inducible nitric oxide synthase with Chlorzoxazone bound

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 

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Conformational Changes in Nitric Oxide Synthases Induced by Chlorzoxazone and Nitroindazoles: Crystallographic and Computational Analyses of Inhibitor Potency

Rosenfeld, R.J.Garcin, E.D.Panda, K.Andersson, G.Aberg, A.Wallace, A.V.Morris, G.M.Olson, A.J.Stuehr, D.J.Tainer, J.A.Getzoff, E.D.

(2002) Biochemistry 41: 13915-13925

  • DOI: https://doi.org/10.1021/bi026313j
  • Primary Citation of Related Structures:  
    1M8D, 1M8E, 1M8H, 1M8I, 1M9J, 1M9K, 1M9M, 1M9Q, 1M9R, 1M9T

  • PubMed Abstract: 

    Nitric oxide is a key signaling molecule in many biological processes, making regulation of nitric oxide levels highly desirable for human medicine and for advancing our understanding of basic physiology. Designing inhibitors to specifically target one of the three nitric oxide synthase (NOS) isozymes that form nitric oxide from the L-Arg substrate poses a significant challenge due to the overwhelmingly conserved active sites. We report here 10 new X-ray crystallographic structures of inducible and endothelial NOS oxygenase domains cocrystallized with chlorzoxazone and four nitroindazoles: 5-nitroindazole, 6-nitroindazole, 7-nitroindazole, and 3-bromo-7-nitroindazole. Each of these bicyclic aromatic inhibitors has only one hydrogen bond donor and therefore cannot form the bidentate hydrogen bonds that the L-Arg substrate makes with Glu371. Instead, all of these inhibitors induce a conformational change in Glu371, creating an active site with altered molecular recognition properties. The cost of this conformational change is approximately 1-2 kcal, based on our measured constants for inhibitor binding to the wild-type and E371A mutant proteins. These inhibitors derive affinity by pi-stacking above the heme and replacing both intramolecular (Glu371-Met368) and intermolecular (substrate-Trp366) hydrogen bonds to the beta-sheet architecture underlying the active site. When bound to NOS, high-affinity inhibitors in this class are planar, whereas weaker inhibitors are nonplanar. Isozyme differences were observed in the pterin cofactor site, the heme propionate, and inhibitor positions. Computational docking predictions match the crystallographic results, including the Glu371 conformational change and inhibitor-binding orientations, and support a combined crystallographic and computational approach to isozyme-specific NOS inhibitor analysis and design.

  • Organizational Affiliation

    Department of Molecular Biology and Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB-4, La Jolla, California 92037, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inducible Nitric Oxide Synthase
A, B
434Mus musculusMutation(s): 0 
Gene Names: iNOS
UniProt & NIH Common Fund Data Resources
Find proteins for P29477 (Mus musculus)
Explore P29477 
Go to UniProtKB:  P29477
IMPC:  MGI:97361
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29477
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

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D [auth A],
I [auth B]
C34 H32 Fe N4 O4
Query on BOG

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G [auth B]octyl beta-D-glucopyranoside
C14 H28 O6
Query on H4B

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E [auth A],
J [auth B]
C9 H15 N5 O3
Query on CLW

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F [auth A],
K [auth B]
C7 H4 Cl N O2
Query on SO4

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C [auth A],
H [auth B]
O4 S
Query on EDO

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L [auth B]1,2-ETHANEDIOL
C2 H6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
CLW Binding MOAD:  1M8D Kd: 4300 (nM) from 1 assay(s)
BindingDB:  1M8D IC50: 1.41e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.238 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.891α = 90
b = 213.891β = 90
c = 115.484γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Refinement description, Structure summary