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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-769

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 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.6

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.2, H2O.3, H2O.3, H2O.5

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

EDO.3: 5 residues within 4Å: Chain A: S.134, F.266, S.281, P.282, C.284 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: 1 residues within 4Å: Chain A: E.144 No protein-ligand interaction detected (PLIP) EDO.5: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.41, A:N.41, A:N.88, A:R.261 Water bridges: A:R.261 EDO.6: 3 residues within 4Å: Chain A: K.188, I.191, D.192 No protein-ligand interaction detected (PLIP) EDO.7: 2 residues within 4Å: Chain A: K.217, V.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.218 EDO.8: 4 residues within 4Å: Chain A: E.292, W.331, Y.332, T.335 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.335, A:T.335 Water bridges: A:D.260, A:Y.332 EDO.9: 6 residues within 4Å: Chain A: F.137, N.140, E.273, M.278, E.279, S.281 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.13: 4 residues within 4Å: Chain A: N.26, K.27, W.28, V.100 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.28 Water bridges: A:D.317

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.10: 2 residues within 4Å: Chain A: E.275, R.276 No protein-ligand interaction detected (PLIP) DMS.11: 3 residues within 4Å: Chain A: N.135, Q.136, I.139 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.135, A:N.135

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

EPE.12: 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 EPE.15: 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.253, A:Q.257 Salt bridges: A:E.37, A:E.37

1 x J2E: 1-cycloheptyl-3-[3-(cyclopentyloxy)-4-methoxyphenyl]-4,4-dimethyl-4,5-dihydro-1H-pyrazol-5-one(Non-covalent)

J2E.14: 14 residues within 4Å: Chain A: Y.85, H.86, M.199, L.245, N.247, W.258, T.259, I.262, M.263, F.266, M.283, S.294, Q.295, F.298 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.245, A:F.266, A:F.298, A:F.298, A:F.298 Hydrogen bonds: A:Q.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A.K. et al., hPDE4D2 structure with inhibitor NPD-769. 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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