2CJI | pdb_00002cji

Crystal structure of a Human Factor Xa inhibitor complex

• PDB DOI: https://doi.org/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 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: other

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: https://doi.org/10.1016/j.bmcl.2006.04.053
• Primary Citation of Related Structures:  
  2CJI


• 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]

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 44.27 kDa 
• Atom Count: 2,323 
• Modeled Residue Count: 286 
• Deposited Residue Count: 388 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ACTIVATED FACTOR XA HEAVY CHAIN	A	254	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FACTOR X LIGHT CHAIN	B	134	Homo sapiens	Mutation(s): 0  EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742  Go to UniProtKB:  P00742
PHAROS:  P00742 GTEx:  ENSG00000126218

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSK	D [auth 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	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GSK	BindingDB:  2CJI	Ki: 6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

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

• 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
• Version 1.3: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary