SMTL ID : 7n7o.1

Crystal Structure of PI5P4KIIAlpha complex with Palbociclib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x LQQ: 6-ACETYL-8-CYCLOPENTYL-5-METHYL-2-[(5-PIPERAZIN-1-YLPYRIDIN-2-YL)AMINO]PYRIDO[2,3-D]PYRIMIDIN-7(8H)-ONE(Non-covalent)

LQQ.1: 15 residues within 4Å: Chain A: D.97, F.106, I.115, K.117, P.148, T.168, R.169, N.170, V.171, F.172, L.202, T.204, L.249, I.330, D.331 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:F.106, A:F.106, A:T.168, A:F.172, A:L.249, A:I.330, A:I.330, A:I.330 Hydrogen bonds: A:D.97, A:N.170, A:V.171, A:D.331 Water bridges: A:N.170 LQQ.4: 15 residues within 4Å: Chain B: D.97, F.106, I.115, K.117, P.148, T.168, R.169, N.170, V.171, F.172, L.202, T.204, L.249, I.330, D.331 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.106, B:F.106, B:T.168, B:F.172, B:L.249, B:I.330, B:I.330, B:I.330 Hydrogen bonds: B:D.97, B:N.170, B:V.171, B:D.331 Water bridges: B:N.170

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

SO4.2: 2 residues within 4Å: Chain A: K.185, R.191 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.185, A:R.191 SO4.3: 3 residues within 4Å: Chain A: K.43, K.63, R.155 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.43, A:K.63, A:R.155 SO4.5: 2 residues within 4Å: Chain B: K.185, R.191 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.185, B:R.191 SO4.6: 3 residues within 4Å: Chain B: K.43, K.63, R.155 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.43, B:K.63, B:R.155

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, S. et al., Pharmacological inhibition of PI5P4K alpha / beta disrupts cell energy metabolism and selectively kills p53-null tumor cells. Proc.Natl.Acad.Sci.USA (2021)

Release Date

2021-06-30

Peptides

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

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