4K5F

Structure of neuronal nitric oxide synthase heme domain in complex with (S)-1,3-bis((2-amino-4-methylpyridin-6-yl)-methoxy)-butan-4-amine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Chiral linkers to improve selectivity of double-headed neuronal nitric oxide synthase inhibitors.

Jing, Q., Li, H., Chreifi, G., Roman, L.J., Martasek, P., Poulos, T.L., Silverman, R.B.

(2013) Bioorg Med Chem Lett 23: 5674-5679

  • DOI: 10.1016/j.bmcl.2013.08.034
  • Primary Citation of Related Structures:  
    4K5F, 4K5G, 4K5H, 4K5I, 4K5J, 4K5K, 4K5D, 4K5E

  • PubMed Abstract: 

    • To develop potent and selective nNOS inhibitors, new double-headed molecules with chiral linkers that derive from natural amino acids or their derivatives have been designed. The new structures contain two ether bonds, which greatly simplifies the synthe ...

    To develop potent and selective nNOS inhibitors, new double-headed molecules with chiral linkers that derive from natural amino acids or their derivatives have been designed. The new structures contain two ether bonds, which greatly simplifies the synthesis and accelerates structure optimization. Inhibitor (R)-6b exhibits a potency of 32nM against nNOS and is 475 and 244 more selective for nNOS over eNOS and iNOS, respectively. Crystal structures show that the additional binding between the aminomethyl moiety of 6b and the two heme propionates in nNOS, but not eNOS, is the structural basis for its high selectivity. This work demonstrates the importance of stereochemistry in this class of molecules, which significantly influences the potency and selectivity of the inhibitors. The structure-activity information gathered here provides a guide for future structure optimization.

    Organizational Affiliation: 

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



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitric oxide synthase, brain A, B422Rattus norvegicusMutation(s): 0 
Gene Names: Nos1, Bnos
EC: 1.14.13.39
Find proteins for P29476 (Rattus norvegicus)
Explore P29476 
Go to UniProtKB:  P29476
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
Q14
Query on Q14
Download Ideal Coordinates CCD File 
A, B
6-[({(2S)-1-amino-4-[(6-amino-4-methylpyridin-2-yl)methoxy]butan-2-yl}oxy)methyl]-4-methylpyridin-2-amine
C18 H27 N5 O2
ZLWWYKPNQBCOKF-INIZCTEOSA-N		 Ligand Interaction
H4B
Query on H4B
Download Ideal Coordinates CCD File 
A, B
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q14Ki:  232   nM  BindingDB
Q14Ki:  232   nM  Binding MOAD
Q14Ki:  232   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.588α = 90
b = 110.742β = 90
c = 164.353γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2013-04-14 
  • Released Date: 2013-09-18 
    • Deposition Author(s): Li, H., Poulos, T.L.

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description