3KQD

Factor xa in complex with the inhibitor 1-(3-(5-oxo-4,5- dihydro-1h-1,2,4-triazol-3-yl)phenyl)-6-(2'-(pyrrolidin-1- ylmethyl)biphenyl-4-yl)-3-(trifluoromethyl)-5,6-dihydro- 1h-pyrazolo[3,4-c]pyridin-7(4h)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


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: 10.1016/j.bmcl.2010.01.011
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
factor Xa heavy chain
A
234Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
factor Xa light chain
L
52Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LGL
Query on LGL

Download CCD File 
A
1-(3-(5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-3-YL)PHENYL)-6-(2'-(PYRROLIDIN-1-YLMETHYL)BIPHENYL-4-YL)-3-(TRIFLUOROMETHYL)-5,6-DIHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-7(4H)-ONE
C32 H28 F3 N7 O2
QNPOXJFBWDKXGC-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LGLKi :  0.4000000059604645   nM  PDBBind
LGLKi:  0.4000000059604645   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.7α = 90
b = 72.1β = 90
c = 76.8γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2009-11-17 
  • Released Date: 2010-02-23 
  • Deposition Author(s): Sheriff, S.

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description