3JX1 | pdb_00003jx1

Structure of rat neuronal nitric oxide synthase D597N mutant heme domain in complex with N1-{(3'R,4'R)-4'-[(6"-amino-4"-methylpyridin-2"-yl)methyl]pyrrolidin-3'-yl}-N2-(3'-fluorophenethyl)ethane-1,2-diamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.216 (Depositor), 0.256 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Unexpected binding modes of nitric oxide synthase inhibitors effective in the prevention of a cerebral palsy phenotype in an animal model.

Delker, S.L.Ji, H.Li, H.Jamal, J.Fang, J.Xue, F.Silverman, R.B.Poulos, T.L.

(2010) J Am Chem Soc 132: 5437-5442

  • DOI: https://doi.org/10.1021/ja910228a
  • Primary Citation Related Structures: 
    3JWS, 3JWT, 3JWU, 3JWV, 3JWW, 3JWX, 3JWY, 3JWZ, 3JX0, 3JX1, 3JX2, 3JX3, 3JX4, 3JX5, 3JX6

  • PubMed Abstract: 

    Selective inhibition of the neuronal isoform of nitric oxide synthase NOS (nNOS) has been shown to prevent brain injury and is important for the treatment of various neurodegenerative disorders. However, given the high active site conservation among all three NOS isoforms, the design of selective inhibitors is an extremely challenging problem. Here we present the structural basis for why novel and potent nNOS inhibitors exhibit the highest level of selectivity over eNOS reported so far (approximately 3,800-fold). By using a combination of crystallography, computational methods, and site-directed mutagenesis, we found that inhibitor chirality and an unanticipated structural change of the target enzyme control both the orientation and selectivity of these novel nNOS inhibitors. A new hot spot generated as a result of enzyme elasticity provides important information for the future fragment-based design of selective NOS inhibitors.


  • Organizational Affiliation
    • Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 100.27 kDa 
  • Atom Count: 7,215 
  • Modeled Residue Count: 817 
  • Deposited Residue Count: 844 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric oxide synthase, brain
A, B
422Rattus norvegicusMutation(s): 1 
Gene Names: Nos1Bnos
EC: 1.14.13.39
UniProt
Find proteins for P29476 (Rattus norvegicus)
Explore P29476 
Go to UniProtKB:  P29476
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29476
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
JI5

Query on JI5



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
N-{(3R,4R)-4-[(6-amino-4-methylpyridin-2-yl)methyl]pyrrolidin-3-yl}-N'-[2-(3-fluorophenyl)ethyl]ethane-1,2-diamine
C21 H30 F N5
PUOKPLCASUFBAN-XLIONFOSSA-N
H4B

Query on H4B



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B]
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.216 (Depositor), 0.256 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.02α = 90
b = 110.884β = 90
c = 164.11γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CNSrefinement
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-06
    Changes: Data collection, Refinement description