6BSK

Human PIM1 kinase in complex with compound 12b


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of 2,6-disubstituted pyrazine derivatives as inhibitors of CK2 and PIM kinases.

Gingipalli, L.Block, M.H.Bao, L.Cooke, E.Dakin, L.A.Denz, C.R.Ferguson, A.D.Johannes, J.W.Larsen, N.A.Lyne, P.D.Pontz, T.W.Wang, T.Wu, X.Wu, A.Zhang, H.J.Zheng, X.Dowling, J.E.Lamb, M.L.

(2018) Bioorg Med Chem Lett 28: 1336-1341

  • DOI: 10.1016/j.bmcl.2018.03.018
  • Primary Citation of Related Structures:  
    6BSK

  • PubMed Abstract: 
  • The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays ...

    The design and synthesis of a novel series of 2,6-disubstituted pyrazine derivatives as CK2 kinase inhibitors is described. Structure-guided optimization of a 5-substituted-3-thiophene carboxylic acid screening hit (3a) led to the development of a lead compound (12b), which shows inhibition in both enzymatic and cellular assays. Subsequent design and hybridization efforts also led to the unexpected identification of analogs with potent PIM kinase activity (14f).


    Organizational Affiliation

    Chemistry, Oncology, IMED Biotech Unit, AstraZeneca, Boston, USA; 35 Gatehouse Drive, Waltham, MA 02451, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1 A276Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Explore P11309 
Go to UniProtKB:  P11309
NIH Common Fund Data Resources
PHAROS:  P11309
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MVG
Query on MVG

Download Ideal Coordinates CCD File 
A
4-{6-[6-(propan-2-ylamino)-1H-indazol-1-yl]pyrazin-2-yl}benzoic acid
C21 H19 N5 O2
RJXWGPDMMDILGJ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.035α = 90
b = 97.035β = 90
c = 81.13γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2017-12-03 
  • Released Date: 2018-03-21 
  • Deposition Author(s): Ferguson, A.D.

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references