SMTL ID : 7n7n.1

Crystal Structure of PI5P4KIIAlpha complex with Volasertib

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x IBI: N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide(Non-covalent)

IBI.1: 15 residues within 4Å: Chain A: N.96, 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 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.106, A:F.106, A:K.117, A:F.172, A:L.202, A:L.249, A:I.330 Hydrogen bonds: A:N.96, A:N.170, A:N.170, A:V.171, A:D.331 IBI.5: 15 residues within 4Å: Chain B: N.96, 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 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.106, B:F.106, B:K.117, B:F.172, B:L.202, B:L.249, B:I.330 Hydrogen bonds: B:N.96, B:N.170, B:N.170, B:V.171, B:D.331

6 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: 4 residues within 4Å: Chain A: K.43, K.63, R.155 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.43, A:K.63, A:R.155 SO4.4: 5 residues within 4Å: Chain A: K.43, K.45, K.61 Chain B: K.45 Ligands: SO4.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Water bridges: B:D.47 Salt bridges: B:K.45, A:K.43, A:K.61 SO4.6: 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 SO4.7: 4 residues within 4Å: Chain B: K.43, K.63, R.155 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:K.43, B:K.63, B:R.155 SO4.8: 5 residues within 4Å: Chain A: K.45 Chain B: K.43, K.45, K.61 Ligands: SO4.7 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:D.47, A:D.47 Salt bridges: A:K.45, B:K.43, B:K.61

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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