6L11

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


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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 60: 3287-3294

  • DOI: 10.1021/acs.jcim.0c00245
  • Primary Citation of Related Structures:  
    6L14, 6L13, 6L16, 6L15, 6L17, 6L12, 6L11, 6KZI

  • 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 Identification by Ligand Competitive Saturation (SILCS) method, we quickly obtained a series of 10-DEBC derivatives with significantly improved activity and selectivity ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A289Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E2C (Subject of Investigation/LOI)
Query on E2C

Download Ideal Coordinates CCD File 
B [auth A]5-(2-chloranylphenoxazin-10-yl)-~{N},~{N}-diethyl-pentan-1-amine
C21 H27 Cl N2 O
UVWATVYWPWOHHD-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: 2.05 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.214 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.915α = 90
b = 97.915β = 90
c = 80.718γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-27
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references