SMTL ID : 6ftw.4 (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.2, H2O.3, H2O.4, H2O.5

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

EDO.3: 2 residues within 4Å: Chain A: S.220, S.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.220 EDO.4: 5 residues within 4Å: Chain A: S.134, F.266, P.282, C.284 Ligands: E6Z.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.282 Water bridges: A:Q.269, A:Q.269 EDO.5: 5 residues within 4Å: Chain A: F.164, L.167, F.175, R.183, R.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.187 Water bridges: A:R.183 EDO.6: 3 residues within 4Å: Chain A: K.188, I.191, D.192 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.192 Water bridges: A:K.188 EDO.7: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.41, A:N.41, A:A.81, A:N.88, A:R.261 Water bridges: A:R.261 EDO.8: 7 residues within 4Å: Chain A: V.100, L.101, T.104, W.310, V.314, D.317, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.310 Water bridges: A:T.104 EDO.9: 6 residues within 4Å: Chain A: Q.176, N.177, L.178, T.179, K.180, R.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.176, A:R.183 Water bridges: A:K.180 EDO.10: 4 residues within 4Å: Chain A: R.55, L.57, D.113, I.116 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.55, A:D.113 EDO.11: 1 residues within 4Å: Chain A: E.108 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.108 EDO.12: 2 residues within 4Å: Chain A: P.316, Q.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.319 EDO.13: 4 residues within 4Å: Chain A: D.24, K.27, G.29, H.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.31 Water bridges: A:H.31 EDO.15: 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:E.169

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

EPE.14: 6 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, L.254, Q.257 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.31, A:F.33, A:R.34, A:Q.257 Salt bridges: A:H.31

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.16: 14 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, T.259, I.262, M.263, F.266, M.283, S.294, Q.295, F.298 Ligands: EDO.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.245, A:F.266 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
D

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

Related Entries With Identical Sequence