- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.75 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 1 x T86: 3-[(2,4-dichlorophenyl)carbonylamino]-4-methoxy-~{N}-oxidanyl-benzamide(Non-covalent)
T86.4: 14 residues within 4Å:- Chain A: K.21, D.101, 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
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:F.217, A:Y.342
- Hydrogen bonds: A:K.21, A:H.143, A:H.293
- Water bridges: A:G.340, A:G.340
- pi-Cation interactions: A:K.21, A:H.293
- 12 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
DMF.5: 6 residues within 4Å:- Chain A: Y.8, R.13, M.30, D.31, N.34
- Ligands: DMF.7
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.13
DMF.6: 3 residues within 4Å:- Chain A: L.91, D.94, S.95
No protein-ligand interaction detected (PLIP)DMF.7: 5 residues within 4Å:- Chain A: I.6, Y.8, I.39, R.44
- Ligands: DMF.5
No protein-ligand interaction detected (PLIP)DMF.8: 4 residues within 4Å:- Chain A: A.62, F.63, R.146
- Ligands: GOL.26
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.146
DMF.9: 7 residues within 4Å:- Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.353
DMF.10: 1 residues within 4Å:- Chain A: G.364
No protein-ligand interaction detected (PLIP)DMF.11: 3 residues within 4Å:- Chain A: K.325, K.326, S.329
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.325
- Water bridges: A:K.326
DMF.12: 4 residues within 4Å:- Chain A: R.13, S.377, Y.378
- Ligands: GOL.17
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.13
DMF.13: 5 residues within 4Å:- Chain A: R.410, S.443, L.444, V.445
- Ligands: GOL.22
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.410
DMF.14: 1 residues within 4Å:- Chain A: T.66
No protein-ligand interaction detected (PLIP)DMF.15: 6 residues within 4Å:- Chain A: Q.11, Y.12, L.15, P.47, Q.49, Q.117
1 PLIP interactions:1 interactions with chain A- Water bridges: A:Q.117
DMF.16: 4 residues within 4Å:- Chain A: W.199, G.237, A.238
- Ligands: GOL.23
No protein-ligand interaction detected (PLIP)- 10 x GOL: GLYCEROL(Non-functional Binders)
GOL.17: 5 residues within 4Å:- Chain A: R.13, C.17, A.27, Y.378
- Ligands: DMF.12
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.13, A:R.13, A:Y.378, A:Y.378
GOL.18: 7 residues within 4Å:- Chain A: E.132, V.133, L.328, K.331, V.332, P.333, V.362
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.132, A:L.328, A:K.331, A:K.331
- Water bridges: A:V.332
GOL.19: 8 residues within 4Å:- Chain A: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247
8 PLIP interactions:8 interactions with chain A- Hydrogen bonds: A:E.195, A:G.221, A:T.222, A:T.222, A:L.235, A:L.235, A:N.247
- Water bridges: A:N.224
GOL.20: 5 residues within 4Å:- Chain A: I.254, D.258, D.403, S.404, I.405
3 PLIP interactions:3 interactions with chain A- Water bridges: A:E.251, A:D.258, A:D.258
GOL.21: 5 residues within 4Å:- Chain A: Y.36, K.37, K.366, M.367, T.368
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.37, A:T.368, A:T.368
- Water bridges: A:E.41
GOL.22: 4 residues within 4Å:- Chain A: R.410, R.411, E.414
- Ligands: DMF.13
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.414, A:E.414
- Water bridges: A:K.407, A:R.411, A:E.414
GOL.23: 3 residues within 4Å:- Chain A: E.196, W.199
- Ligands: DMF.16
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.196, A:E.196, A:W.199
GOL.24: 4 residues within 4Å:- Chain A: D.268, N.271, I.272, W.330
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:N.271, A:W.330
- Water bridges: A:D.268, A:Q.431
GOL.25: 1 residues within 4Å:- Chain A: P.384
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:P.384
GOL.26: 5 residues within 4Å:- Chain A: A.62, F.63, H.163, A.197
- Ligands: DMF.8
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:A.62, A:H.163, A:A.197
- 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
C
SMTL ID : 6hu0.3 (3 other biounits)
Crystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 9
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.2 more...less...6hth.3 | 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 | 6hu0.4 | 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