2Y37 | pdb_00002y37

The discovery of novel, potent and highly selective inhibitors of inducible nitric oxide synthase (iNOS)

• PDB DOI: https://doi.org/10.2210/pdb2Y37/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-12-19 Released: 2011-04-13 
• Deposition Author(s): Cheshire, D.R., Andrews, G., Beaton, H.G., Birkinshaw, T.N., Boughton-Smith, N., Connolly, S., Cook, T.R., Cooper, A., Cooper, S.L., Cox, D., Dixon, J., Gensmantel, N., Hamley, P.J., Harrison, R., Hartopp, P., Kack, H., Luker, T., Mete, A., Millichip, I., Nicholls, D.J., Pimm, A.D., St-Gallay, S.A., Wallace, A.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

The Discovery of Novel, Potent and Highly Selective Inhibitors of Inducible Nitric Oxide Synthase (Inos).

Cheshire, D.R., Berg, A., Andersson, G.M., Andrews, G., Beaton, H.G., Birkinshaw, T.N., Boughton-Smith, N., Connolly, S., Cook, T.R., Cooper, A., Cooper, S.L., Cox, D., Dixon, J., Gensmantel, N., Hamley, P.J., Harrison, R., Hartopp, P., Kack, H., Leeson, P.D., Luker, T., Mete, A., Millichip, I., Nicholls, D.J., Pimm, A.D., St-Gallay, S.A., Wallace, A.V.

(2011) Bioorg Med Chem Lett 21: 2468

• PubMed: 21398123 
• DOI: https://doi.org/10.1016/j.bmcl.2011.02.061
• Primary Citation Related Structures: 
  2Y37, 4UX6


• PubMed Abstract: 
  

  By careful analysis of experimental X-ray ligand crystallographic protein data across several inhibitor series we have discovered a novel, potent and selective series of iNOS inhibitors exemplified by compound 8.

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Organizational Affiliation: 
• Department of Chemistry, AstraZeneca Charnwood, Bakewell Road, Loughborough LE11 5RH, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 103 kDa 
• Atom Count: 7,222 
• Modeled Residue Count: 823 
• Deposited Residue Count: 866 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITRIC OXIDE SYNTHASE, INDUCIBLE	A, B	433	Mus musculus	Mutation(s): 0  EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29477 (Mus musculus) Explore P29477  Go to UniProtKB:  P29477
IMPC:  MGI:97361

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	G [auth A], L [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
A54	F [auth A], K [auth B]	2-[(1R)-3-amino-1-phenyl-propoxy]-4-chloro-benzonitrile C16 H15 Cl N2 O GPCXUXJZOSOVLY-OAHLLOKOSA-N
H4B	H [auth A], M [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N
SO4	C [auth A], D [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
A54	BindingDB:  2Y37	IC50: min: 4, max: 900 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.242 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.492	α = 90
b = 212.492	β = 90
c = 115.372	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Cheshire, D.R., Andrews, G., Beaton, H.G., Birkinshaw, T.N., Boughton-Smith, N., Connolly, S., Cook, T.R., Cooper, A., Cooper, S.L., Cox, D., Dixon, J., Gensmantel, N., Hamley, P.J., Harrison, R., Hartopp, P., Kack, H., Luker, T., Mete, A., Millichip, I., Nicholls, D.J., Pimm, A.D., St-Gallay, S.A., Wallace, A.V.

Revision History  

• Version 1.0: 2011-04-13
  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: 2018-01-17
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other