4N70

Pim1 Complexed with a pyridylcarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure Guided Optimization, in Vitro Activity, and in Vivo Activity of Pan-PIM Kinase Inhibitors.

Burger, M.T.Han, W.Lan, J.Nishiguchi, G.Bellamacina, C.Lindval, M.Atallah, G.Ding, Y.Mathur, M.McBride, C.Beans, E.L.Muller, K.Tamez, V.Zhang, Y.Huh, K.Feucht, P.Zavorotinskaya, T.Dai, Y.Holash, J.Castillo, J.Langowski, J.Wang, Y.Chen, M.Y.Garcia, P.D.

(2013) ACS Med Chem Lett 4: 1193-1197

  • DOI: 10.1021/ml400307j
  • Primary Citation of Related Structures:  
    4N6Y, 4N6Z, 4N70

  • PubMed Abstract: 
  • Proviral insertion of Moloney virus (PIM) 1, 2, and 3 kinases are serine/threonine kinases that normally function in survival and proliferation of hematopoietic cells. As high expression of PIM1, 2, and 3 is frequently observed in many human malignan ...

    Proviral insertion of Moloney virus (PIM) 1, 2, and 3 kinases are serine/threonine kinases that normally function in survival and proliferation of hematopoietic cells. As high expression of PIM1, 2, and 3 is frequently observed in many human malignancies, including multiple myeloma, non-Hodgkins lymphoma, and myeloid leukemias, there is interest in determining whether selective PIM inhibition can improve outcomes of these human cancers. Herein, we describe our efforts toward this goal. The structure guided optimization of a singleton high throughput screening hit in which the potency against all three PIM isoforms was increased >10,000-fold to yield compounds with pan PIM K is < 10 pM, nanomolar cellular potency, and in vivo activity in an acute myeloid leukemia Pim-dependent tumor model is described.


    Organizational Affiliation

    Oncology Research, Novartis Institutes for Biomedical Research , 4560 Horton Street, Emeryville, California 94608, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase pim-1A328Homo sapiensMutation(s): 0 
Gene Names: PIM1
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2HX
Query on 2HX

Download CCD File 
A
N-{4-[(3R,4R,5S)-3-amino-4-hydroxy-5-methylpiperidin-1-yl]pyridin-3-yl}-6-(2,6-difluorophenyl)-5-fluoropyridine-2-carboxamide
C23 H22 F3 N5 O2
ODZZYKUYGVLOTQ-ONJZCGHCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2HXIC50:  1   nM  BindingDB
2HXKi :  0.0010000000474974513   nM  PDBBind
2HXKi:  1   nM  BindingDB
2HXKi:  0   nM  BindingDB
2HXKi:  0.0010000000474974513   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.95α = 90
b = 97.95β = 90
c = 81.08γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references