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: 2.08 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4K0Y, 4K18, 4K1B

  • 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 compound 1 via high throughput screening ...

    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-1A273Homo sapiensMutation(s): 0 
Gene Names: PIM-1PIM1
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OC (Subject of Investigation/LOI)
Query on 1OC

Download Ideal Coordinates CCD File 
C [auth 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
PO4
Query on PO4

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1OC Binding MOAD:  4K1B Ki: 3.00e-3 (nM) from 1 assay(s)
BindingDB:  4K1B Ki: 3.00e-3 (nM) from 1 assay(s)
PDBBind:  4K1B Ki: 3.00e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.993α = 90
b = 97.993β = 90
c = 80.542γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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