SMTL ID : 7a9v.2 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-635

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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.2, H2O.3

6 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: R5Z.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:Q.269 EDO.4: 3 residues within 4Å: Chain A: E.292, W.331, Y.332 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.332 EDO.5: 6 residues within 4Å: Chain A: F.137, N.140, E.273, M.278, E.279, S.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.273 Water bridges: A:S.134, A:S.134 EDO.6: 1 residues within 4Å: Chain A: E.144 No protein-ligand interaction detected (PLIP) EDO.7: 6 residues within 4Å: Chain A: L.101, T.104, W.310, D.317, A.318, I.321 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 EDO.9: 2 residues within 4Å: Chain A: E.275, R.276 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.276

1 x R5Z: 1-cycloheptyl-3-[4-methoxy-3-(2-phenylethoxy)phenyl]-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one(Non-covalent)

R5Z.8: 12 residues within 4Å: Chain A: H.86, M.199, L.245, N.247, T.259, I.262, F.266, M.283, S.294, Q.295, F.298 Ligands: EDO.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:M.199, A:L.245, 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

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-635. To be published

Release Date

2021-10-06

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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