4GV1

PKB alpha in complex with AZD5363

• PDB DOI: https://doi.org/10.2210/pdb4GV1/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2012-08-30 Released: 2013-02-27 
• Deposition Author(s): Addie, M., Ballard, P., Bird, G., Buttar, D., Currie, G., Davies, B., Debreczeni, J., Dry, H., Dudley, P., Greenwood, R., Hatter, G., Jestel, A., Johnson, P.D., Kettle, J.G., Lane, C., Lamont, G., Leach, A., Luke, R.W.A., Ogilvie, D., Page, K., Pass, M., Steinbacher, S., Steuber, H., Pearson, S., Ruston, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 

Literature

Discovery of 4-Amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide (AZD5363), an Orally Bioavailable, Potent Inhibitor of Akt Kinases.

Addie, M., Ballard, P., Buttar, D., Crafter, C., Currie, G., Davies, B.R., Debreczeni, J., Dry, H., Dudley, P., Greenwood, R., Johnson, P.D., Kettle, J.G., Lane, C., Lamont, G., Leach, A., Luke, R.W., Morris, J., Ogilvie, D., Page, K., Pass, M., Pearson, S., Ruston, L.

(2013) J Med Chem 56: 2059-2073

• PubMed: 23394218 
• DOI: https://doi.org/10.1021/jm301762v
• Primary Citation of Related Structures:  
  4GV1


• PubMed Abstract: 
  

  Wide-ranging exploration of analogues of an ATP-competitive pyrrolopyrimidine inhibitor of Akt led to the discovery of clinical candidate AZD5363, which showed increased potency, reduced hERG affinity, and higher selectivity against the closely related AGC kinase ROCK. This compound demonstrated good preclinical drug metabolism and pharmacokinetics (DMPK) properties and, after oral dosing, showed pharmacodynamic knockdown of phosphorylation of Akt and downstream biomarkers in vivo, and inhibition of tumor growth in a breast cancer xenograft model.

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Organizational Affiliation: 

Oncology iMed, AstraZeneca, Alderley Park, Macclesfield SK10 4TG, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.19 kDa 
• Atom Count: 3,232 
• Modelled Residue Count: 330 
• Deposited Residue Count: 340 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAC-alpha serine/threonine-protein kinase	A	340	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0XZ	B [auth A]	4-amino-N-[(1S)-1-(4-chlorophenyl)-3-hydroxypropyl]-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidine-4-carboxamide C21 H25 Cl N6 O2 JDUBGYFRJFOXQC-KRWDZBQOSA-N
GOL	C [auth A], D [auth A], E [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Binding Affinity Annotations
ID	Source	Binding Affinity
0XZ	PDBBind:  4GV1	IC50: 3 (nM) from 1 assay(s)
	BindingDB:  4GV1	IC50: 4.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.49 Å
• R-Value Free: 0.210 
• R-Value Work: 0.181 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.852	α = 90
b = 58.556	β = 90
c = 150.472	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-27 
Deposition Author(s): Addie, M., Ballard, P., Bird, G., Buttar, D., Currie, G., Davies, B., Debreczeni, J., Dry, H., Dudley, P., Greenwood, R., Hatter, G., Jestel, A., Johnson, P.D., Kettle, J.G., Lane, C., Lamont, G., Leach, A., Luke, R.W.A., Ogilvie, D., Page, K., Pass, M., Steinbacher, S., Steuber, H., Pearson, S., Ruston, L.

Revision History  

• Version 1.0: 2013-02-27
  Type: Initial release
  
• Version 1.1: 2013-03-27
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description