3DCV

Crystal structure of human Pim1 kinase complexed with 4-(4-hydroxy-3-methyl-phenyl)-6-phenylpyrimidin-2(1H)-one

• PDB DOI: https://doi.org/10.2210/pdb3DCV/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-04 Released: 2008-08-19 
• Deposition Author(s): Bellamacina, C.R., Shafer, C.M., Lindvall, M., Gesner, T.G., Yabannavar, A., Weiping, J., Song, L., Walter, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 

Starting Model: other

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

• PubMed: 18672368 
• DOI: https://doi.org/10.1016/j.bmcl.2008.07.061
• Primary Citation of Related Structures:  
  3DCV


• 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 metabolic liabilities and improving cellular potency.

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Organizational Affiliation: 

Oncology Division, Novartis Institutes of Biomedical Research, 4560 Horton Street, Emeryville, CA 94608, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 37.88 kDa 
• Atom Count: 2,356 
• Modelled Residue Count: 274 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proto-oncogene serine/threonine-protein kinase Pim-1	A	328	Homo sapiens	Mutation(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 GTEx:  ENSG00000137193

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
55E	B [auth A]	4-(4-hydroxy-3-methylphenyl)-6-phenylpyrimidin-2(5H)-one C17 H14 N2 O2 AZXKZZMGLACNIJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Binding Affinity Annotations
ID	Source	Binding Affinity
55E	PDBBind:  3DCV	IC50: 3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.234 
• R-Value Work: 0.179 
• R-Value Observed: 0.182 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.59	α = 90
b = 97.59	β = 90
c = 81.258	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-19 
Deposition Author(s): Bellamacina, C.R., Shafer, C.M., Lindvall, M., Gesner, T.G., Yabannavar, A., Weiping, J., Song, L., Walter, A.

Revision History  

• Version 1.0: 2008-08-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Refinement description