3TYL

Structure of neuronal nitric oxide synthase heme domain in complex with 6-(((3S,4S)-4-(2-((2-fluorobenzyl)amino)ethoxy)pyrrolidin-3-yl)methyl)-4-methylpyridin-2-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Intramolecular hydrogen bonding: A potential strategy for more bioavailable inhibitors of neuronal nitric oxide synthase.

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

(2012) Bioorg.Med.Chem. 20: 2435-2443

  • DOI: 10.1016/j.bmc.2012.01.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Selective neuronal nitric oxide synthase (nNOS) inhibitors have therapeutic applications in the treatment of numerous neurodegenerative diseases. Here we report the synthesis and evaluation of a series of inhibitors designed to have increased cell me ...

    Selective neuronal nitric oxide synthase (nNOS) inhibitors have therapeutic applications in the treatment of numerous neurodegenerative diseases. Here we report the synthesis and evaluation of a series of inhibitors designed to have increased cell membrane permeability via intramolecular hydrogen bonding. Their potencies were examined in both purified enzyme and cell-based assays; a comparison of these results demonstrates that two of the new inhibitors display significantly increased membrane permeability over previous analogs. NMR spectroscopy provides evidence of intramolecular hydrogen bonding under physiological conditions in two of the inhibitors. Crystal structures of the inhibitors in the nNOS active site confirm the predicted non-intramolecular hydrogen bonded binding mode. Intramolecular hydrogen bonding may be an effective approach for increasing cell membrane permeability without affecting target protein binding.


    Organizational Affiliation

    Department of Chemistry, Department of Molecular Biosciences, Chemistry of Life Processes Institute, Center for Molecular Innovation and Drug Discovery, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nitric oxide synthase, brain
A, B
422Rattus norvegicusMutation(s): 0 
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
ZN
Query on ZN

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Download CCD File 
A
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
AXW
Query on AXW

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Download CCD File 
A, B
6-{[(3S,4S)-4-{2-[(2-fluorobenzyl)amino]ethoxy}pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
C20 H27 F N4 O
PMZVISPCVPVOFN-QFBILLFUSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
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 %)
AXWIC50: 3600 - 11000 nM (100) BINDINGDB
AXWKi: 410 nM (100) BINDINGDB
AXWKi: 410 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.931α = 90.00
b = 110.806β = 90.00
c = 164.294γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-09-26 
  • Released Date: 2012-03-14 
  • Deposition Author(s): Li, H., Poulos, T.L.

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description