4N6Z

Pim1 Complexed with a pyridylcarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 

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:  

  • 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

    Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research , 4560 Horton Street, Emeryville, California 94608, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein kinase pim-1
A
328Homo sapiensGene 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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2HW
Query on 2HW

Download SDF File 
Download CCD File 
A
3-amino-N-{4-[(3S)-3-aminopiperidin-1-yl]pyridin-3-yl}pyrazine-2-carboxamide
C15 H19 N7 O
PKUDLMDWOHMCHC-JTQLQIEISA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2HWKi: 16 nM (98) BINDINGDB
2HWKi: 16 nM BINDINGMOAD
2HWKi: 16 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 97.306α = 90.00
b = 97.306β = 90.00
c = 80.859γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTERrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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