3UMX

Crystal structure of Pim1 kinase in complex with inhibitor (Z)-2-[(1H-indol-3-yl)methylene]-7-(azepan-1-ylmethyl)-6-hydroxybenzofuran-3(2H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177

Literature

Macromolecules
Sequence Display for 3UMX

Classification: TRANSFERASE / INHIBITOR

Total Structure Weight: 34672.25

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase pim-1 A 298 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: KINASE DOMAIN (UNP RESIDUES 120-404)
Gene Name(s): PIM1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
Q18
Query on Q18

A (2Z)-7-(azepan-1-ylmethyl)-6-hydroxy-2-(1H- indol-3-ylmethylidene)-1-benzofuran-3(2H)- one
C24 H24 N2 O3
IARYZBOIUVHJGF-XKZIYDEJSA-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 %)
Q18 IC50: 410 nM (100) BindingDB

N/A in BindingMoad
IC50: 240 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.229
  • R-Value Work: 0.177
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 98.21 α = 90.00
b = 98.21 β = 90.00
c = 80.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-11-15
  • Released Date: 2012-08-08
  • Deposition author(s): Parker, L.J., Handa, N., Yokoyama, S.

Revision History

  • 2012-10-03
    Type: Database references