6L16

Crystal structure of Ser/Thr kinase Pim1 in complex with 10-DEBC derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report



Literature

Structure-Based Optimization of 10-DEBC Derivatives as Potent and Selective Pim-1 Kinase Inhibitors.

Li, G.Zhang, W.Xie, Y.Li, Y.Cao, R.Zheng, G.Huang, N.Zhou, Y.

(2020) J Chem Inf Model 

  • DOI: 10.1021/acs.jcim.0c00245
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pim-1 kinase has been widely regarded as an attractive target for anticancer drugs. Here, we reported our continued efforts in structure-based optimization of compound 10-DEBC, a previously identified micromolar Pim-1 inhibitor. Guided by the Site Id ...

    Pim-1 kinase has been widely regarded as an attractive target for anticancer drugs. Here, we reported our continued efforts in structure-based optimization of compound 10-DEBC, a previously identified micromolar Pim-1 inhibitor. Guided by the Site Identification by Ligand Competitive Saturation (SILCS) method, we quickly obtained a series of 10-DEBC derivatives with significantly improved activity and selectivity. In particular, compound 26 exhibited an IC 50 value of 0.9 nM, as well as 220- and 8-fold selectivity over Pim-2 and Pim-3 kinases, respectively.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing, Beijing 102206, China.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
289Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS  P11309
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E2U
Query on E2U

Download CCD File 
A
2-[4-[2-(7-chloranylpyrido[3,4-b][1,4]benzoxazin-5-yl)ethyl]piperidin-1-yl]ethanamine
C20 H25 Cl N4 O
JTIZNTMOQMLDDF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.031α = 90
b = 98.031β = 90
c = 80.915γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21807007

Revision History 

  • Version 1.0: 2020-05-27
    Type: Initial release