1X7A | pdb_00001x7a

Porcine Factor IXa Complexed to 1-{3-[amino(imino)methyl]phenyl}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb1X7A/pdb

• Classification: blood clotting,hydrolase
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2004-08-13 Released: 2005-08-16 
• Deposition Author(s): Alexander, R.S., Smallwood, A.M., Smallheer, J.M., Wang, J., Wang, S., Nakajima, S., Rossi, K.A., Barbera, F., Burdick, D., Luettgen, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

SAR and factor IXa crystal structure of a dual inhibitor of factors IXa and Xa

Smallheer, J.M., Alexander, R.S., Wang, J., Wang, S., Nakajima, S., Rossi, K.A., Smallwood, A., Barbera, F., Burdick, D., Luettgen, J.M., Knabb, R.M., Wexler, R.R., Jadhav, P.K.

(2004) Bioorg Med Chem Lett 14: 5263-5267

• PubMed: 15454208 
• DOI: https://doi.org/10.1016/j.bmcl.2004.08.034
• Primary Citation Related Structures: 
  1X7A


• PubMed Abstract: 
  

  Modifications to the P4 moiety and pyrazole C3 substituent of factor Xa inhibitor SN-429 provided several new compounds, which are 5-10nM inhibitors of factor IXa. An X-ray crystal structure of one example complexed to factor IXa shows that these compounds adopt a similar binding mode to that previously observed with pyrazole inhibitors in the factor Xa active site both with regard to how the inhibitor binds and the position of Tyr99.

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Organizational Affiliation: 
• Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 43.02 kDa 
• Atom Count: 2,595 
• Modeled Residue Count: 332 
• Deposited Residue Count: 381 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation Factor IXa	A [auth C]	235	Sus scrofa	Mutation(s): 0  EC: 3.4.21.22
UniProt
Find proteins for P16293 (Sus scrofa) Explore P16293  Go to UniProtKB:  P16293

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation Factor IX, light chain	B [auth L]	146	Sus scrofa	Mutation(s): 0  EC: 3.4.21.22
UniProt
Find proteins for P16293 (Sus scrofa) Explore P16293  Go to UniProtKB:  P16293

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
187	C	1-{3-[AMINO(IMINO)METHYL]PHENYL}-N-[4-(1H-BENZIMIDAZOL-1-YL)-2-FLUOROPHENYL]-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE C25 H17 F4 N7 O TWBHVKYRNOGUJS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129	α = 90
b = 129	β = 90
c = 71.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-08-16 
Deposition Author(s): Alexander, R.S., Smallwood, A.M., Smallheer, J.M., Wang, J., Wang, S., Nakajima, S., Rossi, K.A., Barbera, F., Burdick, D., Luettgen, J.M.

Revision History  

• Version 1.0: 2005-08-16
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary