SMTL ID : 9lid.1 (1 other biounit)

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

monomer

Ligands

1 x 01: 4-[7-azanyl-8-(7-fluoranyl-1H-indazol-4-yl)-6-oxidanylidene-5H-1,5-naphthyridin-3-yl]-N,N-dimethyl-benzamide

01.1: 18 residues within 4Å: Chain A: L.42, G.43, Y.47, V.50, A.63, K.65, E.83, H.87, V.97, L.111, T.113, E.114, L.115, C.116, Q.122, F.166, G.176, D.177 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.50, A:K.65, A:T.113, A:F.166 Hydrogen bonds: A:T.113, A:C.116, A:D.177

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

SO4.2: 5 residues within 4Å: Chain A: R.72, G.73, P.74, K.75, D.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.75, A:D.76 SO4.3: 2 residues within 4Å: Chain A: Q.121, R.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.121 Salt bridges: A:R.198 SO4.4: 5 residues within 4Å: Chain A: E.194, G.195, M.200, L.204, Y.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.195, A:Y.209, A:Y.209 SO4.5: 2 residues within 4Å: Chain A: P.5, R.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.7 SO4.6: 3 residues within 4Å: Chain A: P.118, H.123, A.126 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.123 SO4.7: 5 residues within 4Å: Chain A: D.159, K.161, E.194, G.195, D.196 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.196 Water bridges: A:E.194 Salt bridges: A:K.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, B. et al., Discovery of Naphthyridinone Derivatives as Selective and Potent PKMYT1 Inhibitors with Antitumor Efficacy. J.Med.Chem. (2025)

Release Date

2025-05-14

Peptides

Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase

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