4I3L

Crystal structure of a metabolic reductase with 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.293
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 4I3L

Classification: oxidoreductase / oxidoreductase inhibitor

Total Structure Weight: 95300.57

Macromolecule Entities
Molecule Chains Length Organism Details
Isocitrate dehydrogenase [NADP] cytoplasmic A, B 414 Homo sapiens EC#: 1.1.1.42 IUBMB
Mutation: R132H
Gene Name(s): IDH1 Gene View PICD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1BZ
Query on 1BZ

A 6-benzyl-1-hydroxy-4-methylpyridin-2(1H)- one
C13 H13 N O2
AVLZAVSZOAQKRC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1BZ IC50: >30000 nM (99) BindingDB
Ki: 190 - >50000 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.293
  • R-Value Work: 0.220
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 80.85 α = 90.00
b = 80.85 β = 90.00
c = 304.84 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-11-26
  • Released Date: 2013-05-22
  • Deposition author(s): Zheng, B., Yao, Y., Liu, Z., Deng, L., Anglin, J.L., Jiang, H., Prasad, B.V.V., Song, Y.

Revision History

  • 2013-07-10
    Type: Database references