4I3K

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

Structural Biology Knowledgebase: 4I3K SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.206

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4I3K

Classification: oxidoreductase / oxidoreductase inhibitor

Total Structure Weight: 95509.58

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

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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1BX
Query on 1BX

A 1-hydroxy-6-(4-hydroxybenzyl)-4-methylpyridin- 2(1H)-one
C13 H13 N O3
ABLXOGHWKHJQAM-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
1BX IC50: 9700 nM (99) BindingDB
Ki: 280 - >30000 nM (99) BindingDB

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.277
  • R-Value Work: 0.206
  • Space Group: P 43 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 82.86 α = 90.00
b = 82.86 β = 90.00
c = 304.04 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: Citation | Details: Citation update