SMTL ID : 7uk2.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with NN-390

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x O2L: N-hydroxy-4-{[(propan-2-yl)(2,3,4,5-tetrafluorobenzene-1-sulfonyl)amino]methyl}benzamide(Non-covalent)

O2L.1: 13 residues within 4Å: Chain A: H.22, S.90, H.132, H.133, G.141, F.142, D.171, H.173, F.202, D.264, L.271, Y.304 Ligands: ZN.2 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.202, A:F.202, A:F.202, A:L.271 Hydrogen bonds: A:H.133 pi-Stacking: A:F.142

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: D.171, H.173, D.264 Ligands: O2L.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.171, A:D.171, A:H.173, A:D.264

2 x K: POTASSIUM ION(Non-covalent)

K.3: 5 residues within 4Å: Chain A: D.169, D.171, H.173, S.192, L.193 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:D.169, A:D.169, A:D.171, A:H.173, A:S.192 K.4: 4 residues within 4Å: Chain A: F.182, D.185, V.188, Y.221 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:F.182, A:D.185, A:V.188, A:Y.221, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcha, H.K. et al., High Efficacy and Drug Synergy of HDAC6-Selective Inhibitor NN-429 in Natural Killer (NK)/T-Cell Lymphoma. Pharmaceuticals (2022)

Release Date

2022-11-02

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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