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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1021/jm900007a
  • Primary Citation of Related Structures:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase, brain
A, B
422Rattus norvegicusMutation(s): 2 
Gene Names: Nos1 (Bnos)
EC: 1.14.13.39
Find proteins for P29476 (Rattus norvegicus)
Go to UniProtKB:  P29476
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JI2
Query on JI2

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A, B
N-{(3S,4S)-4-[(6-aminopyridin-2-yl)methyl]pyrrolidin-3-yl}ethane-1,2-diamine
(+-)-N1-{cis-4'-[(6"-aminopyridin-2"-yl)methyl]pyrrolidin-3'-yl}ethane-1,2-diamine
C12 H21 N5
BETYXZSFUFTOLC-GXSJLCMTSA-N
 Ligand Interaction
ZN
Query on ZN

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B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

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A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
H4B
Query on H4B

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Download CCD File 
A, B
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JI2Ki: 388 - 58400 nM (99) BINDINGDB
JI2IC50: 6300 - 15300 nM (99) BINDINGDB
JI2Ki: 388 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.870α = 90.00
b = 110.700β = 90.00
c = 164.360γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance