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 

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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:  
    6KZI, 6L11, 6L12, 6L13, 6L14, 6L15, 6L16, 6L17

  • 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)  |  3D 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
E2U (Subject of Investigation/LOI)
Query on E2U
Download Ideal Coordinates CCD File 
B [auth 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		A L-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
E2U Binding MOAD:  6L16 IC50: 1.7 (nM) from 1 assay(s)
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

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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