9C1Y | pdb_00009c1y

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain in complex with 7-((3-(((4-(6-aminopyridin-2-yl)butyl)amino)methyl)phenoxy)methyl)quinolin-2-amine

PDB DOI: https://doi.org/10.2210/pdb9C1Y/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-05-29 Released: 2025-06-11
Deposition Author(s): Li, H., Poulos, T.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.263 (Depositor), 0.257 (DCC)
R-Value Work:
0.194 (Depositor), 0.187 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Discovery of Tetrahydrobiopterin Displacing Potent Neuronal Nitric Oxide Synthase Inhibitor with Unprecedented Binding Mode: Synthesis, Biochemical Evaluation, and Structural Characterization

Weerawarna, P.M., Rathnayaka, A.D., Li, H., Lewis, M., Poulos, T.L., Silverman, R.B.

To be published.

Macromolecule Content

Total Structure Weight: 200.85 kDa
Atom Count: 14,616
Modeled Residue Count: 1,662
Deposited Residue Count: 1,692
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, brain	A, B, C, D	423	Homo sapiens	Mutation(s): 2 Gene Names: NOS1 EC: 1.14.13.39
UniProt & NIH Common Fund Data Resources
Find proteins for P29475 (Homo sapiens) Explore P29475 Go to UniProtKB: P29475
PHAROS: P29475 GTEx: ENSG00000089250
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29475
Sequence Annotations Expand
Reference Sequence

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 E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain R [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain R [auth D]	E [auth A], J [auth B], M [auth C], R [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain R [auth D]
V5D (Subject of Investigation/LOI) Query on V5D Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain S [auth D] MOL2 format, chain F [auth A] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain S [auth D] mmCIF format, chain F [auth A] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain S [auth D]	F [auth A], K [auth B], N [auth C], S [auth D]	7-{[3-({[4-(6-aminopyridin-2-yl)butyl]amino}methyl)phenoxy]methyl}quinolin-2-amine C₂₆ H₂₉ N₅ O QYKBESYQSCLLGR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C]	G [auth A] H [auth A] L [auth B] O [auth C] P [auth C] G [auth A], H [auth A], L [auth B], O [auth C], P [auth C], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain T [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth C] SDF format, chain I [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain I [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain I [auth B]	I [auth B], Q [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth B] Focus chain Q [auth C]