4N6Z

Pim1 Complexed with a pyridylcarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 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 ...

    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
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
2HW (Subject of Investigation/LOI)
Query on 2HW

Download Ideal Coordinates CCD File 
B [auth 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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Binding Affinity Annotations 
IDSourceBinding Affinity
2HW Binding MOAD:  4N6Z Ki: 16 (nM) from 1 assay(s)
PDBBind:  4N6Z Ki: 16 (nM) from 1 assay(s)
BindingDB:  4N6Z Ki: 16 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.306α = 90
b = 97.306β = 90
c = 80.859γ = 120
Software Package:
Software NamePurpose
MOLREPphasing
BUSTERrefinement
DENZOdata reduction
SCALEPACKdata 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: 2013-11-06
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references