5V82

PIM1 kinase in complex with Cpd17 (1-(6-(4,4-difluoropiperidin-3-yl)pyridin-2-yl)-6-(6-methylpyrazin-2-yl)-1H-pyrazolo[4,3-c]pyridine)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Discovery of 5-Azaindazole (GNE-955) as a Potent Pan-Pim Inhibitor with Optimized Bioavailability.

Wang, X.Kolesnikov, A.Tay, S.Chan, G.Chao, Q.Do, S.Drummond, J.Ebens, A.J.Liu, N.Ly, J.Harstad, E.Hu, H.Moffat, J.Munugalavadla, V.Murray, J.Slaga, D.Tsui, V.Volgraf, M.Wallweber, H.Chang, J.H.

(2017) J Med Chem 60: 4458-4473

  • DOI: 10.1021/acs.jmedchem.7b00418
  • Primary Citation of Related Structures:  
    5V80, 5V82

  • PubMed Abstract: 
  • Pim kinases have been identified as promising therapeutic targets for hematologic-oncology indications, including multiple myeloma and certain leukemia. Here, we describe our continued efforts in optimizing a lead series by improving bioavailability while maintaining high inhibitory potency against all three Pim kinase isoforms ...

    Pim kinases have been identified as promising therapeutic targets for hematologic-oncology indications, including multiple myeloma and certain leukemia. Here, we describe our continued efforts in optimizing a lead series by improving bioavailability while maintaining high inhibitory potency against all three Pim kinase isoforms. The discovery of extensive intestinal metabolism and major metabolites helped refine our design strategy, and we observed that optimizing the pharmacokinetic properties first and potency second was a more successful approach than the reverse. In the resulting work, novel analogs such as 20 (GNE-955) were discovered bearing 5-azaindazole core with noncanonical hydrogen bonding to the hinge.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A299Homo 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
96Y (Subject of Investigation/LOI)
Query on 96Y

Download Ideal Coordinates CCD File 
B [auth A]1-{6-[(3R)-4,4-difluoropiperidin-3-yl]pyridin-2-yl}-6-(6-methylpyrazin-2-yl)-1H-pyrazolo[4,3-c]pyridine
C21 H19 F2 N7
OIZRMKSUYVZCDN-OAHLLOKOSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
96Y Binding MOAD:  5V82 Ki: 0.07 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.485α = 90
b = 96.485β = 90
c = 80.628γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-10
    Type: Initial release
  • Version 1.1: 2017-06-07
    Changes: Database references