5DIA

PIM1 in complex with Cpd36 ((1S,3S)-N1-(6-(5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl)pyridin-2-yl)cyclohexane-1,3-diamine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.964 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of 3,5-substituted 6-azaindazoles as potent pan-Pim inhibitors.

Hu, H.Wang, X.Chan, G.K.Chang, J.H.Do, S.Drummond, J.Ebens, A.Lee, W.Ly, J.Lyssikatos, J.P.Murray, J.Moffat, J.G.Chao, Q.Tsui, V.Wallweber, H.Kolesnikov, A.

(2015) Bioorg.Med.Chem.Lett. 25: 5258-5264

  • DOI: 10.1016/j.bmcl.2015.09.052
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pim kinase inhibitors are promising cancer therapeutics. Pim-2, among the three Pim isoforms, plays a critical role in multiple myeloma yet inhibition of Pim-2 is challenging due to its high affinity for ATP. A co-crystal structure of a screening hit ...

    Pim kinase inhibitors are promising cancer therapeutics. Pim-2, among the three Pim isoforms, plays a critical role in multiple myeloma yet inhibition of Pim-2 is challenging due to its high affinity for ATP. A co-crystal structure of a screening hit 1 bound to Pim-1 kinase revealed the key binding interactions of its indazole core within the ATP binding site. Screening of analogous core fragments afforded 1H-pyrazolo[3,4-c]pyridine (6-azaindazole) as a core for the development of pan-Pim inhibitors. Fragment and structure based drug design led to identification of the series with picomolar biochemical potency against all three Pim isoforms. Desirable cellular potency was also achieved.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
299Homo sapiensMutation(s): 0 
Gene Names: PIM1
EC: 2.7.11.1
Find proteins for P11309 (Homo sapiens)
Go to Gene View: PIM1
Go to UniProtKB:  P11309
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5E6
Query on 5E6

Download SDF File 
Download CCD File 
A
(1S,3S)-N-{6-[5-(pyridin-3-yl)-1H-pyrazolo[3,4-c]pyridin-3-yl]pyridin-2-yl}cyclohexane-1,3-diamine
C22 H23 N7
FWMVELRLCYRLLJ-HOTGVXAUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5E6Ki: 0.4 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.964 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.196 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.079α = 90.00
b = 97.079β = 90.00
c = 80.687γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-11
    Type: Database references