SMTL ID : 7b9h.1

Crystal structure of the PDE4D catalytic domain in complex with GEBR-42a

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 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.2, H2O.7 ZN.25: 5 residues within 4Å: Chain B: H.88, H.124, D.125, D.242 Ligands: MG.26 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.16, H2O.20

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

MG.2: 3 residues within 4Å: Chain A: D.125 Ligands: ZN.1, T3K.24 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.125, H2O.2, H2O.5, H2O.5, H2O.5, H2O.10 MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: N.175 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: D.225, D.229 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.225, A:D.229, H2O.1, H2O.4, H2O.8 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain B: D.125 Ligands: ZN.25 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.125, H2O.16, H2O.18, H2O.19, H2O.20, H2O.22 MG.27: 1 residues within 4Å: Chain B: D.258 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Chain B: H.302 No protein-ligand interaction detected (PLIP)

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

EDO.7: 2 residues within 4Å: Chain A: N.133, Q.134 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: K.186, I.189, D.190 Chain B: N.148 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: T.213 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: K.284, H.285, N.286, A.287 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: S.132, F.264, S.279, P.280, C.282 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.75, H.76 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: H.76 Ligands: EDO.12 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: N.138, R.274, M.276 Ligand excluded by PLIP EDO.15: 3 residues within 4Å: Chain A: A.159, V.160 Chain B: M.146 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain A: Q.251, R.254, Q.255, D.258 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: H.29, V.30, F.31, R.32, L.252 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: M.281, G.295, F.296 Ligands: T3K.24 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: A.107, V.108, F.109, T.110 Ligand excluded by PLIP EDO.20: 8 residues within 4Å: Chain A: P.103, A.104, S.219, G.220, V.312, H.313, P.314, D.315 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: S.150, S.151, N.155, L.193 Chain B: S.150 Ligands: EDO.23 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: F.6, T.48, Q.51, E.52 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: S.150, S.151, K.199 Ligands: EDO.21 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain A: N.148 Chain B: K.186, I.189, D.190 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain B: D.22, K.25, W.26, G.27 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: A.205, D.206, T.209 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain B: H.78, D.80, V.81, P.129 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: P.129, V.131, L.136, R.270 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain B: D.321, D.325 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: K.208, P.303 Ligand excluded by PLIP EDO.36: 2 residues within 4Å: Chain B: H.313, P.314 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain B: D.190, L.193, A.194, K.199, Q.235 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain B: A.107, V.108, F.109, T.110 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain B: H.29, V.30, F.31, R.32, Q.251, L.252, Q.255 Ligand excluded by PLIP

2 x T3K: 3-[(~{E})-1-(3-cyclopentyloxy-4-methoxy-phenyl)ethylideneamino]oxy-1-morpholin-4-yl-propan-1-one(Covalent)(Non-covalent)

T3K.24: 18 residues within 4Å: Chain A: Y.83, H.84, T.195, M.197, D.242, L.243, N.245, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 Ligands: MG.2, EDO.18 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.243, A:F.264, A:M.281, A:F.296, A:F.296, A:F.296 Hydrogen bonds: A:Q.293 Water bridges: A:M.197 T3K.40: 12 residues within 4Å: Chain B: Y.83, L.243, N.245, W.256, T.257, I.260, M.261, F.264, M.281, S.292, Q.293, F.296 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.243, B:I.260, B:F.264, B:F.296 Hydrogen bonds: B:Q.293 pi-Stacking: B:F.296

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

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