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: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

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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:  
    4JX3, 4JX7

  • 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, Pim1 is an attractive target for cancer therapeutics, and there has been growing interest in developing small molecule inhibitors for Pim1 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A326Homo 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
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PIM1 consensus peptideB14Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N6
Query on 1N6
Download Ideal Coordinates CCD File 
C [auth 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
Binding Affinity Annotations 
IDSourceBinding Affinity
1N6 Binding MOAD:  4JX7 IC50: 123 (nM) from 1 assay(s)
PDBBind:  4JX7 IC50: 123 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.657α = 90
b = 97.657β = 90
c = 81.106γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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