SMTL ID : 6fdi.1 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-226

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 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.2, H2O.5

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.2, H2O.2, H2O.4, H2O.5, H2O.6

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

EDO.3: 6 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 Ligands: D5T.14 Ligand excluded by PLIP EDO.4: 3 residues within 4Å: Chain A: T.74, H.78, E.169 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.20 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: N.26, K.27, W.28, V.100 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: E.169, E.170, N.171 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: T.60, K.62 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: S.185, K.188, Y.229 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: M.212, T.215, K.216, K.217, L.224, L.225, L.226 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: K.20, E.21, D.24, H.31 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: F.33, A.36, E.37, I.89, R.261 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: V.100, L.101, T.104, W.310, V.314, D.317, A.318, I.321 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 Ligands: EDO.24 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: K.62, I.63, P.64 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: P.64, D.66, T.67, N.171 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: E.144 Ligands: EDO.5 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: K.188, I.191, D.192 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: N.135, D.151, S.152, S.153, D.198, S.200 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: D.192, L.195, A.196, Q.237 Ligand excluded by PLIP EDO.24: 8 residues within 4Å: Chain A: N.41, R.42, E.76, D.77, Y.79, N.88 Ligands: EDO.16, EDO.25 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: D.77, H.78, Y.79, H.80, A.81 Ligands: EDO.24 Ligand excluded by PLIP

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 4 residues within 4Å: Chain A: H.80, D.82, V.83, P.131 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.80, A:D.82

1 x D5T: 1-[2-[4-[(4~{a}~{S},8~{a}~{R})-4-(3,4-dimethoxyphenyl)-1-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-2-yl]piperi din-1-yl]-2-oxidanylidene-ethyl]-4,4-dimethyl-piperidine-2,6-dione(Non-covalent)

D5T.14: 14 residues within 4Å: Chain A: H.86, M.199, D.244, L.245, N.247, T.259, I.262, F.266, M.283, S.294, Q.295, G.297, F.298 Ligands: EDO.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262 Hydrogen bonds: A:Q.295 Water bridges: A:D.198 pi-Stacking: A:F.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Salado, I.G. et al., hPDE4D2 structure with inhibitor NPD-226. 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
A

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

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