SMTL ID : 6ym3.1

Crystal structure of Compound 1 with PIP4K2A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x OYZ: (2~{R})-2-[[3-cyano-2-[4-(2-ethoxyphenyl)phenyl]-5,8-dihydro-1,7-naphthyridin-4-yl]amino]propanoic acid(Non-covalent)

OYZ.1: 16 residues within 4Å: Chain A: F.123, I.132, K.134, I.136, D.140, I.183, T.185, N.187, V.188, F.189, K.198, T.221, L.266, I.347, L.350 Ligands: PO4.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.134, A:I.136, A:I.183, A:L.266, A:I.347, A:L.350 Hydrogen bonds: A:K.134, A:V.188 Water bridges: A:T.185 Salt bridges: A:K.198 OYZ.3: 17 residues within 4Å: Chain B: F.123, I.132, K.134, I.136, D.140, I.183, T.185, R.186, N.187, V.188, K.198, T.221, L.266, I.347, D.348, L.350 Ligands: PO4.4 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:K.134, B:I.136, B:D.140, B:I.183, B:L.266, B:I.347, B:L.350 Hydrogen bonds: B:K.134, B:V.188, B:T.221 Salt bridges: B:K.198

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 3 residues within 4Å: Chain A: D.348, T.351 Ligands: OYZ.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.351, A:T.351 Water bridges: A:D.262 PO4.4: 4 residues within 4Å: Chain B: D.262, D.348, T.351 Ligands: OYZ.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.262 Water bridges: B:T.351, B:T.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wortmann, L. et al., Discovery and Characterization of the Potent and Highly Selective 1,7-Naphthyridine-Based Inhibitors BAY-091 and BAY-297 of the Kinase PIP4K2A. J.Med.Chem. (2021)

Release Date

2021-04-14

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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