5L72 | pdb_00005l72

PI3 kinase delta in complex with N-[6-(5-methanesulfonamido-6-methoxypyridin-3-yl)-1,3-dihydro-2-benzofuran-4-yl]-2-(morpholin-4-yl)acetamide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 
    0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Evolution of a Novel, Orally Bioavailable Series of PI3K delta Inhibitors from an Inhaled Lead for the Treatment of Respiratory Disease.

Amour, A., Barton, N., Cooper, A.W., Inglis, G., Jamieson, C., Luscombe, C.N., Morrell, J., Peace, S., Perez, D., Rowland, P., Tame, C., Uddin, S., Vitulli, G., Wellaway, N.

(2016) J Med Chem 59: 7239-7251

  • DOI: https://doi.org/10.1021/acs.jmedchem.6b00799
  • Primary Citation Related Structures: 
    5L72

  • PubMed Abstract: 

    A four-step process of high-quality modeling of existing data, deconstruction, identification of replacement cores, and an innovative synthetic regrowth strategy led to the rapid discovery of a novel oral series of PI3Kδ inhibitors with promising selectivity and excellent in vivo characteristics.

    • Organizational Affiliation: 
    • GlaxoSmithKline R&D , Gunnels Wood Road, Stevenage SG1 2NY, U.K.

Macromolecule Content 

  • Total Structure Weight: 108.28 kDa 
  • Atom Count: 7,225 
  • Modeled Residue Count: 858 
  • Deposited Residue Count: 940 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform940Mus musculusMutation(s): 0 
Gene Names: Pik3cd
EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data)
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
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6PF

Query on 6PF


Download:Ideal Coordinates CCD File
B [auth A]N-[6-(5-methanesulfonamido-6-methoxypyridin-3-yl)-1,3-dihydro-2-benzofuran-4-yl]-2-(morpholin-4-yl)acetamide
C21 H24 N4 O6 S
BZDMXCRKVCKVEV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.4α = 90
b = 64.36β = 102.88
c = 115.83γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2016-07-27 
    • Deposition Author(s): Rowland, P.

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2021-09-29
    Changes: Database references, Structure summary
  • Version 1.3: 2024-06-19
    Changes: Data collection