SMTL ID : 6rcw.3 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-053

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.08 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.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.1, H2O.1, H2O.2, H2O.2, H2O.5

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: JX2.10 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:S.281 EDO.4: 4 residues within 4Å: Chain A: F.164, F.175, R.183, R.187 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.183, A:R.187 EDO.5: 3 residues within 4Å: Chain A: L.114, K.181, S.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.181, A:S.185, A:S.185 EDO.6: 7 residues within 4Å: Chain A: L.101, T.104, W.310, V.314, D.317, A.318, I.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:W.310, A:D.317 EDO.7: 5 residues within 4Å: Chain A: R.256, E.292, W.331, Y.332, T.335 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.292, A:E.292 EDO.8: 4 residues within 4Å: Chain A: D.129, P.131, L.145, H.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.129

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

EPE.9: 8 residues within 4Å: Chain A: H.31, V.32, F.33, R.34, E.37, Q.253, L.254, Q.257 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:F.33, A:R.34, A:Q.253, A:Q.257 Salt bridges: A:H.31, A:E.37, A:E.37

1 x JX2: 3-[5-[(4~{a}~{R},8~{a}~{S})-3-cycloheptyl-4-oxidanylidene-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-yl]-2-methoxy-phenyl]-~{N}-(furan-2-ylmethyl)prop-2-ynamide(Non-covalent)

JX2.10: 17 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, Y.255, T.259, I.262, F.266, M.283, S.294, Q.295, G.297, F.298, I.302 Ligands: EDO.3 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:I.262, A:F.298, A:F.298, A:I.302 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

de Heuvel, E. et al., Alkynamide phthalazinones as a new class of TbrPDEB1 inhibitors (Part 2). Bioorg.Med.Chem. (2019)

Release Date

2019-07-24

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

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

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