SMTL ID : 2pe2.2 (1 other biounit)

CRYSTAL STRUCTURE OF HUMAN PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 (PDK1) 3-{5-[2-Oxo-5-ureido-1,2-dihydro-indol-(3Z)-ylidenemethyl]-1H-pyrrol-3-yl}-N-(2-piperidin-1-yl-ethyl)-benzamide COMPLEX

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: R.33 Chain B: P.67, H.278 Ligands: GOL.12 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:H.278, A:R.33 Water bridges: A:R.33 SO4.2: 5 residues within 4Å: Chain A: K.3, R.58, T.75, F.76, Q.77 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.75, A:Q.77 Water bridges: A:Q.77 Salt bridges: A:K.3, A:R.58 SO4.3: 4 residues within 4Å: Chain A: R.63, K.126 Chain B: P.1, R.2 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.2, A:R.63 Salt bridges: A:R.63, A:K.126 SO4.13: 4 residues within 4Å: Chain A: P.67, H.278 Chain B: R.33 Ligands: GOL.24 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:H.278, B:R.33 Water bridges: B:R.33 SO4.14: 5 residues within 4Å: Chain B: K.3, R.58, T.75, F.76, Q.77 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.75, B:T.75, B:Q.77 Water bridges: B:Q.77 Salt bridges: B:K.3, B:R.58 SO4.15: 4 residues within 4Å: Chain A: P.1, R.2 Chain B: R.63, K.126 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.63, A:R.2 Salt bridges: B:R.63, B:K.126

2 x 464: 3-[5-({5-[(AMINOCARBONYL)AMINO]-2-OXO-2H-INDOL-3-YL}METHYL)-1H-PYRROL-3-YL]-N-(2-PIPERIDIN-1-YLETHYL)BENZAMIDE(Non-covalent)

464.4: 18 residues within 4Å: Chain A: L.15, V.23, A.36, K.38, L.86, S.87, Y.88, A.89, K.90, N.91, G.92, K.96, Y.97, K.100, L.139, T.149, D.150 Ligands: GOL.5 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.86, A:K.96, A:K.100, A:L.139 Hydrogen bonds: A:K.38, A:S.87, A:A.89, A:N.91, A:D.150, A:D.150, A:D.150 Water bridges: A:S.21, A:N.137 464.16: 18 residues within 4Å: Chain B: L.15, V.23, A.36, K.38, L.86, S.87, Y.88, A.89, K.90, N.91, G.92, K.96, Y.97, K.100, L.139, T.149, D.150 Ligands: GOL.17 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.86, B:K.96, B:K.100, B:L.139 Hydrogen bonds: B:K.38, B:S.87, B:A.89, B:N.91, B:T.149, B:D.150, B:D.150 Water bridges: B:S.21, B:N.137

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: G.16, E.17, G.18, S.21, V.23, E.93 Ligands: 464.4, GOL.11 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: F.9, K.10, F.11 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain A: H.66, W.274, E.275, N.276, L.277, H.278 Chain B: A.30, T.31, S.32 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: L.224, V.245, L.246, D.247, K.250 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: P.6, F.11, K.81, Y.83 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain A: K.38, L.40, Y.53, E.57 Ligands: GOL.11 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: G.18, S.19, F.20, S.21 Ligands: GOL.5, GOL.10 Ligand excluded by PLIP GOL.12: 7 residues within 4Å: Chain A: R.33, E.34, Y.35, Y.73, S.87, Y.88 Ligands: SO4.1 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: G.16, E.17, G.18, S.21, V.23, E.93 Ligands: 464.16, GOL.23 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: F.9, K.10, F.11 Ligand excluded by PLIP GOL.19: 9 residues within 4Å: Chain A: A.30, T.31, S.32 Chain B: H.66, W.274, E.275, N.276, L.277, H.278 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: L.224, V.245, L.246, D.247, K.250 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: P.6, F.11, K.81, Y.83 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain B: K.38, L.40, Y.53, E.57 Ligands: GOL.23 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: G.18, S.19, F.20, S.21 Ligands: GOL.17, GOL.22 Ligand excluded by PLIP GOL.24: 7 residues within 4Å: Chain B: R.33, E.34, Y.35, Y.73, S.87, Y.88 Ligands: SO4.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Islam, I. et al., Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors. Part 2: Optimization of BX-517. Bioorg.Med.Chem.Lett. (2007)

Release Date

2007-06-19

Peptides

3-phosphoinositide-dependent protein kinase 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

3-phosphoinositide-dependent protein kinase 1

Related Entries With Identical Sequence