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

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-768

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 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.2

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.127, E.156 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

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

EDO.3: 6 residues within 4Å: Chain A: S.134, F.266, Q.269, S.281, P.282 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:Q.269, A:P.282 Water bridges: A:S.281, A:S.281 EDO.4: 6 residues within 4Å: Chain A: N.41, A.81, N.87, N.88, I.89, R.261 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:N.41, A:V.83 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:K.188 EDO.6: 2 residues within 4Å: Chain A: K.217, V.218 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.218 EDO.7: 4 residues within 4Å: Chain A: E.292, W.331, Y.332, T.335 No protein-ligand interaction detected (PLIP) EDO.8: 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:Q.269, A:E.273 Water bridges: A:S.281 EDO.9: 6 residues within 4Å: Chain A: H.86, H.130, L.155, F.266 Ligands: EDO.3, RLW.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.86 Water bridges: A:N.135

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

EPE.10: 5 residues within 4Å: Chain A: P.64, D.66, T.67, N.171, Q.176 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.67 EPE.11: 6 residues within 4Å: Chain A: H.31, F.33, R.34, E.37, 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

1 x RLW: 3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,4-dimethyl-1~{H}-pyrazol-5-one(Non-covalent)

RLW.12: 12 residues within 4Å: Chain A: Y.85, M.199, N.247, T.259, I.262, M.263, F.266, M.283, S.294, Q.295, F.298 Ligands: EDO.9 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.266, A:F.266, A:F.298, A:F.298 Hydrogen bonds: A:Q.295 Water bridges: A:H.86, A:M.199, A:D.244 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-768. 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

Related Entries With Identical Sequence