5T8I

PI3Kdelta in complex with the inhibitor GS-9901


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

The Discovery of GS-9901: A Potent, Selective and Metabolically Stable Inhibitor of PI3Kd

Patel, L.Chandrasekhar, J.Evarts, J.Forseth, K.Haran, A.Ip, C.Kashishian, A.Kim, M.Koditek, D.Koppenol, S.Lad, L.Lepist, E.-I.McGrath, M.E.Perreault, S.Puri, K.Villasenor, A.Somoza, J.R.Steiner, B.Therrien, J.Trilberg, J.Phillips, G.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoformA939Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.153 (PDB Primary Data), 2.7.1.137 (UniProt)
UniProt
Find proteins for O35904 (Mus musculus)
Explore O35904 
Go to UniProtKB:  O35904
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO35904
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
77C
Query on 77C

Download Ideal Coordinates CCD File 
B [auth A]2,4-diamino-6-{[(S)-[5-chloro-8-fluoro-4-oxo-3-(pyridin-3-yl)-3,4-dihydroquinazolin-2-yl](cyclopropyl)methyl]amino}pyrimidine-5-carbonitrile
C22 H17 Cl F N9 O
XDSXYMOZKDUASY-INIZCTEOSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
77C BindingDB:  5T8I IC50: 1 (nM) from 1 assay(s)
EC50: min: 0.31, max: 2.4 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.256 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.045α = 90
b = 142.197β = 90
c = 222.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-28
    Type: Initial release