3BGZ

Human Pim-1 kinase in complex with diphenyl indole inhibitor VX3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 3BGZ

Classification: TRANSFERASE

Total Structure Weight: 38297.42

Macromolecule Entities
Molecule Chains Length Organism Details
Proto-oncogene serine/threonine-protein kinase Pim-1 A 333 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: kinase domain residues 92-404
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
VX3
Query on VX3

A 2,3-diphenyl-1H-indole-7-carboxylic acid
C21 H15 N O2
OLUDUXWVPIEHDA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
VX3 IC50: 550 nM (100) BindingDB
Ki: 550 nM (100) BindingDB

Ki: 550 nM  BindingMOAD
Ki: 550 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: 2.4 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.194
  • Space Group: P 65

Unit Cell:

Length (Å) Angle (°)
a = 98.13 α = 90.00
b = 98.13 β = 90.00
c = 80.80 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-27
  • Released Date: 2007-12-11
  • Deposition author(s): Jacobs, M.D.

Revision History

  • Version 1_0: 2007-12-11

    Type: Initial release

  • Version 1_1: 2011-07-13

    Type: Version format compliance