3E88

Crystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors

PDB DOI: https://doi.org/10.2210/pdb3E88/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2008-08-19 Released: 2008-10-14
Deposition Author(s): Concha, N.O., Elkins, P.A., Smallwood, A., Ward, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.273
R-Value Work: 0.230
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Aminofurazans as potent inhibitors of AKT kinase

Rouse, M.B., Seefeld, M.A., Leber, J.D., McNulty, K.C., Sun, L., Miller, W.H., Zhang, S., Minthorn, E.A., Concha, N.O., Choudhry, A.E., Schaber, M.D., Heerding, D.A.

(2009) Bioorg Med Chem Lett 19: 1508-1511

PubMed: 19179070 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.01.002
Primary Citation of Related Structures:
3E87, 3E88, 3E8C, 3E8D, 3E8E

PubMed Abstract:
AKT inhibitors containing an imidazopyridine aminofurazan scaffold have been optimized. We have previously disclosed identification of the AKT inhibitor GSK690693, which has been evaluated in clinical trials in cancer patients. Herein we describe recent efforts focusing on investigating a distinct region of this scaffold that have afforded compounds (30 and 32) with comparable activity profiles to that of GSK690693.

Organizational Affiliation

Oncology Chemistry, GlaxoSmithKline, Collegeville, PA 19426, USA.

Macromolecule Content

Total Structure Weight: 81.31 kDa
Atom Count: 5,556
Modelled Residue Count: 662
Deposited Residue Count: 690
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-beta serine/threonine-protein kinase	A, B	335	Homo sapiens	Mutation(s): 1 Gene Names: AKT2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31751 (Homo sapiens) Explore P31751 Go to UniProtKB: P31751
PHAROS: P31751 GTEx: ENSG00000105221
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31751
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen synthase kinase-3 beta peptide	C, D	10	N/A	Mutation(s): 0 EC: 2.7.11.1 (UniProt), 2.7.11.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P49841 (Homo sapiens) Explore P49841 Go to UniProtKB: P49841
PHAROS: P49841 GTEx: ENSG00000082701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G96 Query on G96 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B]	E [auth A], F [auth B]	4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol C₂₄ H₂₇ N₇ O₃ YFXZFROOGCONFB-MRXNPFEDSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO Query on TPO	A, B	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
G96	BindingDB: 3E88	Ki: min: 0.2, max: 2 (nM) from 2 assay(s)
G96	BindingDB: 3E88	IC50: min: 0.6, max: 10 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.273
R-Value Work: 0.230
R-Value Observed: 0.232
Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.885	α = 90
b = 116.885	β = 90
c = 45.115	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-10-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-10-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-11-13
Changes: Data collection, Refinement description, Structure summary