3DCV

Crystal structure of human Pim1 kinase complexed with 4-(4-hydroxy-3-methyl-phenyl)-6-phenylpyrimidin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.179

Literature

Macromolecules
Sequence Display for 3DCV

Classification: TRANSFERASE

Total Structure Weight: 37875.01

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase Pim-1 A 328 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: Kinase domain: Residues 93-404
Gene Name(s): PIM1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
55E
Query on 55E

A 4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin- 2(5H)-one
C17 H14 N2 O2
AZXKZZMGLACNIJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
55E N/A in BindingDB
N/A in BindingMoad
IC50: 3 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.234
  • R-Value Work: 0.179
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 97.59 α = 90.00
b = 97.59 β = 90.00
c = 81.26 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-04
  • Released Date: 2008-08-19
  • Deposition author(s): Bellamacina, C.R., Shafer, C.M., Lindvall, M., Gesner, T.G., Yabannavar, A., Weiping, J., Song, L., Walter, A.

Revision History

  • Version 1_0: 2008-08-19

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance