SMTL ID : 8a0b.2 (2 other biounits)

Inhibitor binding to HDAC2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.177, H.179, D.265 Ligands: KRU.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.177, A:D.177, A:H.179, A:D.265

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 6 residues within 4Å: Chain A: D.175, D.177, H.179, S.198, F.199, H.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.175, A:D.175, A:D.177, A:H.179, A:S.198

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

NA.3: 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

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

NHE.4: 7 residues within 4Å: Chain A: D.17, G.18, D.19, R.56, K.59, E.109, L.113 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.113 Hydrogen bonds: A:D.17 Water bridges: A:G.18, A:R.56 Salt bridges: A:R.56

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 6 residues within 4Å: Chain A: K.10, D.131, M.132, K.290, N.293, L.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.10, A:D.131 Water bridges: A:L.294 PEG.7: 5 residues within 4Å: Chain A: D.19, N.22, Y.23, D.105, E.109 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.109 PEG.8: 3 residues within 4Å: Chain A: E.336, Y.337, G.339 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.307, A:G.339

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

PG4.6: 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 KRU: 1,3-dihydroisoindol-2-yl-[(2R,4S)-4-phenylpyrrolidin-1-ium-2-yl]methanone(Non-covalent)

KRU.9: 22 residues within 4Å: Chain A: Y.25, M.31, R.35, D.100, G.138, G.139, L.140, H.141, H.142, G.150, F.151, C.152, D.177, H.179, F.206, Q.261, D.265, L.272, G.301, G.302, Y.304 Ligands: ZN.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.140, A:L.140, A:F.151, A:F.206, A:F.206, A:F.206 Hydrogen bonds: A:H.141 pi-Stacking: A:F.151, A:F.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tamanini, E. et al., Fragment-Based Discovery of a Novel, Brain Penetrant, Orally Active HDAC2 Inhibitor. Acs Med.Chem.Lett. (2022)

Release Date

2022-09-21

Peptides

Histone deacetylase 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Histone deacetylase 2

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