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 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    1DMK, 1DMJ

  • 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 cofactor binding, maximally increases enzyme activity and NO production from substrate l-arginine ...

    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: 
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NITRIC OXIDE SYNTHASEA, B444Bos taurusMutation(s): 0 
Gene Names: NOS3
EC: 1.14.13.39
UniProt
Find proteins for P29473 (Bos taurus)
Explore P29473 
Go to UniProtKB:  P29473
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A], N [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
AP4 (Subject of Investigation/LOI)
Query on AP4

Download Ideal Coordinates CCD File 
H [auth A], O [auth B]7-AMINO-3,3A,4,5-TETRAHYDRO-8H-2-OXA-5,6,8,9B-TETRAAZA-CYCLOPENTA[A]NAPHTHALENE-1,9-DIONE
C8 H9 N5 O3
XAZOBOCYEGBXHD-GSVOUGTGSA-N
 Ligand Interaction
CAC
Query on CAC

Download Ideal Coordinates CCD File 
E [auth A], M [auth B]CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
ITU
Query on ITU

Download Ideal Coordinates CCD File 
I [auth A], P [auth B]ETHYLISOTHIOUREA
C3 H8 N2 S
VFIZBHJTOHUOEK-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A], Q [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], K [auth B], L [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ITU BindingDB:  1DMJ IC50: 1300 (nM) from 1 assay(s)
AP4 BindingDB:  1DMJ IC50: 1.01e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.9α = 90
b = 106.49β = 90
c = 156.55γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

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