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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-417

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.90, A:H.126, A:D.127, A:D.244, H2O.1

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: H.126, 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.3, H2O.3

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

EDO.3: 4 residues within 4Å: Chain A: S.134, F.266, P.282 Ligands: 4I7.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:S.281, A:P.282 Water bridges: A:Q.269 EDO.4: 5 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.41, A:N.87, A:N.88, A:R.261 Water bridges: A:Y.79, A:N.88 EDO.5: 3 residues within 4Å: Chain A: K.188, I.191, D.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.192 EDO.6: 1 residues within 4Å: Chain A: V.218 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: E.275, R.276, G.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.276 EDO.8: 4 residues within 4Å: Chain A: A.109, V.110, F.111, T.112 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.113 EDO.9: 2 residues within 4Å: Chain A: K.181, Q.182 No protein-ligand interaction detected (PLIP) EDO.11: 5 residues within 4Å: Chain A: F.137, L.138, T.141, S.143, R.276 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.272, A:R.276, A:R.276 EDO.12: 2 residues within 4Å: Chain A: H.78, E.169 No protein-ligand interaction detected (PLIP)

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

EPE.10: 7 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, L.254, Q.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.31, A:F.33, A:R.34, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

1 x 4I7: (4~{a}~{S},8~{a}~{R})-4-[4-methoxy-3-[[2-(trifluoromethyl)phenyl]methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one(Non-covalent)

4I7.13: 13 residues within 4Å: Chain A: 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.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.266, A:F.266, A:M.283 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298 Halogen bonds: A:S.294

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-417. To be published

Release Date

2019-12-18

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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