SMTL ID : 1okz.1

Structure of human PDK1 kinase domain in complex with UCN-01

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

monomer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: I.62, K.104, Y.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.104, A:K.104 GOL.2: 5 residues within 4Å: Chain A: P.24, K.26, Y.96, F.97, T.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.24, A:Y.96, A:T.98, A:T.98 GOL.3: 4 residues within 4Å: Chain A: L.247, Y.249, F.251, R.260 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.249 Water bridges: A:F.251, A:R.260 GOL.4: 3 residues within 4Å: Chain A: F.32, K.33, F.34 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.32, A:F.34 GOL.5: 8 residues within 4Å: Chain A: R.56, E.57, Y.58, Y.96, S.110, Y.111 Ligands: SO4.8, SO4.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.56, A:Y.96, A:Y.111 GOL.6: 7 residues within 4Å: Chain A: H.89, S.141, W.297, E.298, N.299, L.300, H.301 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.141, A:L.300, A:H.301 Water bridges: A:S.141, A:S.141

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

SO4.7: 5 residues within 4Å: Chain A: K.26, R.81, T.98, F.99, Q.100 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.100 Water bridges: A:R.81, A:Q.100, A:Q.100 Salt bridges: A:K.26, A:R.81 SO4.8: 2 residues within 4Å: Chain A: R.56 Ligands: GOL.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.56 SO4.9: 5 residues within 4Å: Chain A: G.41, S.42, F.43, S.44, K.61 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.42, A:F.43, A:S.44 Water bridges: A:K.61 Salt bridges: A:K.61 SO4.10: 2 residues within 4Å: Chain A: R.86, K.149 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.86, A:K.149 SO4.11: 3 residues within 4Å: Chain A: K.94, Y.96 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.96 Water bridges: A:K.94 Salt bridges: A:K.94

1 x UCN: 7-HYDROXYSTAUROSPORINE(Non-covalent)

UCN.12: 17 residues within 4Å: Chain A: L.38, G.39, V.46, A.59, K.61, V.93, L.109, S.110, Y.111, A.112, G.115, E.116, E.159, N.160, L.162, T.172, D.173 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.38, A:L.38, A:V.46, A:V.46, A:L.109, A:L.162, A:D.173 Hydrogen bonds: A:S.110, A:A.112, A:E.116, A:E.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Komander, D. et al., Structural Basis for Ucn-01 (7-Hydroxystaurosporine) Specificity and Pdk1 (3-Phosphoinositide-Dependent Protein Kinase-1) Inhibition. Biochem.J. (2003)

Release Date

2004-07-29

Peptides

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE 1

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