SMTL ID : 6vhg.1

Crystal structure of phosphorylated RET tyrosine kinase domain complexed with a pyrazolo[1,5-a]pyrimidine inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x QX1: 3-(3,4-dimethoxyphenyl)-N~5~-(1-methylpiperidin-4-yl)-6-phenylpyrazolo[1,5-a]pyrimidine-5,7-diamine(Non-covalent)

QX1.1: 19 residues within 4Å: Chain A: L.28, G.29, F.33, V.36, A.54, K.56, E.73, L.77, I.86, V.102, E.103, Y.104, A.105, G.108, R.176, N.177, L.179, S.189, D.190 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.28, A:L.28, A:F.33, A:K.56, A:L.77, A:I.86, A:V.102, A:L.179 Hydrogen bonds: A:E.103, A:A.105 Water bridges: A:S.109, A:S.109, A:S.189, A:D.190 Salt bridges: A:D.190 pi-Cation interactions: A:K.56

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: S.109, R.111, G.112, R.176 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.109, A:G.112 Water bridges: A:S.109, A:R.111, A:R.176 Salt bridges: A:R.111 SO4.3: 4 residues within 4Å: Chain A: R.115, R.118, G.247, N.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.248 Salt bridges: A:R.115, A:R.118 SO4.4: 3 residues within 4Å: Chain A: P.18, R.19, K.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.19, A:K.20 SO4.5: 5 residues within 4Å: Chain A: R.68, R.171, R.195, R.206, S.207 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.206, A:S.207, A:S.207 Water bridges: A:S.72, A:R.171, A:R.171, A:G.192, A:L.193 Salt bridges: A:R.68, A:R.171, A:R.195

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

CL.6: 4 residues within 4Å: Chain A: R.195, D.196, E.199, R.206 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: Y.107, E.182, G.183 Ligand excluded by PLIP

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 3 residues within 4Å: Chain A: K.38, T.52, Y.104 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.104 Water bridges: A:K.38, A:Y.104 Salt bridges: A:K.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mathison, C.J.N. et al., Efficacy and Tolerability of Pyrazolo[1,5-a]pyrimidine RET Kinase Inhibitors for the Treatment of Lung Adenocarcinoma. Acs Med.Chem.Lett. (2020)

Release Date

2020-02-26

Peptides

Proto-oncogene tyrosine-protein kinase receptor Ret: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Proto-oncogene tyrosine-protein kinase receptor Ret