SMTL ID : 6wi3.2 (2 other biounits)

Histone deacetylases complex with peptide macrocycles

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x U2M- TRP- DTH- ASP- ASN- DSN- MED- DAS- LYS: (SHA)W(DTH)DN(DSN)(DME)(DAS)K peptide macrocycle(Non-covalent)

U2M-TRP-DTH-ASP-ASN-DSN-MED-DAS-LYS.1: 16 residues within 4Å: Chain A: G.28, H.29, P.30, D.100, H.141, H.142, G.150, F.151, D.177, H.179, F.206, P.207, D.265, G.302, Y.304 Ligands: ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.30, A:F.151, A:F.206, A:F.206, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:D.100 Water bridges: A:N.96

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: U2M-TRP-DTH-ASP-ASN-DSN-MED-DAS-LYS.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 7 residues within 4Å: Chain A: D.175, I.176, D.177, H.179, S.198, F.199, H.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.179, A:F.199 NA.4: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.191 Water bridges: A:T.196

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain A: D.19, Y.23, D.105, E.109 No protein-ligand interaction detected (PLIP) PG4.7: 4 residues within 4Å: Chain A: K.280, E.324, N.327, H.345 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.280

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 4 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.337 Water bridges: A:R.307

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

2021-04-21

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 2

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