SMTL ID : 6osp.3 (2 other biounits)

Crystal Structure Analysis of PIP4K2A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

homo-dimer

Ligands

2 x N51: 4-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}-N-(3-{[6-(1H-indol-3-yl)pyrimidin-4-yl]amino}phenyl)benzamide(Non-covalent)

N51.1: 12 residues within 4Å: Chain A: F.123, K.129, I.132, K.134, T.185, R.186, N.187, V.188, F.189, S.194, L.266, I.347 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:K.129, A:K.129, A:K.134, A:F.189, A:F.189 Hydrogen bonds: A:K.129, A:T.185, A:N.187, A:N.187, A:V.188 pi-Stacking: A:F.123 N51.3: 12 residues within 4Å: Chain B: F.123, K.129, I.132, K.134, T.185, R.186, N.187, V.188, F.189, K.198, L.266, I.347 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.123, B:K.129, B:K.134, B:F.189, B:F.189, B:K.198 Hydrogen bonds: B:K.129, B:N.187, B:N.187, B:V.188

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.160, I.161, T.162, L.163, Q.166, K.247, V.327, Y.328 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.162, A:Q.166, A:V.327 Water bridges: A:K.247, A:V.327 GOL.4: 8 residues within 4Å: Chain B: G.160, I.161, T.162, L.163, Q.166, K.247, V.327, Y.328 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.162, B:Q.166, B:K.247, B:V.327

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sivakumaren, S.C. et al., Targeting the PI5P4K Lipid Kinase Family in Cancer Using Covalent Inhibitors. Cell Chem Biol (2020)

Release Date

2020-04-29

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha

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