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

Crystal structure of human PKMYT1 protein kinase domain with Naphthyridinone Inhibitor compound 11

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.1: 4 residues within 4Å: Chain A: G.234, G.235, E.236, Q.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.235 TLA.2: 4 residues within 4Å: Chain A: R.41, L.42, G.43, H.44 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.41, A:R.41 Water bridges: A:R.41, A:Q.122, A:Q.122 Salt bridges: A:R.41, A:H.44

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

01.3: 18 residues within 4Å: Chain A: L.42, G.43, V.50, A.63, K.65, E.83, H.87, V.97, L.111, T.113, E.114, L.115, C.116, G.117, Q.122, F.166, G.176, D.177 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.42, A:V.50, A:K.65, A:T.113, A:F.166 Hydrogen bonds: A:T.113, A:C.116, A:G.117, A:G.117, A:D.177, A:D.177 Water bridges: A:F.178 Halogen bonds: A:Q.122

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: H.93, H.149, S.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.152 EDO.5: 4 residues within 4Å: Chain A: D.159, K.161, E.194, G.195 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.161, A:K.161, A:E.194

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
A

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

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