SMTL ID : 6v7a.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with NF2657

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.178, H.180, D.271 Ligands: QQG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.178, A:D.178, A:H.180, A:D.271

2 x K: POTASSIUM ION(Non-covalent)

K.2: 5 residues within 4Å: Chain A: D.176, D.178, H.180, S.199, L.200 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.176, A:D.178, A:H.180, A:S.199, A:L.200 K.3: 4 residues within 4Å: Chain A: F.189, D.192, V.195, Y.228 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.189, A:D.192, A:V.195, A:Y.228, H2O.1

1 x QQG: N-hydroxy-4-[(1-methyl-1,2-dihydro-1'H-spiro[indole-3,4'-piperidin]-1'-yl)methyl]benzamide(Non-covalent)

QQG.4: 13 residues within 4Å: Chain A: N.96, S.97, H.139, H.140, G.148, F.149, D.178, H.180, F.209, D.271, L.278, Y.311 Ligands: ZN.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.209, A:F.209, A:F.209, A:L.278 Hydrogen bonds: A:H.140 pi-Stacking: A:F.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Saraswati, A.P. et al., Spiroindoline-Capped Selective HDAC6 Inhibitors: Design, Synthesis, Structural Analysis, and Biological Evaluation. Acs Med.Chem.Lett. (2020)

Release Date

2020-12-02

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

Related Entries With Identical Sequence