indicate an allosteric 'switch' mechanism of inhibition involving an activation loop of factor VIIa and represent a new framework for developing inhibitors of serine proteases.

    Organizational Affiliation: 

    Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DES-GLA FACTOR VIIA (HEAVY CHAIN)A [auth H], D [auth I]254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
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Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DES-GLA FACTOR VIIA (LIGHT CHAIN)B [auth L], E [auth M]101Homo 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
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE E-76C [auth X], F [auth Y]20N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseG [auth A]2 O-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Z6
Query on 0Z6
Download Ideal Coordinates CCD File 
 H, N [auth I]D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide
C25 H36 Cl N6 O3
ZKHBINZTIMXMQW-CLAROIROSA-O		 Ligand Interaction
GLC
Query on GLC
Download Ideal Coordinates CCD File 
 Q [auth M]alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N		 Ligand Interaction
FUL
Query on FUL
Download Ideal Coordinates CCD File 
 R [auth M]beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N		 Ligand Interaction
FUC
Query on FUC
Download Ideal Coordinates CCD File 
 K [auth L], Lalpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N		 Ligand Interaction
CAC
Query on CAC
Download Ideal Coordinates CCD File 
 J [auth H], P [auth I]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 I [auth H], M [auth L], O [auth I], S [auth M]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 2 Unique
Entity ID: 5
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000369 (0Z6)
Query on PRD_000369		 H, N [auth I]D-Phe-Phe-Arg ChloromethylketonePeptide-like /  Inhibitor

--

Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900004
Query on PRD_900004		G [auth A]beta-lactoseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.49α = 90
b = 55.26β = 99.48
c = 111.73γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing
X-PLORrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-05-12
    Type: Initial release
  • Version 1.1: 2008-01-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary