SMTL ID : 6lrm.1

Crystal structure of PDE4D catalytic domain in complex with arctigenin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.100, H.136, D.137, D.254 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.100, A:H.136, A:D.137, A:D.254, H2O.2, H2O.6 ZN.21: 5 residues within 4Å: Chain B: H.100, H.136, D.137, D.254 Ligands: MG.20 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.100, B:H.136, B:D.137, B:D.254, H2O.9, H2O.12

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.137 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.137, H2O.2, H2O.2, H2O.3, H2O.4, H2O.7 MG.20: 2 residues within 4Å: Chain B: D.137 Ligands: ZN.21 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.137, H2O.9, H2O.10, H2O.11, H2O.11, H2O.13

2 x EQC: Arctigenin(Non-covalent)

EQC.3: 12 residues within 4Å: Chain A: Y.95, H.96, M.209, N.257, W.268, T.269, I.272, M.293, Q.305, F.308, I.312 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.308 Hydrogen bonds: A:Q.305 Salt bridges: A:H.96 pi-Stacking: A:F.308 EQC.22: 13 residues within 4Å: Chain B: Y.95, H.96, M.209, N.257, Y.265, W.268, T.269, I.272, M.293, Q.305, F.308, I.312 Ligands: EDO.29 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.308 Hydrogen bonds: B:Q.305 Salt bridges: B:H.96 pi-Stacking: B:F.308

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

EDO.4: 6 residues within 4Å: Chain A: S.144, F.276, S.291, P.292, C.294 Ligands: EQC.3 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: H.90, D.92, V.93, P.141 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: N.51, A.91, N.97, N.98, I.99 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: D.337, N.338, W.341 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: K.198, I.201, D.202 Chain B: N.160, S.162 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: T.122, L.124, E.125, S.195, M.199 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: T.70, F.71, K.72, N.187, L.188, Q.192 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: F.174, F.185, R.193, R.197 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: P.261, Q.263 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: L.112, L.117, E.118, A.119, V.120, F.121, I.126 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: Q.194, R.197 Chain B: I.149, D.161 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: M.222, T.225, K.226, K.227, L.235, L.236, D.241 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: R.266, E.302, W.341, Y.342 Ligands: EDO.17 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: R.266, T.269, D.270, V.301, Y.342 Ligands: EDO.16 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: I.309, D.310, H.314, E.336, R.339 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain A: P.115, G.232 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: S.144, F.276, S.291, P.292 Ligands: EDO.29 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: L.235, L.236, D.237, N.238, D.241 Ligand excluded by PLIP EDO.25: 5 residues within 4Å: Chain A: N.160, S.162 Chain B: K.198, I.201, D.202 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: L.111, T.114, W.320, D.327, A.328, I.331 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: F.174, L.177, F.185, R.193, R.197 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: N.51, E.86, D.87, Y.89, A.91, N.98 Ligand excluded by PLIP EDO.29: 10 residues within 4Å: Chain B: H.96, H.140, G.142, V.143, S.144, E.275, F.276, Q.279 Ligands: EQC.22, EDO.23 Ligand excluded by PLIP EDO.30: 2 residues within 4Å: Chain A: M.158 Chain B: A.171 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: H.90, D.92, V.93, P.141 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: R.266, E.302, W.341, Y.342, T.345 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H. et al., Identification of phosphodiesterase-4 as the therapeutic target of arctigenin in alleviating psoriatic skin inflammation. J Adv Res (2021)

Release Date

2021-04-14

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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