6HI9 | pdb_00006hi9

PI3 Kinase Delta in complex with 3[6(oxan4yl)pyridin2yl]phenol

PDB DOI: https://doi.org/10.2210/pdb6HI9/pdb

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

Deposited: 2018-08-29 Released: 2019-09-11
Deposition Author(s): Convery, M.A., Summers, D., Peace, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.213 (Depositor), 0.217 (DCC)
R-Value Work:
0.175 (Depositor), 0.179 (DCC)
R-Value Observed:
0.177 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

A theoretical and experimental investigation into the conformational bias of aryl cyclopropylpyrans, novel bioisosteres for N-aryl morpholines.

Convery, M.A., Summers, D., Hobbs, H., Jamieson, C., Kennedy, A.R., Pal, S., Peace, S., Pogany, P., Upton, R.

To be published.

Macromolecule Content

Total Structure Weight: 108.08 kDa
Atom Count: 7,446
Modeled Residue Count: 858
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

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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: 2.7.1.137 (UniProt), 2.7.1.153 (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
G68 (Subject of Investigation/LOI) Query on G68 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]	3-[6-(oxan-4-yl)pyridin-2-yl]phenol C₁₆ H₁₇ N O₂ JWOOVEVAKYLUGG-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: 2.08 Å
R-Value Free: 0.213 (Depositor), 0.217 (DCC)
R-Value Work: 0.175 (Depositor), 0.179 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.91	α = 90
b = 64.32	β = 102.69
c = 116.14	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
autoBUSTER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-09-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-09-11
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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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.