SMTL ID : 5mrd.1

Human PDK1-PKCiota Kinase Chimera in Complex with Allosteric Compound PS267 Bound to the PIF-Pocket

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x S26: ethyl (2~{S})-1-(6-chloranyl-1,3-benzothiazol-2-yl)-4-oxidanyl-5-oxidanylidene-2-thiophen-2-yl-2~{H}-pyrrole-3-carboxylate(Non-covalent)

S26.1: 12 residues within 4Å: Chain A: K.66, V.69, N.70, I.75, V.78, Q.79, K.82, C.99, F.100, Q.101, L.106, F.108 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.66, A:I.75, A:K.82, A:L.106, A:L.106 Hydrogen bonds: A:Q.79, A:K.82 Halogen bonds: A:K.66

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.2: 8 residues within 4Å: Chain A: F.193, G.195, T.196, A.197, V.200, L.205, E.238, F.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.238

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.3: 2 residues within 4Å: Chain A: T.55, S.56 No protein-ligand interaction detected (PLIP) DMS.4: 5 residues within 4Å: Chain A: P.30, E.31, F.33, K.34, F.35 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:E.31 pi-Cation interactions: A:F.35

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.5: 18 residues within 4Å: Chain A: L.39, G.40, E.41, G.42, S.43, S.45, V.47, A.60, K.62, Y.77, V.94, L.110, S.111, Y.112, A.113, E.117, L.163, D.174 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:S.45, A:Y.77, A:S.111, A:A.113, A:E.117, A:E.117, A:D.174 Water bridges: A:K.62, A:K.62, A:Y.77 Salt bridges: A:K.62, A:K.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arencibia, J.M. et al., An Allosteric Inhibitor Scaffold Targeting the PIF-Pocket of Atypical Protein Kinase C Isoforms. ACS Chem. Biol. (2017)

Release Date

2017-01-18

Peptides

3-phosphoinositide-dependent protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoinositide-dependent protein kinase 1