SMTL ID : 9lgv.2 (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

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

TLA.1: 4 residues within 4Å: Chain A: G.234, G.235, E.236, Q.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.235, A:G.235, A:Q.239

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

EDO.2: 4 residues within 4Å: Chain A: D.196, P.197, R.198, H.233 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.198, A:R.198 EDO.4: 4 residues within 4Å: Chain A: L.184, G.210, T.211, A.212 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.211, A:A.212 EDO.5: 6 residues within 4Å: Chain A: Q.193, E.194, G.195, M.200, L.204, Y.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.193, A:G.195, A:L.204

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

01.3: 16 residues within 4Å: Chain A: L.42, V.50, A.63, K.65, H.87, V.97, L.111, T.113, E.114, L.115, C.116, G.117, Q.122, F.166, G.176, D.177 12 PLIP interactions: 12 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:G.117, A:G.117, A:D.177, A:D.177 Water bridges: A:F.178 Halogen bonds: A:Q.122

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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