SMTL ID : 6pzs.1

Crystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with JR005

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: D.171, H.173, D.264 Ligands: P7J.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.171, A:D.171, A:H.173, A:D.264, H2O.1

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.169, D.171, H.173, S.192, L.193, H.194 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.3: 4 residues within 4Å: Chain A: F.182, D.185, V.188, Y.221 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.185, A:V.188, A:Y.221, H2O.4, H2O.7

1 x P7J: 4-[({[(1R,2R,5R)-6,6-dimethylbicyclo[3.1.1]heptan-2-yl]methyl}amino)methyl]-N-hydroxybenzamide(Non-covalent)

P7J.4: 15 residues within 4Å: Chain A: H.22, P.23, S.90, H.133, G.141, F.142, D.171, H.173, F.202, D.264, L.271, G.302, Y.304 Ligands: ZN.1, NO3.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.23, A:F.142, A:F.142, A:L.271, A:L.271 Hydrogen bonds: A:H.173 pi-Stacking: A:H.173, A:F.202

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: W.18, R.79 Ligand excluded by PLIP

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.6: 3 residues within 4Å: Chain A: A.200, F.201, F.202 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.200, A:F.202 Water bridges: A:L.271 NO3.7: 6 residues within 4Å: Chain A: H.22, S.90, I.91, F.92, F.142 Ligands: P7J.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.16, A:H.22 Water bridges: A:I.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osko, J.D. et al., Exploring Structural Determinants of Inhibitor Affinity and Selectivity in Complexes with Histone Deacetylase 6. J.Med.Chem. (2020)

Release Date

2020-02-05

Peptides

Hdac6 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Hdac6 protein

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