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 

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Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/jm701248t
  • Primary Citation of Related Structures:  
    3BGP, 3BGQ, 3BGZ

  • 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 molecules assayed, had K(i) values between 0 ...

    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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proto-oncogene serine/threonine-protein kinase Pim-1333Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
PHAROS:  P11309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VX3
Query on VX3
Download Ideal Coordinates CCD File 
B [auth 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
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
VX3 BindingDB:  3BGZ Ki: 550 (nM) from 1 assay(s)
IC50: 550 (nM) from 1 assay(s)
PDBBind:  3BGZ Ki: 550 (nM) from 1 assay(s)
Binding MOAD:  3BGZ Ki: 550 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance