Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2277 
• Residue Count: 286 
• Unique protein chains: 2

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

• DOI: 10.2210/pdb2G00/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.269 

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

• PubMed: 16963264 
• DOI: 10.1016/j.bmcl.2006.08.027
• Structures With Same Primary Citation


• 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-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.

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Organizational Affiliation: 

Discovery Chemistry Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor X	A	234	Homo sapiens	Mutation(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 GTEx  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor X	L	52	Homo sapiens	Mutation(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 GTEx  ENSG00000126218

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4QC	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
4QC	Ki :  0.18000000715255737   nM  PDBBind
4QC	Ki:  0.18000000715255737   nM  Binding MOAD
4QC	Ki:  0.18000000715255737   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.284 
• R-Value Work: 0.269 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.6	α = 90
b = 72.4	β = 90
c = 78.9	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing
CNX	refinement

Structure Validation

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description