2UVY | pdb_00002uvy

Structure of PKA-PKB chimera complexed with methyl-(4-(9H-purin-6-yl)- benzyl)-amine

• PDB DOI: https://doi.org/10.2210/pdb2UVY/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Bos taurus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-03-15 Released: 2007-05-08 
• Deposition Author(s): Davies, T.G., Donald, A., McHardy, T., Rowlands, M.G., Hunter, L.J., Boyle, R.G., Aherne, G.W., Garrett, M.D., Collins, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.216 (Depositor) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

Rapid Evolution of 6-Phenylpurine Inhibitors of Protein Kinase B Through Structure-Based Design

Donald, A., Mchardy, T., Rowlands, M.G., Hunter, L.J., Davies, T.G., Berdini, V., Boyle, R.G., Aherne, G.W., Garrett, M.D., Collins, I.

(2007) J Med Chem 50: 2289

• PubMed: 17451235 
• DOI: https://doi.org/10.1021/jm0700924
• Primary Citation Related Structures: 
  2UVX, 2UVY, 2UVZ, 2UW0


• PubMed Abstract: 
  

  6-phenylpurines were identified as novel, ATP-competitive inhibitors of protein kinase B (PKB/Akt) from a fragment-based screen and were rapidly progressed to potent compounds using iterative protein-ligand crystallography with a PKA-PKB chimeric protein. An elaborated lead compound showed cell growth inhibition and effects on cellular signaling pathways characteristic of PKB inhibition.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.38 kDa 
• Atom Count: 3,284 
• Modeled Residue Count: 356 
• Deposited Residue Count: 371 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE, ALPHA-CATALYTIC SUBUNIT	A	351	Bos taurus	Mutation(s): 4  EC: 2.7.11.11
UniProt
Find proteins for P00517 (Bos taurus) Explore P00517  Go to UniProtKB:  P00517

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE INHIBITOR ALPHA	B [auth I]	20	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens) Explore P61925  Go to UniProtKB:  P61925
PHAROS:  P61925 GTEx:  ENSG00000171033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVI	C [auth A]	N-METHYL-1-[4-(9H-PURIN-6-YL)PHENYL]METHANAMINE C13 H13 N5 VRGSDHJXBVCQEL-UHFFFAOYSA-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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.253 (Depositor) 
• R-Value Work:  0.216 (Depositor) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.718	α = 90
b = 74.646	β = 90
c = 80.071	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-08 
Deposition Author(s): Davies, T.G., Donald, A., McHardy, T., Rowlands, M.G., Hunter, L.J., Boyle, R.G., Aherne, G.W., Garrett, M.D., Collins, I.

Revision History  

• Version 1.0: 2007-05-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary