Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 99.93 kDa 
• Atom Count: 7087 
• Modelled Residue Count: 818 
• Deposited Residue Count: 844 
• Unique protein chains: 1

3DQR

Structure of neuronal NOS D597N/M336V mutant heme domain in complex with a inhibitor (+-)-N1-{cis-4'-[(6"-aminopyridin-2"-yl)methyl]pyrrolidin-3'-yl}ethane-1,2-diamine

• PDB DOI: 10.2210/pdb3DQR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-07-09 Released: 2009-03-31 
• Deposition Author(s): Igarashi, J., Li, H., Poulos, T.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.261 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 

Literature

Crystal structures of constitutive nitric oxide synthases in complex with de novo designed inhibitors.

Igarashi, J., Li, H., Jamal, J., Ji, H., Fang, J., Lawton, G.R., Silverman, R.B., Poulos, T.L.

(2009) J Med Chem 52: 2060-2066

• PubMed: 19296678 
• DOI: 10.1021/jm900007a
• Primary Citation of Related Structures:  
  3B3O, 3B3P, 3DQR, 3DQS, 3DQT


• PubMed Abstract: 
  

New nitric oxide synthase (NOS) inhibitors were designed de novo with knowledge gathered from the studies on the nNOS-selective dipeptide inhibitors. Each of the new inhibitors consists of three fragments: an aminopyridine ring, a pyrrolidine, and a tail of various length and polarity. The in vitro inhibitory assays indicate good potency and isoform selectivity for some of the compounds. Crystal structures of these inhibitors bound to either wild type or mutant nNOS and eNOS have confirmed design expectations. The aminopyridine ring mimics the guanidinium group of L-arginine and functions as an anchor to place the compound in the NOS active site where it hydrogen bonds to a conserved Glu. The rigidity of the pyrrolidine ring places the pyrrolidine ring nitrogen between the same conserved Glu and the selective residue nNOS Asp597/eNOS Asn368, which results in similar interactions observed with the alpha-amino group of dipeptide inhibitors bound to nNOS. These structures provide additional information to help in the design of inhibitors with greater potency, physicochemical properties, and isoform selectivity.

---

Organizational Affiliation: 

Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California 92697-3900, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric oxide synthase, brain	A, B	422	Rattus norvegicus	Mutation(s): 2  Gene Names: Nos1, Bnos EC: 1.14.13.39
UniProt
Find proteins for P29476 (Rattus norvegicus) Explore P29476  Go to UniProtKB:  P29476

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], I [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
H4B	E [auth A], J [auth B]	5,6,7,8-TETRAHYDROBIOPTERIN C9 H15 N5 O3 FNKQXYHWGSIFBK-RPDRRWSUSA-N
JI2	F [auth A], K [auth B]	N-{(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}ethane-1,2-diamine C12 H21 N5 BETYXZSFUFTOLC-GXSJLCMTSA-N
ZN	H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	C [auth A], G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
JI2	BindingDB:  3DQR	Ki: min: 388, max: 5.84e+4 (nM) from 3 assay(s)
		IC50: min: 6300, max: 1.53e+4 (nM) from 2 assay(s)
	Binding MOAD:  3DQR	Ki: 388 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.261 
• R-Value Work: 0.205 
• R-Value Observed: 0.205 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.87	α = 90
b = 110.7	β = 90
c = 164.36	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-07-09 
• Released Date: 2009-03-31 
Deposition Author(s): Igarashi, J., Li, H., Poulos, T.L.

Revision History  

• Version 1.0: 2009-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations