2G00

Factor Xa in complex with the inhibitor 3-(6-(2'-((dimethylamino)methyl)-4-biphenylyl)-7-oxo-3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-c]pyridin-1-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.269 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Discovery of potent, efficacious, and orally bioavailable inhibitors of blood coagulation factor Xa with neutral P1 moieties.

Pinto, D.J.Galemmo, R.A.Quan, M.L.Orwat, M.J.Clark, C.Li, R.Wells, B.Woerner, F.Alexander, R.S.Rossi, K.A.Smallwood, A.Wong, P.C.Luettgen, J.M.Rendina, A.R.Knabb, R.M.He, K.Wexler, R.R.Lam, P.Y.

(2006) Bioorg.Med.Chem.Lett. 16: 5584-5589

  • DOI: 10.1016/j.bmcl.2006.08.027

  • PubMed Abstract: 
  • The bicyclic dihydropyrazolopyridinone scaffold allowed for incorporation of multiple P1 moieties with subnanomolar binding affinities for blood coagulation factor Xa. The compound 3-[6-(2'-dimethylaminomethyl-biphenyl-4-yl)-7-oxo-3-trifluoro-methyl- ...

    The bicyclic dihydropyrazolopyridinone scaffold allowed for incorporation of multiple P1 moieties with subnanomolar binding affinities for blood coagulation factor Xa. The compound 3-[6-(2'-dimethylaminomethyl-biphenyl-4-yl)-7-oxo-3-trifluoro-methyl-4,5,6,7-tetrahydro-pyrazolo[3,4-c]pyridine-l-yl]-benzamide 6d shows good fXa potency, selectivity, in vivo efficacy and oral bioavailability. Compound 6d was selected for further pre-clinical evaluations.


    Organizational Affiliation

    Discovery Chemistry Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543, USA. Donald.Pinto@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
A
234Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
L
52Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4QC
Query on 4QC

Download SDF File 
Download CCD File 
A
3-[6-{2'-[(DIMETHYLAMINO)METHYL]BIPHENYL-4-YL}-7-OXO-3-(TRIFLUOROMETHYL)-4,5,6,7-TETRAHYDRO-1H-PYRAZOLO[3,4-C]PYRIDIN-1-YL]BENZAMIDE
C29 H26 F3 N5 O2
PKGPGSWPKRHPKB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4QCKi: 0.2 nM (100) BINDINGDB
4QCKi: 0.18 nM BINDINGMOAD
4QCKi: 0.18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.269 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.600α = 90.00
b = 72.400β = 90.00
c = 78.900γ = 90.00
Software Package:
Software NamePurpose
EPMRphasing
CNXrefinement
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-02-10 
  • Released Date: 2006-10-03 
  • Deposition Author(s): Alexander, R.S.

Revision History 

  • Version 1.0: 2006-10-03
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description