SMTL ID : 7q9q.1

Crystal structure of PDE6D Geranylgeranylated cystein complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x CMT: O-METHYLCYSTEINE(Non-covalent)

CMT.1: 5 residues within 4Å: Chain A: L.57, I.112, A.114, Y.152 Ligands: GER.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.56

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

EDO.2: 5 residues within 4Å: Chain A: R.64, L.66, F.95, W.108, S.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.64, A:R.64, A:S.110, A:S.110 EDO.4: 5 residues within 4Å: Chain A: E.80, K.82, Y.84, E.133, K.135 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.80, A:K.82, A:Y.84, A:E.133, A:K.135 EDO.5: 8 residues within 4Å: Chain A: L.15, F.18, S.42, V.43, P.44, F.136, S.144 Ligands: GER.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.18, A:S.144, A:S.144

1 x GER: GERAN-8-YL GERAN(Non-covalent)

GER.3: 14 residues within 4Å: Chain A: F.18, M.23, S.42, I.56, V.62, R.64, L.66, L.79, Q.81, I.132, T.134, F.136 Ligands: CMT.1, EDO.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.18, A:I.56, A:V.62, A:L.66, A:L.79, A:I.132, A:F.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yelland, T. et al., Stabilization of the RAS:PDE6D Complex Is a Novel Strategy to Inhibit RAS Signaling. J.Med.Chem. (2022)

Release Date

2022-01-19

Peptides

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
BBB

Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta