SMTL ID : 9lgn.2 (1 other biounit)

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 40

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.03 Å

Oligo State

monomer

Ligands

1 x 01: 3-azanyl-4-(7-fluoranyl-2H-indazol-4-yl)-8-methoxy-1H-1,5-naphthyridin-2-one

01.1: 16 residues within 4Å: Chain A: L.41, V.49, A.62, K.64, E.82, H.86, V.96, L.110, T.112, E.113, L.114, C.115, Q.121, F.165, G.175, D.176 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.64, A:T.112, A:F.165 Hydrogen bonds: A:T.112, A:C.115, A:G.116, A:D.176 Water bridges: A:K.64, A:F.177

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

SO4.2: 3 residues within 4Å: Chain A: G.233, G.234, Q.238 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.234, A:Q.238 SO4.3: 2 residues within 4Å: Chain A: Q.120, R.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.120 Salt bridges: A:R.197 SO4.4: 3 residues within 4Å: Chain A: A.128, S.129, N.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.129, A:N.227 Water bridges: A:S.129 SO4.5: 6 residues within 4Å: Chain A: Q.192, E.193, G.194, M.199, L.203, Y.208 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.194, A:Y.208, A:Y.208

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

2025-04-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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