SMTL ID : 7ore.1

Crystal structure of JNK3 in complex with light-activated covalent inhibitor MR-II-249 with both non-covalent and covalent binding modes (compound 4)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.18 Å

Oligo State

monomer

Ligands

2 x 0EI: 4-(dimethylamino)-N-[(5Z)-9-[[4-[5-(4-fluorophenyl)-3-methyl-2-methylsulfanyl-imidazol-4-yl]pyridin-2-yl]amino]-11,12-dihydrobenzo[c][1,2]benzodiazocin-2-yl]butanamide(Covalent)(Non-covalent)

0EI.1: 18 residues within 4Å: Chain A: I.33, V.41, A.54, K.56, I.87, L.89, L.107, V.108, M.109, E.110, L.111, M.112, D.113, N.115, C.117, Q.118, L.169 Ligands: 0EI.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.33, A:I.33, A:V.41, A:A.54, A:K.56, A:K.56, A:I.87, A:Q.118 Hydrogen bonds: A:M.112, A:M.112, A:N.115 0EI.2: 19 residues within 4Å: Chain A: I.33, V.41, A.54, K.56, I.87, L.89, L.107, V.108, M.109, E.110, L.111, M.112, D.113, A.114, Q.118, S.156, N.157, L.169 Ligands: 0EI.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.33, A:I.33, A:I.33, A:V.41, A:A.54, A:K.56, A:K.56, A:I.87 Hydrogen bonds: A:I.33, A:M.112, A:M.112, A:Q.118

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

EDO.3: 5 residues within 4Å: Chain A: N.29, A.43, A.44, Y.45, N.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.29, A:A.43 EDO.4: 6 residues within 4Å: Chain A: R.70, R.73, E.74, D.170, F.171, G.172 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.74, A:F.171, A:G.172 EDO.5: 5 residues within 4Å: Chain A: N.82, H.83, K.84, A.329, A.333 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.84 EDO.6: 4 residues within 4Å: Chain A: N.82, H.83, K.84, S.88 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.82, A:S.88 Water bridges: A:H.83 EDO.7: 5 residues within 4Å: Chain A: V.92, F.93, T.94, V.361, M.362 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.92, A:T.94, A:T.94 EDO.8: 2 residues within 4Å: Chain A: G.202, Y.203 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.203 EDO.9: 5 residues within 4Å: Chain A: H.144, E.205, S.312, V.313, D.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.144, A:V.313, A:D.314, A:D.314 EDO.10: 2 residues within 4Å: Chain A: N.259, N.263 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.260 EDO.11: 3 residues within 4Å: Chain A: E.286, K.289, L.290 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.286, A:E.286, A:L.290

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reynders, M. et al., Controlling the Covalent Reactivity of a Kinase Inhibitor with Light. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2021-07-21

Peptides

Mitogen-activated protein kinase 10: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mitogen-activated protein kinase 10

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