SMTL ID : 6feb.2 (1 other biounit)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-1086

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

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

EDO.1: 3 residues within 4Å: Chain A: K.188, I.191, D.192 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.192 EDO.2: 6 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 Ligands: D5Z.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.134, A:S.134 Water bridges: A:Q.269 EDO.3: 3 residues within 4Å: Chain A: T.179, K.180, K.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.180, A:K.181 EDO.4: 3 residues within 4Å: Chain A: T.74, H.78, E.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.74 Water bridges: A:T.74 EDO.5: 4 residues within 4Å: Chain A: H.80, D.129, P.131, L.145 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.80 EDO.6: 5 residues within 4Å: Chain A: N.41, E.76, D.77, Y.79, N.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.41, A:D.77, A:A.81, A:N.88 EDO.7: 7 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, A.318, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 EDO.12: 3 residues within 4Å: Chain A: F.164, L.167, R.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.183 Water bridges: A:R.183

1 x D5Z: (4aS,8aR)-2-[1-(2-aminoquinazolin-4-yl)piperidin-4-yl]-4-(3,4-dimethoxyphenyl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one(Non-covalent)

D5Z.8: 15 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, T.259, I.262, P.282, M.283, Q.295, G.297, F.298, I.302 Ligands: EDO.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.245, A:F.298 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain A: D.127, E.156 Ligands: ZN.10 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.127, H2O.1, H2O.2, H2O.2, H2O.3, H2O.4

1 x ZN: ZINC ION(Non-covalent)

ZN.10: 5 residues within 4Å: Chain A: H.90, H.126, D.127, D.244 Ligands: MG.9 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 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 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., hPDE4D2 structure with inhibitor NPD-1086. To be published

Release Date

2019-04-10

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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