3RQL | pdb_00003rql

Structure of the neuronal nitric oxide synthase heme domain in complex with 6-(((3R,4R)-4-(2-((1S,2R/1R,2S)-2-(3-Clorophenyl)cyclopropylamino)ethoxy)pyrrolidin-3-yl)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 
    0.235 (Depositor), 0.242 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Cyclopropyl- and methyl-containing inhibitors of neuronal nitric oxide synthase.

Li, H.Xue, F.Kraus, J.M.Ji, H.Labby, K.J.Mataka, J.Delker, S.L.Martasek, P.Roman, L.J.Poulos, T.L.Silverman, R.B.

(2013) Bioorg Med Chem 21: 1333-1343

  • DOI: https://doi.org/10.1016/j.bmc.2012.12.019
  • Primary Citation Related Structures: 
    3RQJ, 3RQK, 3RQL, 3RQM, 3RQN, 3RQO, 3RQP

  • PubMed Abstract: 

    Inhibitors of neuronal nitric oxide synthase have been proposed as therapeutics for the treatment of different types of neurological disorders. On the basis of a cis-3,4-pyrrolidine scaffold, a series of trans-cyclopropyl- and methyl-containing nNOS inhibitors have been synthesized. The insertion of a rigid electron-withdrawing cyclopropyl ring decreases the basicity of the adjacent amino group, which resulted in decreased inhibitory activity of these inhibitors compared to the parent compound. Nonetheless, three of them exhibited double-digit nanomolar inhibition with high nNOS selectivity on the basis of in vitro enzyme assays. Crystal structures of nNOS and eNOS with these inhibitors bound provide a basis for detailed structure-activity relationship (SAR) studies. The conclusions from these studies will be used as a guide in the future development of selective NOS inhibitors.


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

Macromolecule Content 

  • Total Structure Weight: 100.33 kDa 
  • Atom Count: 7,193 
  • Modeled Residue Count: 820 
  • 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): 0 
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
X2D

Query on X2D



Download:Ideal Coordinates CCD File
F [auth A],
J [auth B]
6-{[(3R,4R)-4-(2-{[(1R,2S)-2-(3-chlorophenyl)cyclopropyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
C22 H29 Cl N4 O
SLFXGXAWJWFFCO-RCOXNQKVSA-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
E [auth A],
K [auth B]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free:  0.235 (Depositor), 0.242 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.702α = 90
b = 110.779β = 90
c = 163.93γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2013-04-24
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description