SMTL ID : 7ay6.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-41b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-dimer

Ligands

2 x S8Q: 2-[(~{Z})-1-(3-cyclopentyloxy-4-methoxy-phenyl)ethylideneamino]oxy-1-[(2~{S},6~{S})-2,6-dimethylmorpholin-4-yl]ethanone(Non-covalent)

S8Q.1: 14 residues within 4Å: Chain A: Y.83, H.84, S.132, M.197, N.245, Y.253, T.257, I.260, F.264, M.281, C.282, S.292, Q.293, F.296 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.260, A:F.264, A:F.264, A:F.296, A:F.296, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:Q.267 S8Q.15: 17 residues within 4Å: Chain B: Y.83, H.84, S.132, M.197, N.245, W.256, T.257, I.260, M.261, F.264, Q.267, P.280, M.281, C.282, S.292, Q.293, F.296 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.260, B:F.264, B:F.264, B:F.296, B:F.296, B:F.296 Hydrogen bonds: B:Q.293 Water bridges: B:S.279

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.88, H.124, D.125, D.242 Ligands: MG.3 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.7 ZN.16: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.17 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.17, H2O.21

8 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain A: D.125 Ligands: ZN.2 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.1, H2O.5, H2O.5, H2O.7, H2O.9 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: N.175 No protein-ligand interaction detected (PLIP) MG.6: 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.1, H2O.3 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.16 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.17, H2O.19, H2O.19, H2O.20, H2O.23 MG.18: 1 residues within 4Å: Chain B: D.258 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain B: H.302 No protein-ligand interaction detected (PLIP)

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

EDO.8: 2 residues within 4Å: Chain A: N.133, Q.134 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.133, A:Q.134 Water bridges: A:Q.134, A:D.149, A:D.196, A:S.198 EDO.9: 4 residues within 4Å: Chain A: K.186, I.189, D.190 Chain B: N.148 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.190 Water bridges: A:D.190, B:D.149 EDO.10: 1 residues within 4Å: Chain A: T.213 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.213 EDO.11: 4 residues within 4Å: Chain A: Q.251, R.254, Q.255, D.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.251 Water bridges: A:D.258 EDO.12: 4 residues within 4Å: Chain A: K.284, H.285, N.286, A.287 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.287 EDO.13: 5 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.31, A:R.32 Water bridges: A:F.31 EDO.14: 4 residues within 4Å: Chain A: M.281, S.292, G.295, F.296 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain A: N.148 Chain B: K.186, I.189, D.190 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:D.149 Hydrogen bonds: B:D.190 EDO.21: 4 residues within 4Å: Chain B: D.22, K.25, W.26, G.27 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.26 Water bridges: B:D.22, B:H.29 EDO.22: 3 residues within 4Å: Chain B: A.205, D.206, T.209 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.209, B:T.209 Water bridges: B:D.206 EDO.23: 3 residues within 4Å: Chain B: H.78, D.80, P.129 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.129 EDO.24: 3 residues within 4Å: Chain B: V.131, L.136, R.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.270, B:R.270 Water bridges: B:S.141 EDO.25: 4 residues within 4Å: Chain B: A.107, V.108, F.109, T.110 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.109 EDO.26: 2 residues within 4Å: Chain B: D.321, D.325 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.321, B:D.325 Water bridges: B:D.321, B:T.322, B:D.325

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brullo, C. et al., Design, synthesis, biological evaluation and structural characterization of novel GEBR library PDE4D inhibitors. Eur.J.Med.Chem. (2021)

Release Date

2021-06-30

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

Related Entries With Identical Sequence