SMTL ID : 6i83.1

Crystal structure of phosphorylated RET V804M tyrosine kinase domain complexed with PDD00018366

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x H72: 4-[5-(pyridin-3-ylmethylamino)pyrazolo[1,5-a]pyrimidin-3-yl]benzamide(Non-covalent)

H72.1: 18 residues within 4Å: Chain A: L.31, G.32, F.36, V.39, A.57, K.59, E.76, I.89, M.105, E.106, Y.107, A.108, G.111, S.112, R.179, L.182, S.192, D.193 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.31, A:V.39, A:V.39, A:A.57, A:I.89, A:M.105, A:L.182, A:L.182 Hydrogen bonds: A:L.31, A:K.59, A:E.76, A:A.108, A:D.193 H72.17: 18 residues within 4Å: Chain B: L.31, G.32, F.36, V.39, A.57, K.59, E.76, I.89, M.105, E.106, Y.107, A.108, G.111, S.112, R.179, L.182, S.192, D.193 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.31, B:V.39, B:V.39, B:A.57, B:I.89, B:M.105, B:L.182, B:L.182 Hydrogen bonds: B:L.31, B:K.59, B:E.76, B:A.108, B:D.193, B:D.193

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

FMT.2: 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 Ligand excluded by PLIP FMT.3: 7 residues within 4Å: Chain A: R.22, C.95, Q.97, D.98, G.99, P.100, L.102 Ligand excluded by PLIP FMT.4: 5 residues within 4Å: Chain A: Y.107, A.108, K.109, A.184, E.185 Ligand excluded by PLIP FMT.5: 2 residues within 4Å: Chain A: K.41, T.55 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: H.87, W.157, Q.158, K.188 Ligand excluded by PLIP FMT.7: 5 residues within 4Å: Chain A: R.118, T.247, L.248, G.249, G.250 Ligand excluded by PLIP FMT.8: 7 residues within 4Å: Chain A: Q.211, G.212, M.219, S.223, H.227, Y.229 Chain B: P.67 Ligand excluded by PLIP FMT.9: 5 residues within 4Å: Chain A: K.29, L.31, K.41, Y.107, K.109 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: L.47, K.48, R.50, T.54 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: S.6, R.71, L.74, S.75, N.78 Ligand excluded by PLIP FMT.12: 4 residues within 4Å: Chain A: H.85, Q.161, Q.164, Y.165 Ligand excluded by PLIP FMT.13: 2 residues within 4Å: Chain A: F.225, D.226 Ligand excluded by PLIP FMT.14: 9 residues within 4Å: Chain A: R.174, D.175, L.176, A.177, R.179, I.214, P.215, W.218, S.237 Ligand excluded by PLIP FMT.15: 7 residues within 4Å: Chain A: R.174, L.196, R.198, K.208, G.212, R.213, I.214 Ligand excluded by PLIP FMT.16: 4 residues within 4Å: Chain A: R.270, W.289, K.290, Q.291 Ligand excluded by PLIP FMT.18: 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 Ligand excluded by PLIP FMT.19: 7 residues within 4Å: Chain B: R.22, C.95, Q.97, D.98, G.99, P.100, L.102 Ligand excluded by PLIP FMT.20: 5 residues within 4Å: Chain B: Y.107, A.108, K.109, A.184, E.185 Ligand excluded by PLIP FMT.21: 2 residues within 4Å: Chain B: K.41, T.55 Ligand excluded by PLIP FMT.22: 4 residues within 4Å: Chain B: H.87, W.157, Q.158, K.188 Ligand excluded by PLIP FMT.23: 5 residues within 4Å: Chain B: R.118, T.247, L.248, G.249, G.250 Ligand excluded by PLIP FMT.24: 7 residues within 4Å: Chain A: P.67 Chain B: Q.211, G.212, M.219, S.223, H.227, Y.229 Ligand excluded by PLIP FMT.25: 5 residues within 4Å: Chain B: K.29, L.31, K.41, Y.107, K.109 Ligand excluded by PLIP FMT.26: 4 residues within 4Å: Chain B: L.47, K.48, R.50, T.54 Ligand excluded by PLIP FMT.27: 5 residues within 4Å: Chain B: S.6, R.71, L.74, S.75, N.78 Ligand excluded by PLIP FMT.28: 4 residues within 4Å: Chain B: H.85, Q.161, Q.164, Y.165 Ligand excluded by PLIP FMT.29: 2 residues within 4Å: Chain B: F.225, D.226 Ligand excluded by PLIP FMT.30: 9 residues within 4Å: Chain B: R.174, D.175, L.176, A.177, R.179, I.214, P.215, W.218, S.237 Ligand excluded by PLIP FMT.31: 7 residues within 4Å: Chain B: R.174, L.196, R.198, K.208, G.212, R.213, I.214 Ligand excluded by PLIP FMT.32: 4 residues within 4Å: Chain B: R.270, W.289, K.290, Q.291 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
A

Proto-oncogene tyrosine-protein kinase receptor Ret

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