SMTL ID : 8qlr.1

Human MST3 (STK24) kinase in complex with inhibitor MR24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

2 x VYN: 8-(4-azanylbutyl)-2-[1,3-bis(oxidanyl)propan-2-ylamino]-6-[2-chloranyl-4-(6-methylpyridin-2-yl)phenyl]pyrido[2,3-d]pyrimidin-7-one(Non-covalent)

VYN.1: 21 residues within 4Å: Chain A: I.40, F.45, V.48, A.61, K.63, I.77, E.80, I.81, L.84, I.107, M.109, E.110, Y.111, L.112, G.115, S.116, D.119, A.158, N.159, L.161, D.172 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.45, A:A.61, A:K.63, A:E.80, A:E.80, A:I.81, A:L.84, A:I.107, A:I.107, A:L.161 Hydrogen bonds: A:Y.111, A:Y.111, A:L.112, A:S.116, A:D.119, A:A.158 Water bridges: A:S.44, A:N.159 pi-Cation interactions: A:K.63 VYN.4: 21 residues within 4Å: Chain B: I.40, F.45, V.48, A.61, K.63, I.77, E.80, I.81, L.84, I.107, M.109, E.110, Y.111, L.112, G.115, S.116, D.119, A.158, N.159, L.161, D.172 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:F.45, B:A.61, B:K.63, B:E.80, B:E.80, B:I.81, B:L.84, B:I.107, B:I.107, B:L.161 Hydrogen bonds: B:Y.111, B:L.112, B:A.158 Water bridges: B:D.119, B:D.119, B:N.159, B:D.172 pi-Cation interactions: B:K.63

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

EDO.2: 5 residues within 4Å: Chain A: D.143, S.147, T.274, A.275, K.276 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.275, A:K.276 EDO.3: 3 residues within 4Å: Chain A: I.151, D.207, S.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.207, A:S.208 EDO.5: 5 residues within 4Å: Chain B: D.143, S.147, T.274, A.275, K.276 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.143, B:A.275, B:K.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rak, M. et al., Development of Selective Pyrido[2,3- d ]pyrimidin-7(8 H )-one-Based Mammalian STE20-Like (MST3/4) Kinase Inhibitors. J.Med.Chem. (2024)

Release Date

2023-11-08

Peptides

Serine/threonine-protein kinase 24: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
A

Serine/threonine-protein kinase 24

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