3NW2 | pdb_00003nw2

Novel nanomolar Imidazopyridines as selective Nitric Oxide Synthase (iNOS) inhibitors: SAR and structural insights

PDB DOI: https://doi.org/10.2210/pdb3NW2/pdb

Classification: OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-07-09 Released: 2011-06-22
Deposition Author(s): Graedler, U., Fuchss, T., Ulrich, W.R., Boer, R., Strub, A., Hesslinger, C., Anezo, C., Diederichs, K., Zaliani, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.323 (Depositor), 0.300 (DCC)
R-Value Work:
0.279 (Depositor), 0.250 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Novel nanomolar imidazo[4,5-b]pyridines as selective nitric oxide synthase (iNOS) inhibitors: SAR and structural insights

Graedler, U., Fuchss, T., Ulrich, W.R., Boer, R., Strub, A., Hesslinger, C., Anezo, C., Diederichs, K., Zaliani, A.

(2011) Bioorg Med Chem Lett 21: 4228-4232

PubMed: 21684157 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.05.073
Primary Citation of Related Structures:
3NW2

PubMed Abstract:
Inducible arginine oxidation and subsequent NO production by correspondent synthase (iNOS) are important cellular answers to proinflammatory signals. Prolonged NO production has been proved in higher organisms to cause stroke or septic shock. Several classes of potent NOS inhibitors have been reported, most of them targeting the arginine binding site of the oxygenase domain. Here we disclose the SAR and the rational design of potent and selective iNOS inhibitors which may be useful as anti-inflammatory drugs.

Organizational Affiliation

Nycomed GmbH, Byk-Gulden-Str. 2, D-78467 Konstanz, Germany. ugraedler@hotmail.com

Macromolecule Content

Total Structure Weight: 100.32 kDa
Atom Count: 6,991
Modelled Residue Count: 827
Deposited Residue Count: 846
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric oxide synthase, inducible	A, B	423	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29477
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
MPW Query on MPW Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	2-[2-(4-methoxypyridin-2-yl)ethyl]-3H-imidazo[4,5-b]pyridine C₁₄ H₁₄ N₄ O YBOCDKFRGBOOFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
H4B Query on H4B Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C₉ H₁₅ N₅ O₃ FNKQXYHWGSIFBK-RPDRRWSUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.323 (Depositor), 0.300 (DCC)
R-Value Work: 0.279 (Depositor), 0.250 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 212.6	α = 90
b = 212.6	β = 90
c = 111.5	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-06-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-12-21
Changes: Database references
Version 1.3: 2017-11-08
Changes: Refinement description
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-30
Changes: Structure summary