SMTL ID : 5ml3.1

The crystal structure of PDE6D in complex to Deltasonamide1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x DL3: ~{N}1-[(4-chlorophenyl)methyl]-~{N}1-cyclopentyl-~{N}4-[[2-(methylamino)pyrimidin-4-yl]methyl]-~{N}4-(piperidin-4-ylmethyl)benzene-1,4-disulfonamide(Non-covalent)

DL3.1: 25 residues within 4Å: Chain A: L.16, M.19, L.21, W.31, L.37, S.38, A.46, V.48, I.52, L.53, C.55, K.56, V.58, R.60, Q.77, E.87, W.89, I.108, M.116, L.122, I.128, T.130, F.132, L.146, Y.148 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.31, A:W.31, A:L.37, A:A.46, A:V.48, A:I.52, A:V.58, A:I.108, A:I.128, A:L.146, A:L.146 Hydrogen bonds: A:R.60, A:Q.77, A:E.87, A:Y.148 Water bridges: A:E.87 pi-Stacking: A:W.89

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Martin-Gago, P. et al., A PDE6 delta-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Angew. Chem. Int. Ed. Engl. (2017)

Release Date

2017-02-01

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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