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

Histone deacetylases complex with peptide macrocycles

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

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

U2M-ASN-PRO-TRP-GLY.1: 14 residues within 4Å: Chain A: P.30, D.100, H.142, G.150, F.151, D.177, H.179, E.204, F.206, D.265, R.271, L.272, Y.304 Ligands: ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.151, A:E.204, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:D.100, A:R.271

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: U2M-ASN-PRO-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

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

NA.3: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.177 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 PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: L.165, A.187, F.188, R.193 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.193 PGE.6: 0 residues within 4Å: (No contacts) 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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