2FLB

Discovery of a Novel Hydroxy Pyrazole Based Factor IXa Inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2FLB/pdb

• Classification: HYDROLASE/BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-01-05 Released: 2006-04-04 
• Deposition Author(s): Katz, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.280 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Literature

Discovery of novel hydroxy pyrazole based factor IXa inhibitor.

Vijaykumar, D., Sprengeler, P.A., Shaghafi, M., Spencer, J.R., Katz, B.A., Yu, C., Rai, R., Young, W.B., Schultz, B., Janc, J.

(2006) Bioorg Med Chem Lett 16: 2796-2799

• PubMed: 16487703 
• DOI: https://doi.org/10.1016/j.bmcl.2006.01.123
• Primary Citation of Related Structures:  
  2FLB


• PubMed Abstract: 
  

  Synthesis and biological data of a novel selective and efficacious factor IXa inhibitor are described along with its crystal structure in factor VIIa.

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Organizational Affiliation: 

Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 70.21 kDa 
• Atom Count: 4,278 
• Modelled Residue Count: 501 
• Deposited Residue Count: 624 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6NH	D [auth H]	2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE C17 H14 N6 O CKSIVONWCYACAP-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6NH	PDBBind:  2FLB	Ki: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.280 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.45	α = 90
b = 69.03	β = 90.21
c = 78.76	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Katz, B.A.

Revision History  

• Version 1.0: 2006-04-04
  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: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary