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

Histone deacetylases complex with peptide macrocycles

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

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

U2M-ASN-PRO-LYS-GLN-DLY-TRP-GLY.1: 18 residues within 4Å: Chain A: G.28, H.29, P.30, E.99, D.100, H.141, H.142, G.150, F.151, D.177, H.179, F.206, D.265, R.271, L.272, G.302, Y.304 Ligands: ZN.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:D.100, A:F.151, A:F.151, A:F.206, A:F.206, A:L.272 Hydrogen bonds: A:G.28, A:R.271 Water bridges: A:F.206, A:R.271, 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-LYS-GLN-DLY-TRP-GLY.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.175, A:F.199 NA.4: 4 residues within 4Å: Chain A: F.188, T.191, V.194, Y.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.188

1 x NHE: 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID(Non-covalent)

NHE.5: 8 residues within 4Å: Chain A: D.17, G.18, D.19, Y.23, R.56, K.59, E.109, L.113 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.113 Hydrogen bonds: A:D.17, A:D.19 Water bridges: A:G.18, A:R.56 Salt bridges: A:R.56

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

PGE.6: 4 residues within 4Å: Chain A: R.307, E.336, Y.337, G.339 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.307, A:Y.337 Water bridges: A:R.307 PGE.8: 5 residues within 4Å: Chain A: K.67, L.162, A.187, F.188, T.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.67 Water bridges: A:T.191

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

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

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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