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 PQS (software)

Macromolecule Content

• Total Structure Weight: 44.27 kDa 
• Atom Count: 2323 
• Residue Count: 286 
• Unique protein chains: 2

2CJI

Crystal structure of a Human Factor Xa inhibitor complex

• DOI: 10.2210/pdb2CJI/pdb

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


• Deposited: 2006-04-03 Released: 2006-05-17 
• Deposition Author(s): Watson, N.S., Campbell, M., Chan, C., Convery, M.A., Hamblin, J.N., Kelly, H.A., King, N.P., Mason, A.M., Mitchell, C., Patel, V.K., Senger, S., Shah, G.P., Weston, H.E., Whitworth, C., Young, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Design and Synthesis of Orally Active Pyrrolidin-2-One-Based Factor Xa Inhibitors

Watson, N.S., Brown, D., Campbell, M., Chan, C., Chaudry, L., Convery, M.A., Fenwick, R., Hamblin, J.N., Haslam, C., Kelly, H.A., King, N.P., Kurtis, C.L., Leach, A.R., Manchee, G.R., Mason, A.M., Mitchell, C., Patel, C., Patel, V.K., Senger, S., Shah, G.P., Weston, H.E., Whitworth, C., Young, R.J.

(2006) Bioorg Med Chem Lett 16: 3784

• PubMed: 16697194 
• DOI: 10.1016/j.bmcl.2006.04.053
• Structures With Same Primary Citation


• PubMed Abstract: 
  

A series of novel, non-basic 3-(6-chloronaphth-2-ylsulfonyl)aminopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating an alanylamide P4 group, was designed and synthesised. Within this series, the N-2-(morpholin-4-yl)-2-oxoethyl derivative 24 was shown to be a potent, selective fXa inhibitor with good anticoagulant activity. Moreover, 24 possessed highly encouraging rat and dog pharmacokinetic profiles with excellent oral bioavailabilities in both species.

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Organizational Affiliation: 

GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ACTIVATED FACTOR XA HEAVY CHAIN	A	254	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
FACTOR X LIGHT CHAIN	B	134	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSK	A	6-CHLORO-N-{(3S)-1-[(1S)-1-METHYL-2-(4-MORPHOLINYL)-2-OXO ETHYL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE C21 H24 Cl N3 O5 S ICLOZQFWTRAYPX-LIRRHRJNSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GSK	Ki:  6   nM  BindingDB
GSK	Ki:  6   nM  Binding MOAD
GSK	Ki :  6   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.242 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.968	α = 90
b = 72.633	β = 90
c = 79.784	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-04-03 
• Released Date: 2006-05-17 
Deposition Author(s): Watson, N.S., Campbell, M., Chan, C., Convery, M.A., Hamblin, J.N., Kelly, H.A., King, N.P., Mason, A.M., Mitchell, C., Patel, V.K., Senger, S., Shah, G.P., Weston, H.E., Whitworth, C., Young, R.J.

Revision History 

• Version 1.0: 2006-05-17
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance