Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

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: 43.48 kDa 
• Atom Count: 3257 
• Modelled Residue Count: 356 
• Deposited Residue Count: 371 
• Unique protein chains: 2

2JDT

Structure of PKA-PKB chimera complexed with ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY) ETHYLAMINO)ETHYL)AMIDE

• DOI: 10.2210/pdb2JDT/pdb

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


• Deposited: 2007-01-12 Released: 2007-02-13 
• Deposition Author(s): Davies, T.G., Verdonk, M.L., Graham, B., Saalau-Bethell, S., Hamlett, C.C.F., McHardy, T., Collins, I., Garrett, M.D., Workman, P., Woodhead, S.J., Jhoti, H., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.259 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

A Structural Comparison of Inhibitor Binding to Pkb, Pka and Pka-Pkb Chimera

Davies, T.G., Verdonk, M.L., Graham, B., Saalau-Bethell, S., Hamlett, C.C.F., Mchardy, T., Collins, I., Garrett, M.D., Workman, P., Woodhead, S.J., Jhoti, H., Barford, D.

(2007) J Mol Biol 367: 882

• PubMed: 17275837 
• DOI: 10.1016/j.jmb.2007.01.004
• Primary Citation of Related Structures:  
  2JDO, 2JDR, 2JDS, 2JDT, 2JDV


• PubMed Abstract: 
  

Although the crystal structure of the anti-cancer target protein kinase B (PKBbeta/Akt-2) has been useful in guiding inhibitor design, the closely related kinase PKA has generally been used as a structural mimic due to its facile crystallization with a range of ligands. The use of PKB-inhibitor crystallography would bring important benefits, including a more rigorous understanding of factors dictating PKA/PKB selectivity, and the opportunity to validate the utility of PKA-based surrogates. We present a "back-soaking" method for obtaining PKBbeta-ligand crystal structures, and provide a structural comparison of inhibitor binding to PKB, PKA, and PKA-PKB chimera. One inhibitor presented here exhibits no PKB/PKA selectivity, and the compound adopts a similar binding mode in all three systems. By contrast, the PKB-selective inhibitor A-443654 adopts a conformation in PKB and PKA-PKB that differs from that with PKA. We provide a structural explanation for this difference, and highlight the ability of PKA-PKB to mimic the true PKB binding mode in this case.

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Organizational Affiliation: 

Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE	A	351	Bos taurus	Mutation(s): 4  Gene Names: PRKACA 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  Gene Names: PKIA, PRKACN1
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
I5S (Subject of Investigation/LOI)	C [auth A]	ISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY)ETHYLAMINO)ETHYL)AMIDE C20 H22 Cl N3 O3 S AUHWQSZMVMMRLM-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

Binding Affinity Annotations
ID	Source	Binding Affinity
I5S	PDBBind:  2JDT	IC50: 170 (nM) from 1 assay(s)
	BindingDB:  2JDT	IC50: 170 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.259 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.863	α = 90
b = 75.563	β = 90
c = 80.097	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2007-01-12 
• Released Date: 2007-02-13 
Deposition Author(s): Davies, T.G., Verdonk, M.L., Graham, B., Saalau-Bethell, S., Hamlett, C.C.F., McHardy, T., Collins, I., Garrett, M.D., Workman, P., Woodhead, S.J., Jhoti, H., Barford, D.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance