SMTL ID : 4xx9.1

Crystal structure of PDK1 in complex with ATP and the PIF-pocket ligand RF4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

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

ATP.1: 18 residues within 4Å: Chain A: L.39, G.40, E.41, G.42, S.43, S.45, V.47, A.60, K.62, V.94, L.110, S.111, Y.112, A.113, E.117, E.160, L.163, T.173 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.42, A:S.43, A:S.43, A:S.43, A:S.45, A:S.45, A:S.111, A:A.113, A:E.117, A:E.117 Water bridges: A:K.62, A:N.161 Salt bridges: A:K.62

2 x RF4: (2-{[2-(2,6-dimethylphenoxy)ethyl]sulfanyl}-1H-benzimidazol-1-yl)acetic acid(Non-covalent)

RF4.2: 14 residues within 4Å: Chain A: K.27, K.66, I.69, I.70, V.75, V.78, T.79, R.82, T.99, F.100, Q.101, L.106, Y.107, F.108 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:K.66, A:I.69, A:I.70, A:V.75, A:V.78, A:R.82, A:L.106, A:F.108 Hydrogen bonds: A:T.99 Water bridges: A:K.27 Salt bridges: A:K.27, A:R.82 pi-Cation interactions: A:R.82 RF4.3: 5 residues within 4Å: Chain A: L.119, R.123, G.126, G.229, L.230 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:R.123, A:L.230 Water bridges: A:R.123, A:Q.225, A:Q.225 Salt bridges: A:R.123

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: H.90, P.91, F.92, S.142, W.298, E.299, N.300, L.301, H.302, Q.303 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.90, A:W.298, A:L.301, A:H.302, A:H.302 Water bridges: A:S.142 GOL.5: 4 residues within 4Å: Chain A: E.145, Y.284, G.285, K.288 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.145, A:K.288 Water bridges: A:G.285 GOL.6: 4 residues within 4Å: Chain A: P.258, K.259, D.262, P.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.259 Water bridges: A:P.258, A:D.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rettenmaier, T.J. et al., Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J.Med.Chem. (2015)

Release Date

2015-10-21

Peptides

3-phosphoinositide-dependent protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoinositide-dependent protein kinase 1