SMTL ID : 7q9r.1

Cocrystal structure of PDE6D bound to NRAS peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x FAR: FARNESYL(Non-covalent)

FAR.1: 9 residues within 4Å: Chain A: M.20, L.22, V.59, R.61, L.63, Q.78, W.90, L.147, Y.149 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.22, A:V.59, A:L.63, A:W.90, A:Y.149

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

EDO.2: 3 residues within 4Å: Chain A: W.32, A.47, R.48 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.32, A:R.48, A:R.48 EDO.3: 4 residues within 4Å: Chain A: L.12, P.41, S.141, T.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.142, A:T.142 Water bridges: A:T.142 EDO.4: 5 residues within 4Å: Chain A: E.10, R.13, G.14, T.68, E.69 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.10, A:E.69 EDO.5: 6 residues within 4Å: Chain A: F.15, S.39, L.63, L.76, T.131, F.133 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.39, A:F.133

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

SO4.6: 4 residues within 4Å: Chain A: F.92, E.93, W.105, S.107 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.93, A:E.93 SO4.7: 2 residues within 4Å: Chain A: G.95, F.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.96, A:F.96 SO4.8: 1 residues within 4Å: Chain A: R.9 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.9 Salt bridges: A:R.9

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

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