4JZD

Structure of factor VIIA in complex with the inhibitor 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of nonbenzamidine factor VIIa inhibitors using a biaryl acid scaffold.

Bolton, S.A.Sutton, J.C.Anumula, R.Bisacchi, G.S.Jacobson, B.Slusarchyk, W.A.Treuner, U.D.Wu, S.C.Zhao, G.Pi, Z.Sheriff, S.Smirk, R.A.Bisaha, S.Cheney, D.L.Wei, A.Schumacher, W.A.Hartl, K.S.Liu, E.Zahler, R.Seiler, S.M.

(2013) Bioorg.Med.Chem.Lett. 23: 5239-5243

  • DOI: 10.1016/j.bmcl.2013.06.028
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compou ...

    In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compound 2) wherein potent inhibition of factor VIIa is maintained relative to most other related serine proteases. In an unanticipated result, the m-benzamide P1 (compounds 21a and 21b) proved to be a viable benzamidine replacement, albeit with a 20-40 fold loss in potency against factor VIIa.


    Organizational Affiliation

    Bristol-Myers Squibb Research & Development, Hopewell, NJ 08534-5400, USA. scott.bolton@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Factor VIIa (Heavy Chain)
H
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
Factor VIIa (Light Chain)
L
55Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
1NJ
Query on 1NJ

Download SDF File 
Download CCD File 
H
2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid
C28 H31 N5 O6
KPACBFJTZSMBKD-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1NJIC50: 5 nM (100) BINDINGDB
1NJKi: 10 nM (100) BINDINGDB
1NJIC50: 5 nM BINDINGMOAD
1NJIC50: 5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.164 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.830α = 90.00
b = 94.830β = 90.00
c = 118.490γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description