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 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

4-(1H-indazol-5-yl)-6-phenylpyrimidin-2(1H)-one analogs as potent CDC7 inhibitors.

Shafer, C.M.Lindvall, M.Bellamacina, C.Gesner, T.G.Yabannavar, A.Jia, W.Lin, S.Walter, A.

(2008) Bioorg.Med.Chem.Lett. 18: 4482-4485

  • DOI: 10.1016/j.bmcl.2008.07.061

  • PubMed Abstract: 
  • A series of 4-(4-hydroxyphenyl)-6-phenylpyrimidin-2(1H)-ones were identified by HTS as inhibitors of CDC7. Molecular modeling and medicinal chemistry techniques were employed to explore the SAR for this series with a focus on removing potential metab ...

    A series of 4-(4-hydroxyphenyl)-6-phenylpyrimidin-2(1H)-ones were identified by HTS as inhibitors of CDC7. Molecular modeling and medicinal chemistry techniques were employed to explore the SAR for this series with a focus on removing potential metabolic liabilities and improving cellular potency.


    Organizational Affiliation

    Oncology Division, Novartis Institutes of Biomedical Research, 4560 Horton Street, Emeryville, CA 94608, USA. cynthia_shafer@chiron.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proto-oncogene serine/threonine-protein kinase Pim-1
A
328Homo sapiensGene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
55E
Query on 55E

Download SDF File 
Download CCD File 
A
4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin-2(5H)-one
C17 H14 N2 O2
AZXKZZMGLACNIJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
55EIC50: 3 nM PDBBIND
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 = 97.590α = 90.00
b = 97.590β = 90.00
c = 81.258γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
PHENIXrefinement
SCALAdata scaling
MAR345dtbdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance