SMTL ID : 6whz.3 (2 other biounits)

Histone deacetylases complex with peptide macrocycles

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

monomer

Ligands

1 x U2M- ASN- HYP- LYS- GLN- DLY- TRP- GLY: U2M-ASN-HYP-LYS-GLN-DLY-TRP-GLY peptide macrocycle(Non-covalent)

U2M-ASN-HYP-LYS-GLN-DLY-TRP-GLY.1: 13 residues within 4Å: Chain A: P.30, E.99, D.100, H.141, H.142, G.150, F.151, H.179, Y.205, F.206, L.272, Y.304 Ligands: ZN.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.151, A:F.151, A:F.151, A:F.206 Hydrogen bonds: A:E.99, A:D.100, A:D.100, A:D.100

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: D.177, H.179, D.265, Y.304 Ligands: U2M-ASN-HYP-LYS-GLN-DLY-TRP-GLY.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265

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

NA.3: 7 residues within 4Å: Chain A: D.175, D.177, H.179, H.180, S.198, F.199, H.200 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.175, A:G.181

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

PGE.4: 5 residues within 4Å: Chain A: L.165, A.187, F.188, T.191, R.193 No protein-ligand interaction detected (PLIP)

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
C

Histone deacetylase 2

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