3FFG

Factor XA in complex with the inhibitor (R)-6-(2'-((3- HYDROXYPYRROLIDIN-1-YL)METHYL)BIPHENYL-4-YL)-1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN- 7(4H)-ONE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 

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This is version 1.2 of the entry. See complete history. 


Literature

Phenyltriazolinones as potent factor Xa inhibitors.

Quan, M.L., Pinto, D.J., Rossi, K.A., Sheriff, S., Alexander, R.S., Amparo, E., Kish, K., Knabb, R.M., Luettgen, J.M., Morin, P., Smallwood, A., Woerner, F.J., Wexler, R.R.

(2010) Bioorg Med Chem Lett 20: 1373-1377

  • DOI: https://doi.org/10.1016/j.bmcl.2010.01.011
  • Primary Citation of Related Structures:  
    3FFG, 3KQB, 3KQC, 3KQD, 3KQE

  • PubMed Abstract: 

    We have discovered that phenyltriazolinone is a novel and potent P1 moiety for coagulation factor Xa. X-ray structures of the inhibitors with a phenyltriazolinone in the P1 position revealed that the side chain of Asp189 has reoriented resulting in a novel S1 binding pocket which is larger in size to accommodate the phenyltriazolinone P1 substrate.

    • Organizational Affiliation: 

    Research and Development, Bristol-Myers Squibb, PO Box 5400, Princeton, NJ 08543-5400, USA. mimi.quan@bms.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor X, heavy chain234Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor X, light chainB [auth L]52Homo sapiensMutation(s): 0 
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
GTEx:  ENSG00000126218 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FFG
Query on FFG
Download Ideal Coordinates CCD File 
C [auth A](R)-6-(2'-((3-hydroxypyrrolidin-1-yl)methyl)biphenyl-4-yl)-1-(3-(5-oxo-4,5-dihydro-1h-1,2,4-triazol-3-yl)phenyl)-3-(trifluoromethyl)-5,6-dihydro-1h-pyrazolo[3,4-c]pyridin-7(4h)-one
C32 H28 F3 N7 O3
YBWAYLVOTDFQQI-XMMPIXPASA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FFG PDBBind:  3FFG Ki: 0.84 (nM) from 1 assay(s)
BindingDB:  3FFG Ki: 0.84 (nM) from 1 assay(s)
Binding MOAD:  3FFG Ki: 0.84 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.9α = 90
b = 72.5β = 90
c = 78.8γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations