SMTL ID : 5lbo.1 (3 other biounits)

Crystal structure of human phosphodiesterase 4D2 catalytic domain with inhibitor NPD-001

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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.1

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.4

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

EDO.3: 4 residues within 4Å: Chain A: S.134, F.266, P.282, C.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:P.282 Water bridges: A:Q.269, A:Q.269 EDO.4: 5 residues within 4Å: Chain A: N.41, A.81, N.87, N.88 Ligands: DTT.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:N.88, A:N.88 EDO.5: 5 residues within 4Å: Chain A: T.112, L.114, E.115, S.185, M.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.112, A:T.112, A:S.185, A:S.185 EDO.6: 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.7: 7 residues within 4Å: Chain A: V.100, L.101, T.104, W.310, V.314, D.317, I.321 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.104, A:W.310 Water bridges: A:D.317 EDO.8: 1 residues within 4Å: Chain A: E.144 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: D.192, L.195, A.196, Q.237 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.237 Water bridges: A:Q.237 EDO.12: 2 residues within 4Å: Chain A: H.78, E.169 No protein-ligand interaction detected (PLIP)

2 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.10: 2 residues within 4Å: Chain A: T.60, D.113 No protein-ligand interaction detected (PLIP) DTT.13: 6 residues within 4Å: Chain A: E.76, D.77, Y.79, H.80, A.81 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.81 Water bridges: A:D.77

1 x 6M5: (4~{a}~{S},8~{a}~{R})-2-cycloheptyl-4-[4-methoxy-3-[4-[4-(1~{H}-1,2,3,4-tetrazol-5-yl)phenoxy]butoxy]phenyl]-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one(Non-covalent)

6M5.11: 16 residues within 4Å: Chain A: Y.85, H.86, M.199, D.244, L.245, N.247, T.259, I.262, F.266, M.283, S.294, Q.295, G.297, F.298, Y.301, I.302 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.245, A:I.262, A:F.266, A:F.298, A:I.302 Hydrogen bonds: A:Q.295 pi-Stacking: A:F.298, A:Y.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Blaazer, A.R. et al., Targeting a Subpocket in Trypanosoma brucei Phosphodiesterase B1 (TbrPDEB1) Enables the Structure-Based Discovery of Selective Inhibitors with Trypanocidal Activity. J. Med. Chem. (2018)

Release Date

2018-03-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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