SMTL ID : 4z2b.1

The structure of human PDE12 residues 161-609 in complex with GSK3036342A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Q.224, R.277, S.278, S.279, Y.304 Ligands: EDO.2 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.278, A:S.278, A:S.279 Water bridges: A:R.277, A:R.277, A:S.278 Salt bridges: A:R.277

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

EDO.2: 7 residues within 4Å: Chain A: K.223, S.279, H.302, L.303, Y.304, W.305 Ligands: SO4.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.223, A:H.302, A:W.305 Water bridges: A:S.278 EDO.3: 7 residues within 4Å: Chain A: F.23, P.120, G.121, C.123, F.125, D.126, K.183 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.183

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 4 residues within 4Å: Chain A: H.127, P.425, S.426, E.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.127, A:S.426 Water bridges: A:S.426, A:E.429

1 x 4LC: 3-(6-{[(2S,3S)-3-(hydroxymethyl)-2-phenylmorpholin-4-yl]carbonyl}-1-methyl-1H-benzimidazol-2-yl)-1H-indole-6-carbonitrile(Non-covalent)

4LC.5: 16 residues within 4Å: Chain A: Y.153, T.156, F.158, S.159, L.163, E.197, W.305, P.307, R.313, N.344, S.345, T.346, T.349, F.402, L.406 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.153, A:Y.153, A:F.158, A:W.305, A:W.305, A:P.307, A:F.402 Hydrogen bonds: A:Y.164, A:E.197, A:T.346 Water bridges: A:R.313, A:R.313 pi-Stacking: A:F.402

1 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: Y.164, E.197, D.444 Ligands: 4LC.5 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.444, H2O.2, H2O.2, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wood, E.R. et al., The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. J.Biol.Chem. (2015)

Release Date

2015-06-17

Peptides

2',5'-phosphodiesterase 12: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

2',5'-phosphodiesterase 12