4DK5 | pdb_00004dk5

Crystal structure of human PI3K-gamma in complex with a pyridyl-triazine inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 
    0.289 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.224 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0KOClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Structure-based design of a novel series of potent, selective inhibitors of the class I phosphatidylinositol 3-kinases.

Smith, A.L.D'Angelo, N.D.Bo, Y.Y.Booker, S.K.Cee, V.J.Herberich, B.Hong, F.T.Jackson, C.L.Lanman, B.A.Liu, L.Nishimura, N.Pettus, L.H.Reed, A.B.Tadesse, S.Tamayo, N.A.Wurz, R.P.Yang, K.Andrews, K.L.Whittington, D.A.McCarter, J.D.Miguel, T.S.Zalameda, L.Jiang, J.Subramanian, R.Mullady, E.L.Caenepeel, S.Freeman, D.J.Wang, L.Zhang, N.Wu, T.Hughes, P.E.Norman, M.H.

(2012) J Med Chem 55: 5188-5219

  • DOI: https://doi.org/10.1021/jm300184s
  • Primary Citation of Related Structures:  
    4DK5

  • PubMed Abstract: 

    A highly selective series of inhibitors of the class I phosphatidylinositol 3-kinases (PI3Ks) has been designed and synthesized. Starting from the dual PI3K/mTOR inhibitor 5, a structure-based approach was used to improve potency and selectivity, resulting in the identification of 54 as a potent inhibitor of the class I PI3Ks with excellent selectivity over mTOR, related phosphatidylinositol kinases, and a broad panel of protein kinases. Compound 54 demonstrated a robust PD-PK relationship inhibiting the PI3K/Akt pathway in vivo in a mouse model, and it potently inhibited tumor growth in a U-87 MG xenograft model with an activated PI3K/Akt pathway.


  • Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., One Amgen Center Drive, Thousand Oaks, California 91320-1799, United States. adrians@amgen.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform959Homo sapiensMutation(s): 0 
Gene Names: PIK3CG
EC: 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 2.7.1.137 (UniProt), 2.7.1.154 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P48736 (Homo sapiens)
Explore P48736 
Go to UniProtKB:  P48736
PHAROS:  P48736
GTEx:  ENSG00000105851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48736
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
0KO BindingDB:  4DK5 Ki: min: 4, max: 8 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free:  0.289 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.219 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.224 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.775α = 90
b = 68.233β = 94.99
c = 107.182γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 0KOClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description