- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.95 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 1 x GQN: 4-methoxy-~{N}-oxidanyl-3-[(4-phenylphenyl)carbonylamino]benzamide(Non-covalent)
GQN.4: 13 residues within 4Å:- Chain A: K.21, H.142, H.143, G.151, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342
- Ligands: ZN.1
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:F.217, A:F.217, A:P.292, A:Y.342, A:Y.342
- Hydrogen bonds: A:K.21, A:H.143, A:D.187, A:H.293, A:Y.342
- pi-Cation interactions: A:K.21
- 6 x GOL: GLYCEROL(Non-functional Binders)
GOL.5: 8 residues within 4Å:- Chain A: Q.11, Y.12, L.15, P.47, Q.49, A.114, Q.117
- Ligands: GOL.6
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:P.47, A:Q.49, A:Q.117, A:Q.117
GOL.6: 6 residues within 4Å:- Chain A: L.15, D.110, L.113, A.114, Q.117
- Ligands: GOL.5
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.110, A:D.110, A:Q.117
GOL.7: 8 residues within 4Å:- Chain A: C.16, F.22, R.25, Y.26, Y.111, W.137, G.138, W.141
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:R.25, A:Y.26, A:Y.111, A:W.137, A:W.141
- Water bridges: A:C.16, A:F.22
GOL.8: 9 residues within 4Å:- Chain A: H.190, E.195, T.220, G.221, T.222, I.233, F.234, L.235, N.247
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:I.233, A:L.235, A:N.247
GOL.9: 4 residues within 4Å:- Chain A: A.59, A.62, L.120, R.164
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:A.59, A:R.164
GOL.10: 3 residues within 4Å:- Chain A: A.62, F.63, R.146
No protein-ligand interaction detected (PLIP)- 9 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
DMF.11: 6 residues within 4Å:- Chain A: E.132, V.133, L.328, K.331, V.332, V.362
1 PLIP interactions:1 interactions with chain A- Water bridges: A:V.332
DMF.12: 7 residues within 4Å:- Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369
No protein-ligand interaction detected (PLIP)DMF.13: 5 residues within 4Å:- Chain A: Y.36, K.37, K.366, M.367, T.368
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.368
DMF.14: 5 residues within 4Å:- Chain A: D.385, E.387, D.389, I.390, D.391
No protein-ligand interaction detected (PLIP)DMF.15: 3 residues within 4Å:- Chain A: D.31, H.376, S.377
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:S.377
- Water bridges: A:N.34
DMF.16: 2 residues within 4Å:- Chain A: Y.8, R.44
No protein-ligand interaction detected (PLIP)DMF.17: 5 residues within 4Å:- Chain A: L.250, I.254, D.403, S.404, I.405
No protein-ligand interaction detected (PLIP)DMF.18: 6 residues within 4Å:- Chain A: A.212, T.222, P.249, L.250, E.251, H.408
No protein-ligand interaction detected (PLIP)DMF.19: 4 residues within 4Å:- Chain A: Y.342, N.343, F.344, P.345
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:F.344
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Marek, M. et al., Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants. J. Med. Chem. (2018)
- Release Date
- 2018-10-31
- Peptides
- Histone deacetylase: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
B
SMTL ID : 6hth.2 (3 other biounits)
Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 5
Histone deacetylase
Related Entries With Identical Sequence
6gx3.1 | 6gxa.1 | 6gxa.2 | 6gxa.3 | 6gxa.4 | 6gxu.1 | 6gxu.2 | 6gxu.3 | 6gxu.4 | 6gxw.1 | 6gxw.2 | 6gxw.3 | 6gxw.4 | 6hqy.1 | 6hqy.2 | 6hqy.3 | 6hqy.4 | 6hrq.1 | 6hsh.1 | 6hsh.2 | 6hsh.3 | 6hsh.4 | 6hsz.1 | 6ht8.1 | 6htg.1 | 6htg.2 | 6htg.3 | 6htg.4 | 6hth.1 | 6hth.3 more...less...6hth.4 | 6hti.1 | 6hti.2 | 6hti.3 | 6hti.4 | 6htt.1 | 6htt.2 | 6htt.3 | 6htt.4 | 6htz.1 | 6htz.2 | 6htz.3 | 6htz.4 | 6hu0.1 | 6hu0.2 | 6hu0.3 | 6hu0.4 | 6hu1.1 | 6hu1.2 | 6hu1.3 | 6hu1.4 | 6hu2.1 | 6hu2.2 | 6hu2.3 | 6hu2.4 | 6hu3.1 | 6hu3.2 | 6hu3.3 | 6hu3.4 | 6tld.1 | 6tld.2 | 6tld.3 | 6tld.4 | 7p3s.1 | 7p3s.2 | 7p3s.3 | 7p3s.4