4ANV | pdb_00004anv

Complexes of PI3Kgamma with isoform selective inhibitors.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 
    0.297 (Depositor), 0.291 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 
    0.243 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 4ANV

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

The Discovery of a Novel Series of Potent and Orally Bioavailable Phosphoinositide 3-Kinase Gamma Inhibitors

Leahy, J.W.Buhr, C.A.Johnson, H.W.B.Kim, B.G.Baik, T.Cannoy, J.Forsyth, T.P.Jeong, J.W.Lee, M.S.Ma, S.Noson, K.Wang, L.Williams, M.Nuss, J.M.Brooks, E.Heald, N.Holst, C.Jaeger, C.Lam, S.Lougheed, J.C.Nguyen, L.Plonowski, A.Stout, T.Foster, P.G.Wu, X.Yakes, M.F.Yu, R.Zhang, W.Lamb, P.Raeber, O.

(2012) J Med Chem 55: 5467

  • DOI: https://doi.org/10.1021/jm300403a
  • Primary Citation Related Structures: 
    4ANU, 4ANV, 4ANW, 4ANX

  • PubMed Abstract: 

    The phosphoinositide 3-kinases (PI3Ks) have been linked to an extraordinarily diversified group of cellular functions making these enzymes compelling targets for the treatment of disease. A large body of evidence has linked PI3Kγ to the modulation of autoimmune and inflammatory processes making it an intriguing target for drug discovery. Our high-throughput screening (HTS) campaign revealed two hits that were nominated for further optimization studies. The in vitro activity of the first HTS hit, designated as the sulfonylpiperazine scaffold, was optimized utilizing structure-based design. However, nonoptimal pharmacokinetic properties precluded this series from further studies. An overlay of the X-ray structures of the sulfonylpiperazine scaffold and the second HTS hit within their complexes with PI3Kγ revealed a high degree of overlap. This feature was utilized to design a series of hybrid analogues including advanced leads such as 31 with desirable potency, selectivity, and oral bioavailability.


  • Organizational Affiliation
    • Department of Drug Discovery, Exelixis, 169 Harbor Way, South San Francisco, California 94083, United States.

Macromolecule Content 

  • Total Structure Weight: 112.71 kDa 
  • Atom Count: 7,111 
  • Modeled Residue Count: 848 
  • Deposited Residue Count: 980 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 3-KINASE CATALYTIC SUBUNIT GAMMA ISOFORM980Homo sapiensMutation(s): 0 
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data), 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
751

Query on 751



Download:Ideal Coordinates CCD File
C [auth A]2-{4-[(4'-METHOXYBIPHENYL-3-YL)SULFONYL]PIPERAZIN-1-YL}-3-(4-METHOXYPHENYL)PYRAZINE
C28 H28 N4 O4 S
IQVDMFYVPSHFEP-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free:  0.297 (Depositor), 0.291 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.236 (DCC) 
  • R-Value Observed: 0.243 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.337α = 90
b = 68.729β = 94.91
c = 106.773γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Other
  • Version 1.2: 2012-06-27
    Changes: Other
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description