3QKL

Spirochromane Akt Inhibitors

PDB DOI: https://doi.org/10.2210/pdb3QKL/pdb

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

Deposited: 2011-02-01 Released: 2011-03-30
Deposition Author(s): Kallan, N.C., Spencer, K.L., Blake, J.F., Xu, R., Heizer, J., Bencsik, J.R., Mitchell, I.S., Gloor, S.L., Martinson, M., Risom, T., Gross, S.D., Morales, T., Vigers, G.P.A., Brandhuber, B.J., Skelton, N.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243
R-Value Work: 0.193
R-Value Observed: 0.196

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery and SAR of spirochromane Akt inhibitors.

Kallan, N.C., Spencer, K.L., Blake, J.F., Xu, R., Heizer, J., Bencsik, J.R., Mitchell, I.S., Gloor, S.L., Martinson, M., Risom, T., Gross, S.D., Morales, T.H., Wu, W.I., Vigers, G.P., Brandhuber, B.J., Skelton, N.J.

(2011) Bioorg Med Chem Lett 21: 2410-2414

PubMed: 21392984 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.02.073
Primary Citation of Related Structures:
3QKK, 3QKL

PubMed Abstract:
A novel series of spirochromane pan-Akt inhibitors is reported. SAR optimization furnished compounds with improved enzyme potencies and excellent selectivity over the related AGC kinase PKA. Attempted replacement of the phenol hinge binder provided compounds with excellent Akt enzyme and cell activities but greatly diminished selectivity over PKA.

Organizational Affiliation

Array BioPharma, Inc., 3200 Walnut Street, Boulder, CO 80301, USA. nkallan@arraybiopharma.com

Macromolecule Content

Total Structure Weight: 41.15 kDa
Atom Count: 2,959
Modelled Residue Count: 328
Deposited Residue Count: 351
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-alpha serine/threonine-protein kinase	A	341	Homo sapiens	Mutation(s): 1 Gene Names: AKT1, PKB, RAC EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P31749 (Homo sapiens) Explore P31749 Go to UniProtKB: P31749
PHAROS: P31749 GTEx: ENSG00000142208
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31749
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	B [auth C]	10	Homo sapiens	Mutation(s): 0 EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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
SMR Query on SMR Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-{(2S)-3-[(3S)-8',9'-dihydro-1H,3'H-spiro[piperidine-3,7'-pyrano[3,2-e]indazol]-1-yl]-2-hydroxypropyl}-N-(2-ethoxyethyl)-2,6-dimethylbenzenesulfonamide C₂₉ H₄₀ N₄ O₅ S ZSKFBGIRLVOQAD-MUAVYFROSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

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

Binding Affinity Annotations
ID	Source	Binding Affinity
SMR	PDBBind: 3QKL	IC50: 9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243
R-Value Work: 0.193
R-Value Observed: 0.196
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.741	α = 90
b = 55.72	β = 101.84
c = 91.019	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary