4K1B

Structure of PIM-1 kinase bound to N-(5-(2-fluorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl)-5-((((3R,4R)-3-fluoropiperidin-4-yl)methyl)amino)pyrazolo[1,5-a]pyrimidine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.082 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
273Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
1OC
Query on 1OC

Download SDF File 
Download CCD File 
A
N-[5-(2-fluorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-5-({[(3R,4R)-3-fluoropiperidin-4-yl]methyl}amino)pyrazolo[1,5-a]pyrimidine-3-carboxamide
C26 H24 F2 N8 O
BEXSRDRFSVXXPU-VFNWGFHPSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1OCKi: 0 nM (100) BINDINGDB
1OCKi: 0.003 nM BINDINGMOAD
1OCKi: 0.003 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.082 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.993α = 90.00
b = 97.993β = 90.00
c = 80.542γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXrefinement
SCALAdata scaling
PHASERphasing
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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