3OCB | pdb_00003ocb

Akt1 kinase domain with pyrrolopyrimidine inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3OCB/pdb

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


• Deposited: 2010-08-09 Released: 2010-09-15 
• Deposition Author(s): Morales, T.H., Vigers, G.P.A., Brandhuber, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Literature

Discovery of pyrrolopyrimidine inhibitors of Akt.

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

(2010) Bioorg Med Chem Lett 20: 5607-5612

• PubMed: 20810279 
• DOI: https://doi.org/10.1016/j.bmcl.2010.08.053
• Primary Citation Related Structures: 
  3OCB


• PubMed Abstract: 
  

  The discovery and optimization of a series of pyrrolopyrimidine based protein kinase B (Pkb/Akt) inhibitors discovered via HTS and structure based drug design is reported. The compounds demonstrate potent inhibition of all three Akt isoforms and knockdown of phospho-PRAS40 levels in LNCaP cells and tumor xenografts.

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Organizational Affiliation: 
• Array BioPharma Inc, 3200 Walnut Street, Boulder, CO 80301, 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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.98 kDa 
• Atom Count: 5,519 
• Modeled Residue Count: 656 
• Deposited Residue Count: 702 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
v-akt murine thymoma viral oncogene homolog 1 (AKT1)	A, B	341	Homo sapiens	Mutation(s): 1  Gene Names: AKT1 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GSK 3 beta peptide	C, D	10	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XM1	E [auth A], F [auth B]	(2S)-2-(4-chlorobenzyl)-3-oxo-3-[4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperazin-1-yl]propan-1-amine C20 H23 Cl N6 O IYQSFRNHWXBIKV-HNNXBMFYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.282 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.265	α = 90
b = 56.013	β = 104.27
c = 91.65	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Morales, T.H., Vigers, G.P.A., Brandhuber, B.J.

Revision History  

• Version 1.0: 2010-09-15
  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, Structure summary