SMTL ID : 5laq.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.166, H.202, D.203, D.320 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.166, A:H.202, A:D.203, A:D.320, H2O.3

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.203, E.232 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.203, H2O.1, H2O.2, H2O.2, H2O.2, H2O.3

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: N.117, S.157, S.164 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.117, A:L.165 Water bridges: A:S.164 ACT.4: 5 residues within 4Å: Chain A: F.342, Q.345, P.358, C.360 Ligands: 6M5.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.342 Hydrogen bonds: A:P.358 ACT.6: 2 residues within 4Å: Chain A: D.399, D.403 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.403

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)

6M5.5: 16 residues within 4Å: Chain A: M.275, D.320, L.321, N.323, W.334, T.335, I.338, M.339, F.342, S.370, Q.371, G.373, F.374, Y.377, I.378 Ligands: ACT.4 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.321, A:F.374, A:Y.377, A:Y.377 Hydrogen bonds: A:Q.371 pi-Stacking: A:F.374, A:Y.377

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

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

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