PDBsum entry 4z84

Transferase

PDB id: 4z84

Contents

Protein chains

337 a.a.

20 a.a.

Ligands

NVX

MOH ×2

Waters ×457

PDB id:

4z84

Name:

Transferase

Title:

Pkab3 in complex with pyrrolidine inhibitor 34a

Structure:

Camp-dependent protein kinase catalytic subunit alpha. Chain: a. Synonym: pka c-alpha. Engineered: yes. Mutation: yes. Camp-dependent protein kinase inhibitor alpha. Chain: i. Synonym: pki-alpha,camp-dependent protein kinase inhibitor, muscle/brain isoform.

Source:

Bos taurus. Bovine. Organism_taxid: 9913. Gene: prkaca. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens. Human.

Resolution:

1.55Å R-factor: 0.209 R-free: 0.234

Authors:

B.A.Lund,K.A.Alam,R.A.Engh

Key ref:

B.S.Lauber et al. (2016). Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of PKA and a PKB Mimic. Chemistry, 22, 211-221. PubMed id: 26578105 DOI: 10.1002/chem.201503552

Date:

08-Apr-15 Release date: 02-Dec-15

Protein chain

P00517  (KAPCA_BOVIN) -  cAMP-dependent protein kinase catalytic subunit alpha from Bos taurus

Seq: 351 a.a.

Struc: 337 a.a.*

Protein chain

P61925  (IPKA_HUMAN) -  cAMP-dependent protein kinase inhibitor alpha from Homo sapiens

Seq: 76 a.a.

Struc: 20 a.a.

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.11.11 - cAMP-dependent protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1002/chem.201503552

Chemistry 22:211-221 (2016)

PubMed id: 26578105

Addressing the Glycine-Rich Loop of Protein Kinases by a Multi-Facetted Interaction Network: Inhibition of PKA and a PKB Mimic.

B.S.Lauber, L.A.Hardegger, A.K.Asraful, B.A.Lund, O.Dumele, M.Harder, B.Kuhn, R.A.Engh, F.Diederich.

ABSTRACT

Protein kinases continue to be hot targets in drug discovery research, as they are involved in many essential cellular processes and their deregulation can lead to a variety of diseases. A series of 32 enantiomerically pure inhibitors was synthesized and tested towards protein kinase A (PKA) and protein kinase B mimic PKAB3 (PKA triple mutant). The ligands bind to the hinge region, ribose pocket, and glycine-rich loop at the ATP site. Biological assays showed high potency against PKA, with Ki values in the low nanomolar range. The investigation demonstrates the significance of targeting the often neglected glycine-rich loop for gaining high binding potency. X-ray co-crystal structures revealed a multi-facetted network of ligand-loop interactions for the tightest binders, involving orthogonal dipolar contacts, sulfur and other dispersive contacts, amide-π stacking, and H-bonding to organofluorine, besides efficient water replacement. The network was analyzed in a computational approach.