7POR | pdb_00007por

PI3 kinase delta in complex with N-[2-(2-fluoro-4-{[4-(propan-2-yl)piperazin-1-yl]methyl}phenyl)pyridin-4-yl]-2-methoxy-5-(morpholin-4-yl)pyridine-3-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb7POR/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2021-09-09 Released: 2021-09-29
Deposition Author(s): Rowland, P., Convery, M.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.188 (Depositor), 0.191 (DCC)
R-Value Observed:
0.190 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7POR

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Discovery of GSK251: A Highly Potent, Highly Selective, Orally Bioavailable Inhibitor of PI3K delta with a Novel Binding Mode.

Down, K., Amour, A., Anderson, N.A., Barton, N., Campos, S., Cannons, E.P., Clissold, C., Convery, M.A., Coward, J.J., Doyle, K., Duempelfeld, B., Edwards, C.D., Goldsmith, M.D., Krause, J., Mallett, D.N., McGonagle, G.A., Patel, V.K., Rowedder, J., Rowland, P., Sharpe, A., Sriskantharajah, S., Thomas, D.A., Thomson, D.W., Uddin, S., Hamblin, J.N., Hessel, E.M.

(2021) J Med Chem 64: 13780-13792

PubMed: 34510892 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.1c01102
Primary Citation Related Structures:
7POP, 7POR, 7POS, 7POT

PubMed Abstract:
Optimization of a previously reported lead series of PI3Kδ inhibitors with a novel binding mode led to the identification of a clinical candidate compound 31 (GSK251). Removal of an embedded Ames-positive heteroaromatic amine by reversing a sulfonamide followed by locating an interaction with Trp760 led to a highly selective compound 9 . Further optimization to avoid glutathione trapping, to enhance potency and selectivity, and to optimize an oral pharmacokinetic profile led to the discovery of compound 31 (GSK215) that had a low predicted daily dose (45 mg, b.i.d) and a rat toxicity profile suitable for further development.

Organizational Affiliation

Medicines Research Centre, GlaxoSmithKline R&D, Gunnels Wood Road, Stevenage SG1 2NY, U.K.

Macromolecule Content

Total Structure Weight: 108.41 kDa
Atom Count: 7,272
Modeled Residue Count: 859
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform	A	940	Mus musculus	Mutation(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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7XH (Subject of Investigation/LOI) Query on 7XH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	~{N}-[2-[2-fluoranyl-4-[(4-propan-2-ylpiperazin-1-yl)methyl]phenyl]pyridin-4-yl]-2-methoxy-5-morpholin-4-yl-pyridine-3-sulfonamide C₂₉ H₃₇ F N₆ O₄ S ODQVPYNCHSLNGV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.188 (Depositor), 0.191 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142	α = 90
b = 64.2	β = 102.27
c = 115.46	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-09-29

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2021-09-29
Type: Initial release
Version 1.1: 2021-10-06
Changes: Data collection, Database references
Version 1.2: 2024-06-19
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.