4K0Y

Structure of PIM-1 kinase bound to N-(4-fluorophenyl)-7-hydroxy-5-(piperidin-4-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of novel pyrazolo[1,5-a]pyrimidines as potent pan-Pim inhibitors by structure- and property-based drug design.

Wang, X.Magnuson, S.Pastor, R.Fan, E.Hu, H.Tsui, V.Deng, W.Murray, J.Steffek, M.Wallweber, H.Moffat, J.Drummond, J.Chan, G.Harstad, E.Ebens, A.J.

(2013) Bioorg Med Chem Lett 23: 3149-3153

  • DOI: 10.1016/j.bmcl.2013.04.020
  • Primary Citation of Related Structures:  
    4K18, 4K1B, 4K0Y

  • PubMed Abstract: 
  • Pim kinases are promising targets for the development of cancer therapeutics. Among the three Pim isoforms, Pim-2 is particularly important in multiple myeloma, yet is the most difficult to inhibit due to its high affinity for ATP. We identified comp ...

    Pim kinases are promising targets for the development of cancer therapeutics. Among the three Pim isoforms, Pim-2 is particularly important in multiple myeloma, yet is the most difficult to inhibit due to its high affinity for ATP. We identified compound 1 via high throughput screening. Using property-based drug design and co-crystal structures with Pim-1 kinase to guide analog design, we were able to improve potency against all three Pim isoforms including a significant 10,000-fold gain against Pim-2. Compound 17 is a novel lead with low picomolar potency on all three Pim kinase isoforms.


    Organizational Affiliation

    Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. wang.xiaojing@gene.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A274Homo sapiensMutation(s): 0 
Gene Names: PIM-1PIM1
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
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OA
Query on 1OA

Download CCD File 
A
N-(4-fluorophenyl)-7-hydroxy-5-(piperidin-4-yl)pyrazolo[1,5-a]pyrimidine-3-carboxamide
C18 H18 F N5 O2
SBDJADVTLNKDBC-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1OAKi:  15   nM  Binding MOAD
1OAKi :  15   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.83α = 90
b = 96.83β = 90
c = 80.716γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references