2VH0

Structure and property based design of factor Xa inhibitors:biaryl pyrrolidin-2-ones incorporating basic heterocyclic motifs

• PDB DOI: https://doi.org/10.2210/pdb2VH0/pdb

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


• Deposited: 2007-11-16 Released: 2008-11-25 
• Deposition Author(s): Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Convery, M.A., Diallo, H., Hortense, E., Irving, W.R., Kelly, H.A., King, N.P., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E., Zhou, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

Literature

Structure and property based design of factor Xa inhibitors: biaryl pyrrolidin-2-ones incorporating basic heterocyclic motifs.

Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Convery, M.A., Diallo, H., Hortense, E., Irving, W.R., 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., Zhou, P.

(2008) Bioorg Med Chem Lett 18: 28-33

• PubMed: 18053714 
• DOI: https://doi.org/10.1016/j.bmcl.2007.11.019
• Primary Citation of Related Structures:  
  2VH0


• PubMed Abstract: 
  

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

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Organizational Affiliation: 

GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom. [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: 44.35 kDa 
• Atom Count: 2,518 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSI	E [auth A]	2-(5-chlorothiophen-2-yl)-N-[(3S)-1-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-2-oxopyrrolidin-3-yl]ethanesulfonamide C22 H25 Cl F N5 O3 S2 JENHCPNBBPPGMN-SFHVURJKSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GSI	Binding MOAD:  2VH0	Ki: 1 (nM) from 1 assay(s)
	PDBBind:  2VH0	Ki: 3.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.216 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.542	α = 90
b = 72.156	β = 90
c = 78.657	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: 2008-11-25 
Deposition Author(s): Young, R.J., Borthwick, A.D., Brown, D., Burns-Kurtis, C.L., Campbell, M., Chan, C., Charbaut, M., Convery, M.A., Diallo, H., Hortense, E., Irving, W.R., Kelly, H.A., King, N.P., Kleanthous, S., Mason, A.M., Pateman, A.J., Patikis, A., Pinto, I.L., Pollard, D.R., Senger, S., Shah, G.P., Toomey, J.R., Watson, N.S., Weston, H.E., Zhou, P.

Revision History  

• Version 1.0: 2008-11-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-01-23
  Changes: Data collection, Database references, Non-polymer description
• Version 2.1: 2019-05-08
  Changes: Data collection, Experimental preparation