3TEM

Quinone Oxidoreductase (NQ02) bound to the imidazoacridin-6-one 6a1

Structural Biology Knowledgebase: 3TEM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.149

Literature

Macromolecules
Sequence Display for 3TEM

Classification: OXIDOREDUCTASE / OXIDOREDUCTASE INHIBITOR

Total Structure Weight: 53786.46

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosyldihydronicotinamide dehydrogenase [quinone] A, B 228 Homo sapiens EC#: 1.10.5.1 IUBMB
Mutation: L46F
Gene Name(s): NQO2 Gene View NMOR2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FAD
Query on FAD

A, B FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
6A1
Query on 6A1

A, B hydroxy(2-{[(5S)-6-hydroxy-8-methoxy-4,5- dihydro-3H-imidazo[4,5,1-de]acridin-5-yl]amino}ethyl)dimethylammonium
C19 H25 N4 O3
VTPADFJSUDVABF-AWEZNQCLSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
6A1 N/A in BindingDB
IC50: 14 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.165
  • R-Value Work: 0.149
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.76 α = 90.00
b = 83.57 β = 90.00
c = 106.28 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-08-15
  • Released Date: 2011-09-21
  • Deposition author(s): Dunstan, M.S., Leys, D.

Revision History

  • 2011-10-19
    Type: Citation | Details: Citation update
  • 2011-10-05
    Type: Citation | Details: Citation update