SMTL ID : 6rcw.2 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 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.4

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.127 Ligands: ZN.1, JX2.14 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.1, H2O.2, H2O.2, H2O.3

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

EDO.3: 7 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, M.283, C.284 Ligands: JX2.14 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:Q.269, A:S.281 EDO.4: 1 residues within 4Å: Chain A: E.144 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.144 EDO.5: 3 residues within 4Å: Chain A: Q.136, N.140 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.136, A:N.140 Water bridges: A:Q.136 EDO.6: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:N.41, A:N.88, A:R.261 EDO.7: 2 residues within 4Å: Chain A: K.188, D.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 EDO.8: 5 residues within 4Å: Chain A: H.80, D.129, P.131, L.145, H.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.80 EDO.9: 2 residues within 4Å: Chain A: K.217, V.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.218 EDO.10: 8 residues within 4Å: Chain A: Q.136, F.137, N.140, E.273, M.278, E.279, S.281 Ligands: EDO.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.140, A:Q.269, A:E.273 Water bridges: A:S.134, A:S.281 EDO.11: 2 residues within 4Å: Chain A: N.135, Q.136 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.135, A:Q.136 Water bridges: A:Q.136, A:S.153, A:S.200, A:S.200 EDO.12: 5 residues within 4Å: Chain A: M.212, T.215, K.216, K.217, L.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.215, A:K.217, A:K.217

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

EPE.13: 5 residues within 4Å: Chain A: P.64, D.66, T.67, N.171, Q.176 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.66 Water bridges: A:Q.176

1 x JX2: 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide(Non-covalent)

JX2.14: 16 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, W.258, T.259, I.262, M.283, S.294, Q.295, G.297, F.298 Ligands: MG.2, EDO.3 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.298, A:F.298, A:F.298 Hydrogen bonds: 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 (Part 2). Bioorg.Med.Chem. (2019)

Release Date

2019-07-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

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

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