4NGA | pdb_00004nga

Factor viia in complex with the inhibitor (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-N-[2-(propan-2-ylsulfonyl)benzyl]ethanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.228 (Depositor), 0.223 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4NGA

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Design and Synthesis of Phenylpyrrolidine Phenylglycinamides As Highly Potent and Selective TF-FVIIa Inhibitors.

Zhang, X.Jiang, W.Jacutin-Porte, S.Glunz, P.W.Zou, Y.Cheng, X.Nirschl, A.H.Wurtz, N.R.Luettgen, J.M.Rendina, A.R.Luo, G.Harper, T.M.Wei, A.Anumula, R.Cheney, D.L.Knabb, R.M.Wong, P.C.Wexler, R.R.Priestley, E.S.

(2014) ACS Med Chem Lett 5: 188-192

  • DOI: https://doi.org/10.1021/ml400453z
  • Primary Citation Related Structures: 
    4NG9, 4NGA

  • PubMed Abstract: 

    Inhibitors of the Tissue Factor/Factor VIIa (TF-FVIIa) complex are promising novel anticoagulants that show excellent efficacy and minimal bleeding in preclinical models. On the basis of a zwitterionic phenylglycine acylsulfonamide 1, a phenylglycine benzylamide 2 was shown to possess improved permeability and oral bioavailability. Optimization of the benzylamide, guided by X-ray crystallography, led to a potent TF-FVIIa inhibitor 18i with promising oral bioavailability, but promiscuous activity in an in vitro safety panel of receptors and enzymes. Introducing an acid on the pyrrolidine ring, guided by molecular modeling, resulted in highly potent, selective, and efficacious TF-FVIIa inhibitors with clean in vitro safety profile. The pyrrolidine acid 20 showed a moderate clearance, low volume of distribution, and a short t 1/2 in dog PK studies.


  • Organizational Affiliation
    • Bristol-Myers Squibb R&D , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534-2130, United States.

Macromolecule Content 

  • Total Structure Weight: 35.43 kDa 
  • Atom Count: 2,706 
  • Modeled Residue Count: 309 
  • Deposited Residue Count: 309 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Factor VIIa (Heavy Chain)A [auth H]254Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Factor VIIa (Light Chain)B [auth L]55Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
2KF

Query on 2KF



Download:Ideal Coordinates CCD File
C [auth H](2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-N-[2-(propan-2-ylsulfonyl)benzyl]ethanamide
C32 H38 N4 O5 S
QHJUWQXHNUKLAP-SSEXGKCCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth H],
F [auth H],
G [auth H],
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth H],
J [auth H],
K [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.228 (Depositor), 0.223 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.13α = 90
b = 95.13β = 90
c = 117.06γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.3: 2024-11-27
    Changes: Structure summary