3N5P

Structure of endothelial nitric oxide synthase heme domain complexed with 4-(2-(6-(2-(6-amino-4-methylpyridin-2-yl)ethyl)pyridin-2-yl)ethyl)-6-methylpyridin-2-amine

Structural Biology Knowledgebase: 3N5P SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3N5P

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 102751.04

Macromolecule Entities
Molecule Chains Length Organism Details
Nitric oxide synthase A, B 444 Bos taurus EC#: 1.14.13.39 IUBMB
Mutation: C100R
Gene Name(s): NOS3 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
HEM
Query on HEM

A, B PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
XFM
Query on XFM

A, B 6-(2-{6-[2-(2-amino-6-methylpyridin-4-yl)ethyl]pyridin- 2-yl}ethyl)-4-methylpyridin-2-amine
C21 H25 N5
ZMKGFXFDYMNDSP-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
H4B
Query on H4B

A, B 5,6,7,8-TETRAHYDROBIOPTERIN
C9 H15 N5 O3
FNKQXYHWGSIFBK-RPDRRWSUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CAD
Query on CAD

A, B CACODYLIC ACID
HYDROXYDIMETHYLARSINE OXIDE (Synonym)
C2 H7 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
XFM Ki: 20000 nM (93) BindingDB

Ki: 20000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.260
  • R-Value Work: 0.206
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.04 α = 90.00
b = 106.10 β = 90.00
c = 158.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-05-25
  • Released Date: 2011-02-09
  • Deposition author(s): Delker, S.L., Li, H., Poulos, T.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4