SMTL ID : 7nzn.1

Structure of RET kinase domain bound to inhibitor JB-48

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

homo-dimer

Ligands

2 x VJH: 2-[4-[[4-[1-[2-(dimethylamino)ethyl]pyrazol-4-yl]-6-[(3-methyl-1~{H}-pyrazol-5-yl)amino]pyrimidin-2-yl]amino]phenyl]-~{N}-(3-fluorophenyl)ethanamide(Non-covalent)

VJH.1: 23 residues within 4Å: Chain A: K.29, L.31, G.32, E.33, G.34, E.35, V.39, A.57, K.59, I.89, V.105, E.106, Y.107, A.108, K.109, G.111, S.112, D.175, R.179, N.180, L.182, S.192, D.193 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.35, A:V.39, A:L.182 Hydrogen bonds: A:L.31, A:E.35, A:E.106, A:A.108, A:A.108, A:D.193 pi-Cation interactions: A:K.29 Halogen bonds: A:D.175 VJH.5: 23 residues within 4Å: Chain B: K.29, L.31, G.32, E.33, G.34, E.35, V.39, A.57, K.59, I.89, V.105, E.106, Y.107, A.108, K.109, G.111, S.112, D.175, R.179, N.180, L.182, S.192, D.193 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.35, B:V.39, B:L.182 Hydrogen bonds: B:L.31, B:E.35, B:E.106, B:A.108, B:A.108, B:D.193 pi-Cation interactions: B:K.29 Halogen bonds: B:D.175

6 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 10 residues within 4Å: Chain A: V.216, K.217, W.218, M.219, A.220, W.236, V.240, Y.253, L.261, L.265 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.219, A:M.219, A:W.236, A:Y.253 FMT.3: 9 residues within 4Å: Chain A: G.1, P.2, L.3, S.4 Chain B: Q.211, L.224, F.225, H.227, F.262 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.1, A:L.3, A:S.4, A:S.4 FMT.4: 10 residues within 4Å: Chain A: K.208, S.210, Q.211, G.212, M.219, S.223, L.224, H.227, Y.229 Chain B: P.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.211, A:G.212 Water bridges: A:Y.229 FMT.6: 10 residues within 4Å: Chain B: V.216, K.217, W.218, M.219, A.220, W.236, V.240, Y.253, L.261, L.265 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.219, B:M.219, B:W.236, B:Y.253 FMT.7: 9 residues within 4Å: Chain A: Q.211, L.224, F.225, H.227, F.262 Chain B: G.1, P.2, L.3, S.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.3, B:S.4, B:S.4 FMT.8: 10 residues within 4Å: Chain A: P.67 Chain B: K.208, S.210, Q.211, G.212, M.219, S.223, L.224, H.227, Y.229 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.211, B:G.212 Water bridges: B:Y.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Discovery of N-Trisubstituted Pyrimidine Derivatives as Type I RET and RET Gatekeeper Mutant Inhibitors with a Novel Kinase Binding Pose. J.Med.Chem. (2022)

Release Date

2022-02-09

Peptides

Proto-oncogene tyrosine-protein kinase receptor Ret: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proto-oncogene tyrosine-protein kinase receptor Ret

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