SMTL ID : 3rwp.1 (1 other biounit)

Discovery of a Novel, Potent and Selective Inhibitor of 3-Phosphoinositide Dependent Kinase (PDK1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: R.58, E.59, Y.60, Y.98, S.112, Y.113 Ligands: SO4.4, SO4.7, SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.58, A:Y.113 Water bridges: A:E.59, A:E.59 GOL.2: 7 residues within 4Å: Chain A: H.91, S.143, W.299, E.300, N.301, L.302, H.303 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.143, A:L.302, A:H.303, A:H.303 Water bridges: A:S.143, A:S.143, A:E.146 GOL.3: 3 residues within 4Å: Chain A: E.280, E.283, G.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.283, A:E.283 GOL.10: 4 residues within 4Å: Chain A: G.43, S.44, F.45 Ligands: ABQ.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.44, A:F.45, A:S.46 Water bridges: A:S.46, A:K.159, A:D.175

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.58 Ligands: GOL.1, SO4.8 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.58 SO4.5: 5 residues within 4Å: Chain A: K.28, R.83, T.100, F.101, Q.102 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.102 Water bridges: A:R.83, A:R.83, A:Q.102 Salt bridges: A:K.28, A:R.83 SO4.6: 3 residues within 4Å: Chain A: K.96, Y.98 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.98 Salt bridges: A:K.96 SO4.7: 5 residues within 4Å: Chain A: Y.98, S.112, Q.172 Ligands: GOL.1, SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.112, A:Q.172 Water bridges: A:Y.113, A:Q.172 SO4.8: 5 residues within 4Å: Chain A: S.57, R.58, E.59 Ligands: GOL.1, SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.59 Water bridges: A:E.59, A:E.59 Salt bridges: A:K.115 SO4.9: 2 residues within 4Å: Chain A: R.88, K.151 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.88, A:K.151

1 x ABQ: [4-amino-7-(propan-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl](6-{[(3S,4R)-4-(4-fluorophenyl)tetrahydrofuran-3-yl]amino}pyrazin-2-yl)methanone(Non-covalent)

ABQ.11: 22 residues within 4Å: Chain A: L.40, G.41, E.42, G.43, S.46, T.47, V.48, A.61, K.63, V.95, L.111, S.112, Y.113, A.114, E.118, K.159, E.161, N.162, L.164, T.174, D.175 Ligands: GOL.10 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.118, A:L.164 Hydrogen bonds: A:S.112, A:A.114, A:D.175 Water bridges: A:K.159, A:E.161, A:F.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murphy, S.T. et al., Discovery of Novel, Potent, and Selective Inhibitors of 3-Phosphoinositide-Dependent Kinase (PDK1). J.Med.Chem. (2011)

Release Date

2011-11-16

Peptides

3-phosphoinositide-dependent protein kinase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-phosphoinositide-dependent protein kinase 1

Related Entries With Identical Sequence