4JX7

Crystal structure of Pim1 kinase in complex with inhibitor 2-[(trans-4-aminocyclohexyl)amino]-4-{[3-(trifluoromethyl)phenyl]amino}pyrido[4,3-d]pyrimidin-5(6H)-one

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Crystal structure of pim1 kinase in complex with a pyrido[4,3-d]pyrimidine derivative suggests a unique binding mode.

Lee, S.J., Han, B.G., Cho, J.W., Choi, J.S., Lee, J., Song, H.J., Koh, J.S., Lee, B.I.

(2013) Plos One 8: e70358-e70358

  • DOI: 10.1371/journal.pone.0070358
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human Pim1 kinase is a serine/threonine protein kinase that plays important biological roles in cell survival, apoptosis, proliferation, and differentiation. Moreover, Pim1 is up-regulated in various hematopoietic malignancies and solid tumors. Thus, ...

    Human Pim1 kinase is a serine/threonine protein kinase that plays important biological roles in cell survival, apoptosis, proliferation, and differentiation. Moreover, Pim1 is up-regulated in various hematopoietic malignancies and solid tumors. Thus, Pim1 is an attractive target for cancer therapeutics, and there has been growing interest in developing small molecule inhibitors for Pim1. Here, we describe the crystal structure of Pim1 in complex with a newly developed pyrido[4,3-d]pyrimidine-derivative inhibitor (SKI-O-068). Our inhibitor exhibits a half maximum inhibitory concentration (IC50) of 123 (±14) nM and has an unusual binding mode in complex with Pim1 kinase. The interactions between SKI-O-068 and the Pim1 active site pocket residue are different from those of other scaffold inhibitor-bound structures. The binding mode analysis suggests that the SKI-O-068 inhibitor can be improved by introducing functional groups that facilitate direct interaction with Lys67, which aid in the design of an optimized inhibitor.

    Organizational Affiliation: 

    Biomolecular Function Research Branch, Research Institute, National Cancer Center, Goyang, Gyeonggi, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
326Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PIM1 consensus peptide
B
14N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N6
Query on 1N6
Download SDF File 
Download CCD File 
A
2-[(trans-4-aminocyclohexyl)amino]-4-{[3-(trifluoromethyl)phenyl]amino}pyrido[4,3-d]pyrimidin-5(6H)-one
C20 H21 F3 N6 O
VWACYUAZKMPNOH-JOCQHMNTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1N6IC50: 123 nM BINDINGMOAD
1N6IC50: 123 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.657α = 90.00
b = 97.657β = 90.00
c = 81.106γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release