PDBsum entry 4mk0

Signaling protein/inhibitor

PDB id: 4mk0

Contents

Protein chains

631 a.a.

339 a.a.

59 a.a.

Ligands

GOL

29X

Waters ×131

PDB id:

4mk0

Name:

Signaling protein/inhibitor

Title:

Crystal structure of g protein-coupled receptor kinase 2 in complex with a a rationally designed paroxetine derivative

Structure:

Beta-adrenergic receptor kinase 1. Chain: a. Fragment: unp residues 30-668. Synonym: beta-ark-1, g-protein coupled receptor kinase 2. Engineered: yes. Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1. Chain: b. Synonym: transducin beta chain 1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: adrbk1, bark, bark1, grk2. Expressed in: trichoplusia ni. Expression_system_taxid: 7111. Bos taurus. Cow. Organism_taxid: 9913.

Resolution:

2.40Å R-factor: 0.179 R-free: 0.238

Authors:

K.T.Homan,J.J.G.Tesmer

Key ref:

K.T.Homan et al. (2014). Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog. Mol Pharmacol, 85, 237-248. PubMed id: 24220010 DOI: 10.1124/mol.113.089631

Date:

04-Sep-13 Release date: 22-Jan-14

Protein chain

P25098  (ARBK1_HUMAN) -  Beta-adrenergic receptor kinase 1 from Homo sapiens

Seq: 689 a.a.

Struc: 631 a.a.*

Protein chain

P62871  (GBB1_BOVIN) -  Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 from Bos taurus

Seq: 340 a.a.

Struc: 339 a.a.

Protein chain

P63212  (GBG2_BOVIN) -  Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 from Bos taurus

Seq: 71 a.a.

Struc: 59 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.11.15 - [beta-adrenergic-receptor] kinase.
• Reaction: [beta-adrenergic receptor] + ATP = [beta-adrenergic receptor]-phosphate + ADP + H⁺

[beta-adrenergic receptor] (Bound ligand (Het Group name = GOL) matches with 41.67% similarity) + ATP = [beta-adrenergic receptor]-phosphate + ADP + H(+)

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

reference

DOI no: 10.1124/mol.113.089631

Mol Pharmacol 85:237-248 (2014)

PubMed id: 24220010

Structural and functional analysis of g protein-coupled receptor kinase inhibition by paroxetine and a rationally designed analog.

K.T.Homan, E.Wu, M.W.Wilson, P.Singh, S.D.Larsen, J.J.Tesmer.

ABSTRACT

Recently we identified the serotonin reuptake inhibitor paroxetine as an inhibitor of G protein-coupled receptor kinase 2 (GRK2) that improves cardiac performance in live animals. Paroxetine exhibits up to 50-fold selectivity for GRK2 versus other GRKs. A better understanding of the molecular basis of this selectivity is important for the development of even more selective and potent small molecule therapeutics and chemical genetic probes. We first sought to understand the molecular mechanisms underlying paroxetine selectivity among GRKs. We directly measured the KD for paroxetine and assessed its mechanism of inhibition for each of the GRK subfamilies and then determined the atomic structure of its complex with GRK1, the most weakly inhibited GRK tested. Our results suggest that the selectivity of paroxetine for GRK2 largely reflects its lower affinity for adenine nucleotides. Thus, stabilization of off-pathway conformational states unique to GRK2 will likely be key for the development of even more selective inhibitors. Next, we designed a benzolactam derivative of paroxetine that has optimized interactions with the hinge of the GRK2 kinase domain. The crystal structure of this compound in complex with GRK2 confirmed the predicted interactions. Although the benzolactam derivative did not significantly alter potency of inhibition among GRKs, it exhibited 20-fold lower inhibition of serotonin reuptake. However, there was an associated increase in the potency for inhibition of other AGC kinases, suggesting that the unconventional hydrogen bond formed by the benzodioxole ring of paroxetine is better accommodated by GRKs.