3BGZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Docking study yields four novel inhibitors of the protooncogene pim-1 kinase.

Pierce, A.C., Jacobs, M., Stuver-Moody, C.

(2008) J Med Chem 51: 1972-1975

  • DOI: 10.1021/jm701248t
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • To supplement the hits from a high throughput screen, docking was performed against Pim-1 kinase. Glide docking was augmented with a filter to require traditional or aromatic CH..O hydrogen bonds to the kinase hinge. Four diverse actives, of 96 molec ...

    To supplement the hits from a high throughput screen, docking was performed against Pim-1 kinase. Glide docking was augmented with a filter to require traditional or aromatic CH..O hydrogen bonds to the kinase hinge. Four diverse actives, of 96 molecules assayed, had K(i) values between 0.091 and 4.5 microM. This gives a 14-fold enrichment over the earlier HTS run, and the two crystal structures solved confirmed the binding modes predicted by docking.

    Organizational Affiliation: 

    Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA. al_pierce@vrtx.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase Pim-1
A
333Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
GTEx  ENSG00000137193
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VX3
Query on VX3
Download CCD File 
A
2,3-diphenyl-1H-indole-7-carboxylic acid
C21 H15 N O2
OLUDUXWVPIEHDA-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		AL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VX3IC50:  550   nM  BindingDB
VX3Ki:  550   nM  BindingDB
VX3Ki:  550   nM  Binding MOAD
VX3Ki :  550   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.13α = 90
b = 98.13β = 90
c = 80.8γ = 120
Software Package:
Software NamePurpose
d*TREKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
d*TREKdata reduction
CNXrefinement

Structure Validation

View Full Validation Report


View more in-depth experimental data

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
    Changes: Version format compliance