SMTL ID : 6i82.1

Crystal structure of partially phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018412

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

2 x H6W: ~{N}-[3-(1,3-benzodioxol-5-yl)pyrazolo[1,5-a]pyrimidin-5-yl]-~{N}',~{N}'-dimethyl-propane-1,3-diamine(Non-covalent)

H6W.1: 16 residues within 4Å: Chain A: L.31, G.32, F.36, V.39, A.57, K.59, E.106, Y.107, A.108, G.111, R.179, N.180, L.182, S.192, D.193 Ligands: FMT.10 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.31, A:V.39, A:A.57, A:L.182, A:L.182 Hydrogen bonds: A:A.108, A:S.192 Water bridges: A:S.112, A:S.112 Salt bridges: A:D.193 H6W.13: 16 residues within 4Å: Chain B: L.31, G.32, F.36, V.39, A.57, M.105, E.106, Y.107, A.108, G.111, R.179, N.180, L.182, S.192, D.193 Ligands: CL.12 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.31, B:L.31, B:A.57, B:L.182, B:L.182 Hydrogen bonds: B:A.108, B:S.192 Water bridges: B:S.112 Salt bridges: B:D.193

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

EDO.2: 2 residues within 4Å: Chain A: L.147 Ligands: FMT.11 No protein-ligand interaction detected (PLIP) EDO.3: 4 residues within 4Å: Chain A: G.268, H.269, R.270, E.272 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.268, A:R.270, A:E.272 EDO.14: 7 residues within 4Å: Chain B: R.22, C.95, Q.97, D.98, G.99, P.100, L.102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.98, B:P.100 EDO.15: 4 residues within 4Å: Chain B: D.199, V.200, Y.201, E.202 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.199, B:E.202 EDO.16: 2 residues within 4Å: Chain B: K.41, T.55 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.41, B:K.41, B:T.55 Water bridges: B:T.55

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

FMT.4: 8 residues within 4Å: Chain A: G.1, P.2, L.3, S.4 Chain B: Q.211, L.224, F.225, H.227 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.1, A:L.3, A:S.4, B:Q.211, B:L.224 FMT.5: 4 residues within 4Å: Chain A: S.4, L.5, D.8 Chain B: K.266 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.1, A:G.1, B:K.266 FMT.6: 3 residues within 4Å: Chain A: V.26, T.43, Y.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.43, A:T.43 FMT.7: 6 residues within 4Å: Chain A: Q.164, A.167, T.231, V.298, F.299, A.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.299, A:A.300 FMT.8: 4 residues within 4Å: Chain A: K.23, N.24, F.45, Y.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.23 Water bridges: A:F.45 FMT.9: 6 residues within 4Å: Chain A: P.2, L.3, S.6, R.71, L.74, S.75 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.2, A:S.6, A:S.75 FMT.10: 6 residues within 4Å: Chain A: E.76, M.105, S.192, D.193, F.194 Ligands: H6W.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.76, A:D.193, A:F.194 FMT.11: 6 residues within 4Å: Chain A: S.120, R.145, A.146, L.147, L.248 Ligands: EDO.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.145, A:L.147 FMT.17: 4 residues within 4Å: Chain B: R.22, L.25, V.26, L.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.22, B:R.22, B:L.27 FMT.18: 8 residues within 4Å: Chain B: R.174, L.196, R.198, K.208, G.212, R.213, I.214, Y.229 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.174, B:R.174, B:R.198, B:K.208, B:R.213, B:R.213, B:R.213 FMT.19: 5 residues within 4Å: Chain B: A.167, T.231, Q.232, V.298, F.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:F.299 Water bridges: B:A.300 FMT.20: 4 residues within 4Å: Chain B: I.153, S.278, M.309, R.313 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.278, B:R.313 FMT.21: 5 residues within 4Å: Chain B: K.29, L.31, K.41, Y.107, K.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.29, B:Y.107, B:K.109 FMT.22: 2 residues within 4Å: Chain B: I.221, D.226 No protein-ligand interaction detected (PLIP) FMT.23: 3 residues within 4Å: Chain B: H.85, Q.161, Y.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.161, B:Y.165

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.12: 6 residues within 4Å: Chain B: K.59, E.76, M.105, S.192, D.193 Ligands: H6W.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Newton, R. et al., Discovery and Optimization of wt-RET/KDR-Selective Inhibitors of RETV804MKinase. Acs Med.Chem.Lett. (2020)

Release Date

2020-03-11

Peptides

Proto-oncogene tyrosine-protein kinase receptor Ret: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Proto-oncogene tyrosine-protein kinase receptor Ret

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