SMTL ID : 6f8x.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-26g

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.88, A:H.124, A:D.125, A:D.242, H2O.1, H2O.6 ZN.8: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.9 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.88, B:H.124, B:D.125, B:D.242, H2O.12, H2O.13

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.4, H2O.5, H2O.6, H2O.7 MG.3: 1 residues within 4Å: Chain A: D.22 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain A: D.225, D.229 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.225, A:D.229, H2O.3, H2O.4 MG.9: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.8 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.12, H2O.13, H2O.14, H2O.14, H2O.15

2 x D08: 2-[(5~{R})-3-(3-cyclopentyloxy-4-methoxy-phenyl)-4,5-dihydro-1,2-oxazol-5-yl]-~{N},~{N}-bis(2-hydroxyethyl)ethanamide(Non-covalent)

D08.5: 21 residues within 4Å: Chain A: Y.83, H.84, H.128, S.132, N.133, Q.134, E.154, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: EDO.6 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.296, A:F.296, A:F.296, A:F.296 Hydrogen bonds: A:N.133, A:Q.293 Water bridges: A:H.84, A:H.84, A:H.128, A:N.133, A:Q.134 D08.11: 19 residues within 4Å: Chain B: Y.83, H.84, H.128, S.132, N.133, E.154, M.197, L.243, N.245, Y.253, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.260, B:F.296 Hydrogen bonds: B:N.133, B:Q.293 Water bridges: B:H.84, B:V.131, B:N.133, B:N.133, B:N.133, B:Q.134, B:E.154, B:E.154, B:E.154, B:D.196 pi-Stacking: B:F.296

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

EDO.6: 8 residues within 4Å: Chain A: S.132, F.264, Q.267, S.279, P.280, M.281, C.282 Ligands: D08.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.267, A:P.280 Water bridges: A:S.279 EDO.7: 8 residues within 4Å: Chain A: P.103, A.104, S.219, G.220, V.312, H.313, P.314, D.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.313

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

DMS.10: 4 residues within 4Å: Chain B: D.298, H.302, P.303, E.306 2 PLIP interactions: 2 interactions with chain B Water bridges: B:D.298 Salt bridges: B:E.306

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prosdocimi, T. et al., Molecular Bases of PDE4D Inhibition by Memory-Enhancing GEBR Library Compounds. Biochemistry (2018)

Release Date

2018-05-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

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