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 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.3 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

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DES-GLA FACTOR VIIA (HEAVY CHAIN)
H, I
254Homo sapiensGene 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
DES-GLA FACTOR VIIA (LIGHT CHAIN)
L, M
101Homo sapiensGene 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
PEPTIDE E-76
X, Y
20N/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Z6
Query on 0Z6

Download SDF File 
Download CCD File 
H, I
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide
FFRCK
C25 H36 Cl N6 O3
ZKHBINZTIMXMQW-CLAROIROSA-O
 Ligand Interaction
CA
Query on CA

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

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

Download SDF File 
Download CCD File 
L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
L
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
M
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
CAC
Query on CAC

Download SDF File 
Download CCD File 
H, I
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
M
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000369 (0Z6)
Query on PRD_000369
H,ID-Phe-Phe-Arg ChloromethylketonePeptide-like / Inhibitor

--

Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
X, Y
NON-POLYMERH2 N

--

ACE
Query on ACE
X, Y
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.225 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.490α = 90.00
b = 55.260β = 99.48
c = 111.730γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
X-PLORrefinement
MOSFLMdata reduction
TRUNCATEdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-05-12
    Type: Initial release
  • Version 1.1: 2008-01-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other