2C1B

Structure of cAMP-dependent protein kinase complexed with (4R,2S)-5'-(4-(4-Chlorobenzyloxy)pyrrolidin-2-ylmethanesulfonyl)isoquinoline

• PDB DOI: https://doi.org/10.2210/pdb2C1B/pdb

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


• Deposited: 2005-09-12 Released: 2005-11-02 
• Deposition Author(s): Collins, I., Caldwell, J., Fonseca, T., Donald, A., Bavetsias, V., Hunter, L.J., Garrett, M.D., Rowlands, M.G., Aherne, G.W., Davies, T.G., Berdini, V., Woodhead, S.J., Seavers, L.C.A., Wyatt, P.G., Workman, P., McDonald, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Literature

Structure-based design of isoquinoline-5-sulfonamide inhibitors of protein kinase B.

Collins, I., Caldwell, J., Fonseca, T., Donald, A., Bavetsias, V., Hunter, L.J., Garrett, M.D., Rowlands, M.G., Aherne, G.W., Davies, T.G., Berdini, V., Woodhead, S.J., Davis, D., Seavers, L.C., Wyatt, P.G., Workman, P., McDonald, E.

(2006) Bioorg Med Chem 14: 1255-1273

• PubMed: 16249095 
• DOI: https://doi.org/10.1016/j.bmc.2005.09.055
• Primary Citation of Related Structures:  
  2C1A, 2C1B


• PubMed Abstract: 
  

  Structure-based drug design of novel isoquinoline-5-sulfonamide inhibitors of PKB as potential antitumour agents was investigated. Constrained pyrrolidine analogues that mimicked the bound conformation of linear prototypes were identified and investigated by co-crystal structure determinations with the related protein PKA. Detailed variation in the binding modes between inhibitors with similar overall conformations was observed. Potent PKB inhibitors from this series inhibited GSK3beta phosphorylation in cellular assays, consistent with inhibition of PKB kinase activity in cells.

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Organizational Affiliation: 

Cancer Research, UK Centre for Cancer Therapeutics, The Institute of Cancer Research, Sutton, Surrey. [e-mail]

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: 43.5 kDa 
• Atom Count: 3,416 
• Modelled Residue Count: 357 
• Deposited Residue Count: 371 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CAMP-DEPENDENT PROTEIN KINASE	A	351	Bos taurus	Mutation(s): 0  EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
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	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
CQP	C [auth A]	(4R,2S)-5'-(4-(4-CHLOROBENZYLOXY)PYRROLIDIN-2-YLMETHANESULFONYL)ISOQUINOLINE C21 H22 Cl N3 O3 S RLNNFNGBXLTQOB-RBUKOAKNSA-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
CQP	PDBBind:  2C1B	IC50: 400 (nM) from 1 assay(s)
	BindingDB:  2C1B	IC50: 400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.211 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.31	α = 90
b = 75.16	β = 90
c = 80.052	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-02 
Deposition Author(s): Collins, I., Caldwell, J., Fonseca, T., Donald, A., Bavetsias, V., Hunter, L.J., Garrett, M.D., Rowlands, M.G., Aherne, G.W., Davies, T.G., Berdini, V., Woodhead, S.J., Seavers, L.C.A., Wyatt, P.G., Workman, P., McDonald, E.

Revision History  

• Version 1.0: 2005-11-02
  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: 2018-02-28
  Changes: Database references, Structure summary
• Version 1.4: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary