1DMJ

BOVINE ENDOTHELIAL NITRIC OXIDE SYNTHASE HEME DOMAIN COMPLEXED WITH 5,6-CYCLIC-TETRAHYDROPTERIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for pterin antagonism in nitric-oxide synthase. Development of novel 4-oxo-pteridine antagonists of (6R)-5,6,7,8-tetrahydrobiopterin

Kotsonis, P.Frohlich, L.G.Raman, C.S.Li, H.Berg, M.Gerwig, R.Groehn, V.Kang, Y.Al-Masoudi, N.Taghavi-Moghadam, S.Mohr, D.Munch, U.Schnabel, J.Martasek, P.Masters, B.S.Strobel, H.Poulos, T.Matter, H.Pfleiderer, W.Schmidt, H.H.

(2001) J.Biol.Chem. 276: 49133-49141

  • DOI: 10.1074/jbc.M011469200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pathological nitric oxide (NO) generation in sepsis, inflammation, and stroke may be therapeutically controlled by inhibiting NO synthases (NOS). Here we targeted the (6R)-5,6,7,8-tetrahydro-l-biopterin (H(4)Bip)-binding site of NOS, which, upon cofa ...

    Pathological nitric oxide (NO) generation in sepsis, inflammation, and stroke may be therapeutically controlled by inhibiting NO synthases (NOS). Here we targeted the (6R)-5,6,7,8-tetrahydro-l-biopterin (H(4)Bip)-binding site of NOS, which, upon cofactor binding, maximally increases enzyme activity and NO production from substrate l-arginine. The first generation of H(4)Bip-based NOS inhibitors employed a 4-amino pharmacophore of H(4)Bip analogous to antifolates such as methotrexate. We developed a novel series of 4-oxo-pteridine derivatives that were screened for inhibition against neuronal NOS (NOS-I) and a structure-activity relationship was determined. To understand the structural basis for pterin antagonism, selected derivatives were docked into the NOS pterin binding cavity. Using a reduced 4-oxo-pteridine scaffold, derivatives with certain modifications such as electron-rich aromatic phenyl or benzoyl groups at the 5- and 6-positions, were discovered to markedly inhibit NOS-I, possibly due to hydrophobic and electrostatic interactions with Phe(462) and Ser(104), respectively, within the pterin binding pocket. One of the most effective 4-oxo compounds and, for comparisons an active 4-amino derivative, were then co-crystallized with the endothelial NOS (NOS-III) oxygenase domain and this structure solved to confirm the hypothetical binding modes. Collectively, these findings suggest (i) that, unlike the antifolate principle, the 4-amino substituent is not essential for developing pterin-based NOS inhibitors and (ii), provide a steric and electrostatic basis for their rational design.


    Related Citations: 
    • Anti-Pterins as Tools to Characterize the Function of Tetrahydrobiopterin in NO Synthase
      Bommel, H.M.,Reif, A.,Frohlich, L.G.,Frey, A.,Hofmann, H.,Marecak, D.M.,Groehn, V.,Kotsonis, P.,La, M.,Koster, S.,Meinecke, M.,Bernhardt, M.,Weeger, M.,Ghisla, S.,Prestwich, G.D.,Pfleiderer, W.,Schmidt, H.H.H.W.
      (1998) J.Biol.Chem. 273: 33142
    • Crystal Structure of Constitutive Endothelial Nitric Oxide Synthase: A Paradigm for Pterin Function Involving a Novel Metal Center
      Raman, C.S.,Li, H.,Martasek, P.,Kral, V.,Masters, B.S.S.,Poulos, T.L.
      (1998) Cell 95: 939
    • Structure of Nitric Oxide Synthase Oxygenase Dimer with Pterin and Substrate
      Crane, B.R.,Arvai, A.S.,Ghosh, D.K.,Wu, C.,Getzoff, E.D.,Stuehr, D.J.,Tainer, A.
      (1998) Science 279: 2121


    Organizational Affiliation

    Department of Pharmacology and Toxicology, Julius-Maximilians University, Versbacher Strasse 9, W├╝rzburg 97078, Germany. peter.kotsonis@pharma.novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NITRIC OXIDE SYNTHASE
A, B
444Bos taurusMutation(s): 0 
Gene Names: NOS3
EC: 1.14.13.39
Find proteins for P29473 (Bos taurus)
Go to Gene View: NOS3
Go to UniProtKB:  P29473
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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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
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
ITU
Query on ITU

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A, B
ETHYLISOTHIOUREA
C3 H8 N2 S
VFIZBHJTOHUOEK-UHFFFAOYSA-N
 Ligand Interaction
CAC
Query on CAC

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A, B
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
AP4
Query on AP4

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A, B
7-AMINO-3,3A,4,5-TETRAHYDRO-8H-2-OXA-5,6,8,9B-TETRAAZA-CYCLOPENTA[A]NAPHTHALENE-1,9-DIONE
5,6-CYCLIC-TETRAHYDROPTERIDINE
C8 H9 N5 O3
XAZOBOCYEGBXHD-GSVOUGTGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ITUIC50: 1300 nM (93) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.900α = 90.00
b = 106.490β = 90.00
c = 156.550γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2000-12-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance