1ZZQ

Rat nNOS D597N mutant with L-N(omega)-Nitroarginine-(4R)-amino-L-proline amide bound

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


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


Literature

Exploring the Binding Conformations of Bulkier Dipeptide Amide Inhibitors in Constitutive Nitric Oxide Synthases.

Li, H., Flinspach, M.L., Igarashi, J., Jamal, J., Yang, W., Litzinger, E.A., Huang, H., Erdal, E.P., Silverman, R.B., Poulos, T.L.

(2005) Biochemistry 44: 15222-15229

  • DOI: 10.1021/bi0513610
  • Primary Citation of Related Structures:  
    1ZZU, 1ZZT, 1ZZS, 1ZZR, 1ZZQ

  • PubMed Abstract: 

    • A series of L-nitroarginine-based dipeptide inhibitors are highly selective for neuronal nitric oxide synthase (nNOS) over the endothelial isoform (eNOS). Crystal structures of these dipeptides bound to both isoforms revealed two different conformations, curled in nNOS and extended in eNOS, corresponding to higher and lower binding affinity to the two isoforms, respectively ...

    A series of L-nitroarginine-based dipeptide inhibitors are highly selective for neuronal nitric oxide synthase (nNOS) over the endothelial isoform (eNOS). Crystal structures of these dipeptides bound to both isoforms revealed two different conformations, curled in nNOS and extended in eNOS, corresponding to higher and lower binding affinity to the two isoforms, respectively. In previous studies we found that the primary reason for selectivity is that Asp597 in nNOS, which is Asn368 in eNOS, provides greater electrostatic stabilization in the inhibitor complex. While this is the case for smaller dipeptide inhibitors, electrostatic stabilization may no longer be the sole determinant for isoform selectivity with bulkier dipeptide inhibitors. Another residue farther away from the active site, Met336 in nNOS (Val106 in eNOS), is in contact with bulkier dipeptide inhibitors. Double mutants were made to exchange the D597/M336 pair in nNOS with N368/V106 in eNOS. Here we report crystal structures and inhibition constants for bulkier dipeptide inhibitors bound to nNOS and eNOS that illustrate the important role played by residues near the entry to the active site in isoform selective inhibition.

    Related Citations: 
    • Structural Basis for Dipeptide Amide Isoform-Selective Inhibition of Neuronal Nitric Oxide Synthase
      Flinspach, M.L., Li, H., Jamal, J., Yang, W., Huang, H., Hah, J.M., Gomez-Vidal, J.A., Litzinger, E.A., Silverman, R.B., Poulos, T.L.
      (2004) Nat Struct Mol Biol 11: 54
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nitric-oxide synthase, brainA, B420Rattus norvegicusMutation(s): 1 
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 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
DP9
Query on DP9
Download CCD File 
A, B
L-N(OMEGA)-NITROARGININE-(4R)-AMINO-L-PROLINE AMIDE
C11 H22 N8 O4
IUFRDGFKAVLPFZ-CSMHCCOUSA-N		 Ligand Interaction
H4B
Query on H4B
Download CCD File 
A, B
5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N		 Ligand Interaction
MTL
Query on MTL
Download CCD File 
A, B
D-MANNITOL
C6 H14 O6
FBPFZTCFMRRESA-KVTDHHQDSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DP9Ki:  100   nM  BindingDB
DP9IC50:  640   nM  BindingDB
DP9Ki:  20000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.86α = 90
b = 110.32β = 90
c = 164.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance