4NA9 | pdb_00004na9

Factor VIIa in complex with the inhibitor 3'-amino-5'-[(2s,4r)-6-carbamimidoyl-4-phenyl-1,2,3,4-tetrahydroquinolin-2-yl]biphenyl-2-carboxylic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.222 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4NA9

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Tetrahydroquinoline Derivatives as Potent and Selective Factor XIa Inhibitors.

Quan, M.L.Wong, P.C.Wang, C.Woerner, F.Smallheer, J.M.Barbera, F.A.Bozarth, J.M.Brown, R.L.Harpel, M.R.Luettgen, J.M.Morin, P.E.Peterson, T.Ramamurthy, V.Rendina, A.R.Rossi, K.A.Watson, C.A.Wei, A.Zhang, G.Seiffert, D.Wexler, R.R.

(2014) J Med Chem 57: 955-969

  • DOI: https://doi.org/10.1021/jm401670x
  • Primary Citation Related Structures: 
    4NA7, 4NA8, 4NA9

  • PubMed Abstract: 

    Antithrombotic agents that are inhibitors of factor XIa (FXIa) have the potential to demonstrate robust efficacy with a low bleeding risk profile. Herein, we describe a series of tetrahydroquinoline (THQ) derivatives as FXIa inhibitors. Compound 1 was identified as a potent and selective tool compound for proof of concept studies. It exhibited excellent antithrombotic efficacy in rabbit thrombosis models and did not prolong bleeding times. This demonstrates proof of concept for the FXIa mechanism in animal models with a reversible, small molecule inhibitor.


  • Organizational Affiliation
    • Discovery Chemistry and Cardiovascular Biology, Research and Development, Bristol-Myers Squibb Company , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08543, United States.

Macromolecule Content 

  • Total Structure Weight: 34.64 kDa 
  • Atom Count: 2,621 
  • 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
Coagulation factor VII heavy chainA [auth H]254Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor VII light chainB [auth L]55Homo 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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1T7

Query on 1T7



Download:Ideal Coordinates CCD File
C [auth H]3'-amino-5'-[(2S,4R)-6-carbamimidoyl-4-phenyl-1,2,3,4-tetrahydroquinolin-2-yl]biphenyl-2-carboxylic acid
C29 H26 N4 O2
XUJJWQQLMFLJKO-SQHAQQRYSA-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: 2.24 Å
  • R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.222 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.21α = 90
b = 95.21β = 90
c = 115.71γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2014-02-12 
  • Deposition Author(s): Wei, A.

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-02-26
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary