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
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



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