SMTL ID : 7zzs.3 (2 other biounits)

HDAC2 complexed with an inhibitory ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.177, H.179, D.265, G.302 Ligands: SHH.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.191

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: L.165, K.166, Y.167, H.168, Q.169, R.193 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.165, A:R.193, A:R.193 Water bridges: A:Y.167, A:Q.169 EDO.5: 3 residues within 4Å: Chain A: D.19, N.22, Y.23 No protein-ligand interaction detected (PLIP)

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

PEG.6: 5 residues within 4Å: Chain A: L.162, L.165, A.187, F.188, T.191 No protein-ligand interaction detected (PLIP)

1 x SHH: OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE(Non-covalent)

SHH.7: 17 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, D.265, L.272, G.302, Y.304 Ligands: ZN.1, KK0.8 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.30, A:F.151, A:F.151, A:F.206, A:F.206 Hydrogen bonds: A:D.100, A:H.141, A:H.142, A:Y.304

1 x KK0: (5~{S})-5-(4-chlorophenyl)pyrrolidin-2-one(Non-covalent)

KK0.8: 19 residues within 4Å: Chain A: I.20, Y.25, M.31, P.33, R.35, I.36, F.110, S.114, A.137, G.138, G.139, L.140, H.141, G.150, F.151, C.152, G.301, G.302 Ligands: SHH.7 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.110, A:L.140, A:L.140, A:L.140, A:F.151 Hydrogen bonds: A:R.35

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
C

Histone deacetylase 2

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