6HI2

PI3 Kinase Delta in complex with 3{6[(1S,6R)3oxabicyclo[4.1.0]heptan6yl]pyridin2yl}phenol

PDB DOI: https://doi.org/10.2210/pdb6HI2/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: 1.90 Å
R-Value Free: 0.196
R-Value Work: 0.175
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 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: 108.09 kDa
Atom Count: 7,552
Modelled Residue Count: 860
Deposited Residue Count: 940
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for O35904 (Mus musculus) Explore O35904 Go to UniProtKB: O35904
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35904
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G62 (Subject of Investigation/LOI) Query on G62 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	3-[6-[(1~{S},6~{R})-3-oxabicyclo[4.1.0]heptan-6-yl]pyridin-2-yl]phenol C₁₇ H₁₇ N O₂ LKFXAVVNPRARMY-DYVFJYSZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.196
R-Value Work: 0.175
R-Value Observed: 0.176
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 141.74	α = 90
b = 64.49	β = 103.17
c = 116.4	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.