9MWA | pdb_00009mwa

Structure of human neuronal nitric oxide synthase R354A/G357D mutant heme domain bound with N-(4-(2-((3-(thiophene-2-carboximidamido)benzyl)amino)ethyl)phenyl)thiophene-2-carboximidamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.230 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

New Inhibitors of Neuronal Nitric Oxide Synthase for the Treatment of Melanoma.

Awasthi, A.Patel, A.Li, H.Kang, K.M.Hardy, C.D.Ansari, A.Nowar, R.Hasan, M.E.Yang, S.Poulos, T.L.Silverman, R.B.

(2026) J Med Chem 69: 2310-2329

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02154
  • Primary Citation Related Structures: 
    9MWA, 9MWB, 9MWC, 9MWD, 9MWE, 9MWF, 9MWG, 9MWH, 9MWI, 9MWJ, 9MWK, 9MWL, 9MWM, 9MWN, 9MWO, 9MWP, 9MWQ, 9MWR, 9MWS, 9MWT, 9MWU, 9MWV, 9MWW, 9MWX

  • PubMed Abstract: 

    In 2024, an estimated 100,640 new cases of invasive melanoma were diagnosed in the U.S., with 9290 deaths. Our previous studies revealed that neuronal nitric oxide synthase (nNOS) derived nitric oxide plays a critical role in melanoma progression, making nNOS inhibition a promising strategy. High structural similarity among NOS isoforms requires careful design of nNOS inhibitors to avoid off-target effects. Our previous lead, HH044, demonstrated potent antimelanoma activity but exhibited only moderate nNOS selectivity. Here, we utilized a structure-based approach to design nNOS inhibitors that promote interactions with human nNOS-specific residue His342. Compound 9 exhibited inhibition of both human ( K i = 1.7 nM) and rat nNOS ( K i = 2.3 nM), with 5654-fold selectivity over human eNOS and 250-fold selectivity over iNOS. X-ray crystallography and molecular modeling revealed a novel SAR, forming the basis for nNOS inhibition and providing a foundation for further innovative design of nNOS inhibitors for melanoma treatment.


  • Organizational Affiliation
    • Department of Chemistry, Chemistry of Life Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide synthase, brain
A, B, C, D
423Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29475
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
T [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
H44 (Subject of Investigation/LOI)
Query on H44

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
V [auth D]
N-(4-{2-[(3-{[(E)-imino(thiophen-2-yl)methyl]amino}benzyl)amino]ethyl}phenyl)thiophene-2-carboximidamide
C25 H25 N5 S2
RWYJTZOFPFOVAE-UHFFFAOYSA-N
H4B
Query on H4B

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
U [auth D]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
M [auth B]
Q [auth C]
R [auth C]
W [auth D]
H [auth A],
M [auth B],
Q [auth C],
R [auth C],
W [auth D],
X [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
I [auth A],
S [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.230 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.334α = 90
b = 118.708β = 90.19
c = 165.454γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM131920

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-26
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Database references