SMTL ID : 6wsj.1

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.3.1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

1 x DAL- DSN- ASP- DAR- U2M- PHE- DNE- LYS: cyclopeptide des4.3.1(Non-covalent)

DAL-DSN-ASP-DAR-U2M-PHE-DNE-LYS.1: 18 residues within 4Å: Chain A: H.29, P.30, N.96, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, N.211, D.271, L.278, G.309, Y.311 Ligands: ZN.2, EDO.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.30, A:F.149, A:F.149, A:F.149, A:F.209, A:F.209 Hydrogen bonds: A:N.96, A:S.97, A:S.97 Water bridges: A:N.96, A:N.211

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: DAL-DSN-ASP-DAR-U2M-PHE-DNE-LYS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.3: 6 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200, H.201 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.176, A:D.178, A:H.180, A:S.199 K.4: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.192, A:V.195, A:Y.228, H2O.3, H2O.5

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

EDO.5: 6 residues within 4Å: Chain A: A.207, F.208, F.209, N.211 Ligands: DAL-DSN-ASP-DAR-U2M-PHE-DNE-LYS.1, DAL-DSN-ASP-DAR-U2M-PHE-DNE-LYS.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.207, A:F.209, A:N.211 EDO.6: 7 residues within 4Å: Chain A: E.190, D.218, K.219, V.220, G.221, L.222, R.226 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.190, A:E.190, A:V.220, A:G.221, A:R.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hosseinzadeh, P. et al., Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nat Commun (2021)

Release Date

2021-04-28

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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