SMTL ID : 8zqw.1

The crystal structure of PDE4D with isoaurostatin derivatives 2-9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.164, H.200, D.201, D.318 Ligands: MG.2 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.164, A:H.200, A:D.201, A:D.318, H2O.2, H2O.3 ZN.4: 5 residues within 4Å: Chain B: H.164, H.200, D.201, D.318 Ligands: MG.5 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.164, B:H.200, B:D.201, B:D.318, H2O.6, H2O.6

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.201 Ligands: ZN.1 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.201, H2O.1, H2O.2, H2O.2, H2O.3, H2O.4 MG.5: 3 residues within 4Å: Chain B: H.200, D.201 Ligands: ZN.4 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.201, H2O.5, H2O.5, H2O.6, H2O.6, H2O.7

2 x 01: (3~{Z})-3-[[4-[bis(fluoranyl)methoxy]-3-cyclopentyloxy-phenyl]methylidene]-6-oxidanyl-1~{H}-indol-2-one

01.3: 18 residues within 4Å: Chain A: Y.159, E.230, T.271, D.272, M.273, D.318, N.321, P.322, Y.329, W.332, T.333, I.336, M.337, F.340, M.357, S.368, Q.369, F.372 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.273, A:I.336, A:F.340, A:F.372, A:F.372 Hydrogen bonds: A:T.271, A:M.273, A:Q.369 pi-Stacking: A:F.372 pi-Cation interactions: A:H.160 01.6: 18 residues within 4Å: Chain B: Y.159, E.230, T.271, D.272, M.273, D.318, N.321, P.322, Y.329, W.332, T.333, I.336, M.337, F.340, M.357, S.368, Q.369, F.372 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:M.273, B:I.336, B:F.340, B:F.372, B:F.372, B:F.372, B:F.372 Hydrogen bonds: B:E.230, B:T.271, B:M.273, B:Q.369 pi-Cation interactions: B:H.160, B:H.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, Y.Y. et al., Structure-based optimization of isoaurostatin as novel PDE4 inhibitors with anti-fibrotic effects. Chin.Chem.Lett. (2024)

Release Date

2025-02-12

Peptides

3',5'-cyclic-AMP phosphodiesterase 4D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3',5'-cyclic-AMP phosphodiesterase 4D

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