SMTL ID : 6ftw.3 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-048

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.90, A:H.126, A:D.127, A:D.244, H2O.1, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.127 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.1, H2O.1, H2O.2, H2O.3, H2O.3

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

EDO.3: 3 residues within 4Å: Chain A: F.175, R.183, R.187 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.187 EDO.4: 6 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, A.318, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 EDO.5: 1 residues within 4Å: Chain A: E.144 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.144, A:E.144 EDO.6: 3 residues within 4Å: Chain A: T.74, H.78, E.169 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.74, A:T.74 EDO.7: 6 residues within 4Å: Chain A: N.41, R.42, E.76, D.77, Y.79, N.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:D.77, A:Y.79 EDO.8: 5 residues within 4Å: Chain A: S.134, S.281, P.282, C.284 Ligands: E6Z.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.282 Water bridges: A:Q.269, A:Q.269 EDO.9: 2 residues within 4Å: Chain A: K.188, D.192 No protein-ligand interaction detected (PLIP) EDO.10: 1 residues within 4Å: Chain A: R.268 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.268 EDO.13: 3 residues within 4Å: Chain A: N.140, M.278, E.279 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.279

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

EPE.11: 8 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, Q.253, L.254, Q.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.253, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

1 x E6Z: 3-{5-[(4aR,8aS)-3-cycloheptyl-4-oxo-3,4,4a,5,8,8a-hexahydrophthalazin-1-yl]-2-methoxyphenyl}prop-2-ynamide(Non-covalent)

E6Z.12: 16 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, Y.255, T.259, I.262, M.263, F.266, M.283, V.291, S.294, Q.295, F.298 Ligands: EDO.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.199, A:L.245, A:I.262, A:I.262, A:F.298 Hydrogen bonds: A:S.294, A:S.294, A:Q.295 pi-Stacking: A:F.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Heuvel, E. et al., Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors. Bioorg.Med.Chem. (2019)

Release Date

2019-03-20

Peptides

cAMP-specific 3',5'-cyclic phosphodiesterase 4D: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

cAMP-specific 3',5'-cyclic phosphodiesterase 4D

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