2VH6

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs

• PDB DOI: https://doi.org/10.2210/pdb2VH6/pdb

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


• Deposited: 2007-11-19 Released: 2008-12-16 
• Deposition Author(s): Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Chung, C.W., Convery, M.A., Kelly, H.A., King, N.P., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A.N., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 

Literature

Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Biaryl P4 Motifs.

Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Chung, C.W., Convery, M.A., Kelly, H.A., Paul King, N., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A.N., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E.

(2008) Bioorg Med Chem Lett 18: 23

• PubMed: 18054228 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.023
• Primary Citation of Related Structures:  
  2VH6


• PubMed Abstract: 
  

  Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating biaryl P4 groups, producing highly potent inhibitors with encouraging oral pharmacokinetic profiles and significant but sub-optimal anticoagulant activities.

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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: 44.32 kDa 
• Atom Count: 2,433 
• Modelled 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
ACTIVATED FACTOR XA 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSV	C [auth A]	2-(5-chlorothiophen-2-yl)-N-{(3S)-1-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-2-oxopyrrolidin-3-yl}ethanesulfonamide C23 H22 Cl F N2 O5 S3 MRKBPFVJGAHTFU-IBGZPJMESA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GSV	PDBBind:  2VH6	Ki: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.197 
• R-Value Observed: 0.199 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.959	α = 90
b = 72.309	β = 90
c = 78.976	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-16 
Deposition Author(s): Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Chung, C.W., Convery, M.A., Kelly, H.A., King, N.P., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A.N., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E.

Revision History  

• Version 1.0: 2008-12-16
  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: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2024-10-23
  Changes: Data collection, Database references, Structure summary