- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.84 Å
- Oligo State
- homo-tetramer
- Ligands
- 4 x ZN: ZINC ION(Non-covalent)
- 8 x K: POTASSIUM ION(Non-covalent)
K.2: 7 residues within 4Å:- Chain A: D.185, L.186, D.187, H.189, S.208, V.209, H.210
5 PLIP interactions:5 interactions with chain A- Metal complexes: A:D.185, A:D.185, A:D.187, A:H.189, A:S.208
K.3: 4 residues within 4Å:- Chain A: F.198, S.201, V.204, S.244
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:F.198, A:S.201, A:V.204, A:S.244, H2O.6
K.13: 4 residues within 4Å:- Chain B: F.198, S.201, V.204, S.244
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:F.198, B:S.201, B:V.204, B:S.244, H2O.18
K.14: 7 residues within 4Å:- Chain B: D.185, L.186, D.187, H.189, S.208, V.209, H.210
5 PLIP interactions:5 interactions with chain B- Metal complexes: B:D.185, B:D.185, B:D.187, B:H.189, B:S.208
K.31: 4 residues within 4Å:- Chain C: F.198, S.201, V.204, S.244
5 PLIP interactions:4 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:F.198, C:S.201, C:V.204, C:S.244, H2O.30
K.32: 7 residues within 4Å:- Chain C: D.185, L.186, D.187, H.189, S.208, V.209, H.210
5 PLIP interactions:5 interactions with chain C- Metal complexes: C:D.185, C:D.185, C:D.187, C:H.189, C:S.208
K.44: 4 residues within 4Å:- Chain D: F.198, S.201, V.204, S.244
5 PLIP interactions:4 interactions with chain D, 1 Ligand-Water interactions- Metal complexes: D:F.198, D:S.201, D:V.204, D:S.244, H2O.41
K.45: 7 residues within 4Å:- Chain D: D.185, L.186, D.187, H.189, S.208, V.209, H.210
5 PLIP interactions:5 interactions with chain D- Metal complexes: D:D.185, D:D.185, D:D.187, D:H.189, D:S.208
- 4 x GM5: ~{N}-oxidanyl-3-[1-(phenylsulfanylmethyl)-1,2,3-triazol-4-yl]benzamide(Non-covalent)
GM5.4: 14 residues within 4Å:- Chain A: K.21, H.142, H.143, G.151, F.152, 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.152, A:F.217, A:F.217, A:P.292, A:Y.342
- Hydrogen bonds: A:H.143
- Water bridges: A:Q.282, A:Q.282
- pi-Stacking: A:H.293, A:H.293, A:Y.342
GM5.15: 15 residues within 4Å:- Chain A: D.51, R.55
- Chain B: H.142, H.143, G.151, F.152, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342
- Ligands: ZN.12
15 PLIP interactions:14 interactions with chain B, 1 interactions with chain A- Hydrophobic interactions: B:F.152, B:F.152, B:F.217, B:F.217, B:P.292, B:Y.342, A:D.51
- Hydrogen bonds: B:H.143, B:D.187, B:Y.342
- Water bridges: B:Q.282, B:Q.282
- pi-Stacking: B:H.293, B:H.293, B:Y.342
GM5.33: 16 residues within 4Å:- Chain C: K.21, H.142, H.143, G.151, F.152, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342
- Chain D: D.51, R.55
- Ligands: ZN.30
12 PLIP interactions:11 interactions with chain C, 1 interactions with chain D- Hydrophobic interactions: C:F.152, C:F.217, C:F.217, C:P.292, C:Y.342, D:D.51
- Hydrogen bonds: C:H.143, C:D.187, C:H.189
- pi-Stacking: C:H.293, C:H.293, C:Y.342
GM5.46: 13 residues within 4Å:- Chain D: H.142, H.143, G.151, F.152, D.187, H.189, F.217, D.286, P.292, H.293, G.340, Y.342
- Ligands: ZN.43
10 PLIP interactions:10 interactions with chain D- Hydrophobic interactions: D:F.152, D:F.152, D:F.217, D:P.292, D:Y.342
- Hydrogen bonds: D:H.143, D:Y.342
- pi-Stacking: D:H.293, D:H.293, D:Y.342
- 28 x DMF: DIMETHYLFORMAMIDE(Non-covalent)
DMF.5: 8 residues within 4Å:- Chain A: Y.8, I.39, L.42, S.43, R.44
- Chain B: L.91, D.94, S.95
Ligand excluded by PLIPDMF.6: 7 residues within 4Å:- Chain A: Y.302, R.353, A.356, L.357, E.360, M.367, I.369
Ligand excluded by PLIPDMF.7: 5 residues within 4Å:- Chain A: E.132, V.133, K.331, V.332, P.333
Ligand excluded by PLIPDMF.8: 5 residues within 4Å:- Chain A: R.13, Q.14, C.17, D.24, Y.378
Ligand excluded by PLIPDMF.9: 6 residues within 4Å:- Chain A: Y.36, K.37, L.38, K.366, M.367, T.368
Ligand excluded by PLIPDMF.11: 9 residues within 4Å:- Chain A: S.19, P.20, K.21, F.22, D.101, F.105, Y.111, F.152, Y.154
Ligand excluded by PLIPDMF.16: 4 residues within 4Å:- Chain B: Y.8, M.30, D.31, N.34
Ligand excluded by PLIPDMF.17: 4 residues within 4Å:- Chain B: R.13, C.17, D.24, Y.378
Ligand excluded by PLIPDMF.18: 6 residues within 4Å:- Chain B: Y.302, R.353, A.356, L.357, M.367, I.369
Ligand excluded by PLIPDMF.19: 5 residues within 4Å:- Chain B: Y.36, K.37, K.366, M.367, T.368
Ligand excluded by PLIPDMF.20: 2 residues within 4Å:- Chain B: E.196, W.199
Ligand excluded by PLIPDMF.21: 4 residues within 4Å:- Chain B: A.62, V.159, H.163, A.197
Ligand excluded by PLIPDMF.22: 3 residues within 4Å:- Chain B: K.325, K.326, S.329
Ligand excluded by PLIPDMF.23: 2 residues within 4Å:- Chain B: Y.8, R.44
Ligand excluded by PLIPDMF.24: 5 residues within 4Å:- Chain B: I.254, D.258, D.403, S.404, I.405
Ligand excluded by PLIPDMF.25: 6 residues within 4Å:- Chain B: E.132, V.133, K.331, V.332, P.333, V.362
Ligand excluded by PLIPDMF.34: 6 residues within 4Å:- Chain C: Y.8, R.13, M.30, D.31, N.34, I.39
Ligand excluded by PLIPDMF.35: 5 residues within 4Å:- Chain C: Y.36, K.37, K.366, M.367, T.368
Ligand excluded by PLIPDMF.36: 3 residues within 4Å:- Chain C: R.13, C.17, Y.378
Ligand excluded by PLIPDMF.37: 6 residues within 4Å:- Chain C: L.78, H.79, E.81, E.82, K.83, L.85
Ligand excluded by PLIPDMF.38: 6 residues within 4Å:- Chain C: E.132, V.133, K.331, V.332, P.333, V.362
Ligand excluded by PLIPDMF.39: 5 residues within 4Å:- Chain C: I.254, D.258, D.403, S.404, I.405
Ligand excluded by PLIPDMF.40: 7 residues within 4Å:- Chain C: Y.302, R.353, A.356, L.357, E.360, M.367, I.369
Ligand excluded by PLIPDMF.47: 6 residues within 4Å:- Chain D: Y.302, R.353, A.356, L.357, E.360, I.369
Ligand excluded by PLIPDMF.48: 5 residues within 4Å:- Chain D: E.132, V.133, K.331, V.332, V.362
Ligand excluded by PLIPDMF.49: 2 residues within 4Å:- Chain D: S.377, Y.378
Ligand excluded by PLIPDMF.50: 6 residues within 4Å:- Chain D: Y.36, K.37, L.38, K.366, M.367, T.368
Ligand excluded by PLIPDMF.51: 5 residues within 4Å:- Chain D: A.212, W.223, P.249, E.251, H.408
Ligand excluded by PLIP- 13 x GOL: GLYCEROL(Non-functional Binders)
GOL.10: 9 residues within 4Å:- Chain A: H.190, E.195, T.220, G.221, T.222, N.224, F.234, L.235, N.247
7 PLIP interactions:7 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
GOL.26: 8 residues within 4Å:- Chain B: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:E.195, B:G.221, B:T.222, B:L.235, B:N.247
GOL.27: 2 residues within 4Å:- Chain B: P.384, F.386
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:P.384
GOL.28: 7 residues within 4Å:- Chain B: Q.11, Y.12, L.15, P.47, Q.49, A.114, Q.117
2 PLIP interactions:2 interactions with chain B- Water bridges: B:Q.117, B:Q.117
GOL.29: 3 residues within 4Å:- Chain B: A.62, F.63, R.146
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:A.62, B:R.146, B:R.146
GOL.41: 8 residues within 4Å:- Chain C: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247
7 PLIP interactions:7 interactions with chain C- Hydrogen bonds: C:E.195, C:G.221, C:T.222, C:T.222, C:I.233, C:L.235, C:N.247
GOL.42: 6 residues within 4Å:- Chain C: Q.11, Y.12, L.15, P.47, Q.49, Q.117
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:Q.49, C:Q.117
GOL.52: 8 residues within 4Å:- Chain D: H.190, E.195, T.220, G.221, T.222, F.234, L.235, N.247
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:E.195, D:G.221, D:T.222, D:T.222, D:L.235, D:L.235, D:N.247
GOL.53: 5 residues within 4Å:- Chain D: Q.11, L.15, P.47, Q.49, Q.117
5 PLIP interactions:3 interactions with chain D, 2 interactions with chain C- Hydrogen bonds: D:Q.117
- Water bridges: D:P.47, D:Q.49, C:G.215, C:G.215
GOL.54: 7 residues within 4Å:- Chain D: L.75, H.79, L.85, M.93, L.98, P.103, G.104
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:L.98, D:G.104
GOL.55: 5 residues within 4Å:- Chain D: Y.8, R.13, M.30, D.31, I.39
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:R.13, D:M.30, D:D.31
- Water bridges: D:N.34
GOL.56: 5 residues within 4Å:- Chain D: R.13, Q.14, C.17, D.24, Y.378
6 PLIP interactions:6 interactions with chain D- Hydrogen bonds: D:R.13, D:Q.14, D:Q.14
- Water bridges: D:R.13, D:Y.378, D:Y.378
GOL.57: 8 residues within 4Å:- Chain D: F.22, Y.111, S.112, W.141, F.152, C.153, Y.154, L.155
7 PLIP interactions:7 interactions with chain D- Hydrogen bonds: D:Y.111, D:S.112, D:F.152, D:Y.154, D:L.155
- Water bridges: D:Y.111, D:A.115
- 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: ABCD
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
D
SMTL ID : 6hrq.1
Crystal structure of Schistosoma mansoni HDAC8 complexed with NCC-149
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 | 6hsh.1 | 6hsh.2 | 6hsh.3 | 6hsh.4 | 6hsz.1 | 6ht8.1 | 6htg.1 | 6htg.2 | 6htg.3 | 6htg.4 | 6hth.1 | 6hth.2 | 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