4X8V

FACTOR VIIA IN COMPLEX WITH THE INHIBITOR (methyl {3-[(2R)-1-{(2R)-2-(3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]acetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}carbamate)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of Novel P1 Groups for Coagulation Factor VIIa Inhibition Using Fragment-Based Screening.

Cheney, D.L.Bozarth, J.M.Metzler, W.J.Morin, P.E.Mueller, L.Newitt, J.A.Nirschl, A.H.Rendina, A.R.Tamura, J.K.Wei, A.Wen, X.Wurtz, N.R.Seiffert, D.A.Wexler, R.R.Priestley, E.S.

(2015) J Med Chem 58: 2799-2808

  • DOI: 10.1021/jm501982k
  • Primary Citation of Related Structures:  
    4X8S, 4X8T, 4X8U, 4X8V

  • PubMed Abstract: 
  • A multidisciplinary, fragment-based screening approach involving protein ensemble docking and biochemical and NMR assays is described. This approach led to the discovery of several structurally diverse, neutral surrogates for cationic factor VIIa P1 ...

    A multidisciplinary, fragment-based screening approach involving protein ensemble docking and biochemical and NMR assays is described. This approach led to the discovery of several structurally diverse, neutral surrogates for cationic factor VIIa P1 groups, which are generally associated with poor pharmacokinetic (PK) properties. Among the novel factor VIIa inhibitory fragments identified were aryl halides, lactams, and heterocycles. Crystallographic structures for several bound fragments were obtained, leading to the successful design of a potent factor VIIa inhibitor with a neutral lactam P1 and improved permeability.


    Organizational Affiliation

    †Bristol-Myers Squibb Co., Research and Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VIIa (Heavy Chain)H254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS  P08709
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VIIa (Light Chain)L55Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS  P08709
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3Z9
Query on 3Z9

Download CCD File 
H
methyl {3-[(2R)-1-{(2R)-2-(3,4-dimethoxyphenyl)-2-[(1-oxo-1,2,3,4-tetrahydroisoquinolin-7-yl)amino]acetyl}pyrrolidin-2-yl]-4-(propan-2-ylsulfonyl)phenyl}carbamate
C34 H40 N4 O8 S
XGQHTIIEXCNFSG-DLFZDVPBSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3Z9Ki:  130   nM  BindingDB
3Z9Ki:  130   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.3α = 90
b = 95.3β = 90
c = 116.3γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2014-12-10 
  • Released Date: 2015-03-25 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references