2GU8

Discovery of 2-Pyrimidyl-5-Amidothiophenes as Novel and Potent Inhibitors for AKT: Synthesis and SAR Studies

• PDB DOI: https://doi.org/10.2210/pdb2GU8/pdb

• Classification: SIGNALING PROTEIN,TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-04-28 Released: 2007-05-01 
• Deposition Author(s): Murray, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 

Literature

Discovery of 2-pyrimidyl-5-amidothiophenes as potent inhibitors for AKT: synthesis and SAR studies

Lin, X., Murray, J.M., Rico, A.C., Wang, M.X., Chu, D.T., Zhou, Y., Del Rosario, M., Kaufman, S., Ma, S., Fang, E., Crawford, K., Jefferson, A.B.

(2006) Bioorg Med Chem Lett 16: 4163-4168

• PubMed: 16765046 
• DOI: https://doi.org/10.1016/j.bmcl.2006.05.092
• Primary Citation of Related Structures:  
  2GU8


• PubMed Abstract: 
  

  A series of 2-pyrimidyl-5-amidothiophenes has been synthesized and evaluated for AKT inhibition. SAR studies resulted in potent inhibitors of AKT with IC(50) values as low as single digit nanomolar as represented by compound 2aa. Compound 2aa showed cellular activity including antiproliferation and downstream target modulation. Selectivity profile is described. A co-crystal of 2aa with PKA is determined and discussed.

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Organizational Affiliation: 

Small Molecule Drug Discovery, Biopharma Research, Chiron Corporation, Emeryville, CA, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 42.08 kDa 
• Atom Count: 3,123 
• Modelled Residue Count: 357 
• Deposited Residue Count: 357 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-dependent protein kinase, alpha-catalytic subunit	A	337	Homo sapiens	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P17612 (Homo sapiens) Explore P17612  Go to UniProtKB:  P17612
PHAROS:  P17612 GTEx:  ENSG00000072062

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
inhibitor of CAMP-dependent protein kinase	B [auth C]	20	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
796	C [auth A]	N-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]-5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE-2-CARBOXAMIDE C19 H19 Cl2 N5 O S HHOVRZGUSBMKKU-ZDUSSCGKSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	A	L-PEPTIDE LINKING	C3 H8 N O6 P		SER
TPO	A	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Binding Affinity Annotations
ID	Source	Binding Affinity
796	PDBBind:  2GU8	IC50: 2.6 (nM) from 1 assay(s)
	BindingDB:  2GU8	IC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.203 
• R-Value Observed: 0.206 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.72	α = 90
b = 75.165	β = 90
c = 79.844	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-01 
Deposition Author(s): Murray, J.M.

Revision History  

• Version 1.0: 2007-05-01
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary