SMTL ID : 7pad.1

The crystal structure of DW-0254 in complex with PDE6D

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

monomer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 1 residues within 4Å: Chain A: S.18 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.18

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: W.106, F.107, F.108, L.124, I.125, E.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.107, A:F.107, A:L.124, A:E.126 Water bridges: A:E.126

1 x O7W: ~{N}-[(4-ethylphenyl)methyl]-3-[5-[2-(1~{H}-indol-3-yl)ethyl]-1,3,4-oxadiazol-2-yl]-~{N}-methyl-propanamide(Non-covalent)

O7W.3: 21 residues within 4Å: Chain A: M.36, L.38, A.63, V.65, I.69, R.77, L.79, L.92, Q.94, V.96, L.103, E.104, W.106, A.127, S.131, I.145, T.147, F.149, V.161, L.163, Y.165 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.38, A:I.69, A:L.79, A:L.79, A:L.92, A:V.96, A:L.103, A:W.106, A:T.147, A:F.149, A:V.161 Hydrogen bonds: A:E.104, A:E.104, A:Y.165

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 6 residues within 4Å: Chain A: F.108, E.109, F.110, W.121, Q.122, S.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.109 Water bridges: A:L.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Canovas Nunes, S. et al., Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects. Blood Cancer J (2022)

Release Date

2022-06-08

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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