Binding Site Information of Target

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Target General Information
Drug Binding Sites of Target
References
Target General Information  Top
Target ID T22274 Target Info
Target Name Histone deacetylase 6 (HDAC6)
Synonyms KIAA0901; JM21; HD6
Target Type Clinical trial Target
Gene Name HDAC6
Biochemical Class Carbon-nitrogen hydrolase
UniProt ID
HDAC6_HUMAN
Drug Binding Sites of Target  Top
Ligand Name: N-(4-Methylthiazol-2-yl)acetamide Ligand Info
Structure Description Crystal structure of a low occupancy fragment candidate (N-(4-Methyl-1,3-thiazol-2-yl)propanamide) bound adjacent to the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5B8D
Method X-ray diffraction Resolution 1.05 Å Mutation No [1]
PDB Sequence
PLPWCPHLVA
1118
VCPIPAAGLD
1128
VTQPCGDCGT
1138
IQENWVCLSC
1148
YQVYCGRYIN
1158

GHMLQHHGNS
1168
GHPLVLSYID
1178
LSAWCYYCQA
1188
YVHHQALLDV
1198
KNIAHQNKFG
1208
Residue
Distance (Å)
GLU1141
3.592
ASN1142
3.322
TRP1143
3.350
GLY1154
4.971
SER1175
2.710
Residue
Distance (Å)
TYR1176
4.350
ILE1177
3.899
ASP1178
2.802
SER1180
4.205
TYR1189
3.684
Ligand Name: 6-Methyl-5-[(4-Propan-2-Ylphenyl)amino]-2~{h}-1,2,4-Triazin-3-One Ligand Info
Structure Description Crystal structure of a low occupancy fragment candidate (5-[(4-Isopropylphenyl)amino]-6-methyl-1,2,4-triazin-3(2H)-one) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5KH9
Method X-ray diffraction Resolution 1.07 Å Mutation No [1]
PDB Sequence
PLPWCPHLVA
1118
VCPIPAAGLD
1128
VTQPCGDCGT
1138
IQENWVCLSC
1148
YQVYCGRYIN
1158

GHMLQHHGNS
1168
GHPLVLSYID
1178
LSAWCYYCQA
1188
YVHHQALLDV
1198
KNIAHQNKFG
1208
Residue
Distance (Å)
TRP1143
3.677
ARG1155
3.374
Residue
Distance (Å)
TRP1182
3.385
TYR1189
2.975
Ligand Name: 2-(Benzo[d]thiazol-2-yl)acetic acid Ligand Info
Structure Description Crystal structure of fragment 2-(Benzo[d]thiazol-2-yl)acetic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CE8
Method X-ray diffraction Resolution 1.55 Å Mutation No [2]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYV or .EYV2 or .EYV3 or :3EYV;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.650
CYS1153
4.758
GLY1154
3.478
ARG1155
2.866
MET1161
4.346
Residue
Distance (Å)
LEU1162
4.035
VAL1173
4.846
TRP1182
3.509
TYR1184
2.628
TYR1189
3.375
Ligand Name: 3-(3-Methoxyquinoxalin-2-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(3-Methoxy-2-quinoxalinyl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CEC
Method X-ray diffraction Resolution 1.55 Å Mutation No [2]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EY7 or .EY72 or .EY73 or :3EY7;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1187 or .A:1189; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.461
CYS1153
4.735
GLY1154
3.620
ARG1155
2.904
MET1161
4.261
LEU1162
3.994
Residue
Distance (Å)
VAL1173
4.435
TRP1182
3.317
TYR1184
2.605
GLN1187
4.686
TYR1189
3.329
Ligand Name: 3-(4-Methyl-3-oxo-3,4-dihydroquinoxalin-2-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(1-Methyl-2-oxo-1,2-dihydroquinoxalin-3-yl)propionic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CEE
Method X-ray diffraction Resolution 1.55 Å Mutation No [2]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYM or .EYM2 or .EYM3 or :3EYM;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.266
CYS1153
4.714
GLY1154
3.514
ARG1155
2.875
MET1161
4.287
Residue
Distance (Å)
LEU1162
3.950
VAL1173
4.546
TRP1182
3.263
TYR1184
2.651
TYR1189
2.640
Ligand Name: 2-Quinolinepropanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(quinolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CEA
Method X-ray diffraction Resolution 1.60 Å Mutation No [2]
PDB Sequence
PLPWCPHLVA
1118
VCPIPAAGLD
1128
VTQPCGDCGT
1138
IQENWVCLSC
1148
YQVYCGRYIN
1158

GHMLQHHGNS
1168
GHPLVLSYID
1178
LSAWCYYCQA
1188
YVHHQALLDV
1198
KNIAHQNKF
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYY or .EYY2 or .EYY3 or :3EYY;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.447
CYS1153
4.794
GLY1154
3.475
ARG1155
2.852
MET1161
4.290
Residue
Distance (Å)
LEU1162
3.893
VAL1173
4.376
TRP1182
3.241
TYR1184
2.667
TYR1189
3.211
Ligand Name: 3,3'-(Benzo[1,2-d:5,4-d']bis[1,3]thiazole-2,6-diyl)dipropanoic acid Ligand Info
Structure Description Structure of HDAC6 zinc-finger ubiquitin binding domain soaked with 3,3'-(benzo[1,2-d:5,4-d']bis(thiazole)-2,6-diyl)dipropionic acid PDB:6CE6
Method X-ray diffraction Resolution 1.60 Å Mutation No [2]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYP or .EYP2 or .EYP3 or :3EYP;style chemicals stick;color identity;select .A:1141 or .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1156 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLU1141
4.901
TRP1143
3.250
CYS1153
4.807
GLY1154
3.514
ARG1155
2.829
TYR1156
4.931
Residue
Distance (Å)
MET1161
4.488
LEU1162
4.092
VAL1173
4.268
TRP1182
3.488
TYR1184
2.662
TYR1189
3.472
Ligand Name: 3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment (3-(5-Chloro-1,3-benzothiazol-2-yl)propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5KH3
Method X-ray diffraction Resolution 1.60 Å Mutation No [1]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6U6 or .6U62 or .6U63 or :36U6;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.337
CYS1153
4.838
GLY1154
3.503
ARG1155
2.870
MET1161
4.355
Residue
Distance (Å)
LEU1162
3.887
VAL1173
4.306
TRP1182
3.460
TYR1184
2.666
TYR1189
3.187
Ligand Name: 3-(3-Benzyl-2-oxo-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5WBN
Method X-ray diffraction Resolution 1.64 Å Mutation No [3]
PDB Sequence
GSPLPWCPHL
1116
VAVCPIPAAG
1126
LDVTQPCGDC
1136
GTIQENWVCL
1146
SCYQVYCGRY
1156

INGHMLQHHG
1166
NSGHPLVLSY
1176
IDLSAWCYYC
1186
QAYVHHQALL
1196
DVKNIAHQNK
1206

FGE
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .9ZV or .9ZV2 or .9ZV3 or :39ZV;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1156 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.449
CYS1153
4.717
GLY1154
3.661
ARG1155
2.892
TYR1156
4.265
MET1161
4.175
Residue
Distance (Å)
LEU1162
3.791
VAL1173
4.181
TRP1182
3.163
TYR1184
2.549
TYR1189
3.035
Ligand Name: 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(3-Methyl-4-oxo-3,4-dihydroquinazolin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CED
Method X-ray diffraction Resolution 1.70 Å Mutation No [2]
PDB Sequence
PLPWCPHLVA
1118
VCPIPAAGLD
1128
VTQPCGDCGT
1138
IQENWVCLSC
1148
YQVYCGRYIN
1158

GHMLQHHGNS
1168
GHPLVLSYID
1178
LSAWCYYCQA
1188
YVHHQALLDV
1198
KNIAHQNKF
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYA or .EYA2 or .EYA3 or :3EYA;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.422
CYS1153
4.713
GLY1154
3.576
ARG1155
2.937
MET1161
4.246
Residue
Distance (Å)
LEU1162
3.973
VAL1173
4.465
TRP1182
3.350
TYR1184
2.613
TYR1189
3.154
Ligand Name: 3-(6-Oxidanylidene-3-Pyridin-3-Yl-Pyridazin-1-Yl)propanoic Acid Ligand Info
Structure Description Crystal structure of fragment (3-[6-Oxo-3-(3-pyridinyl)-1(6H)-pyridazinyl]propanoic acid) bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5KH7
Method X-ray diffraction Resolution 1.70 Å Mutation No [1]
PDB Sequence
SPLPWCPHLV
1117
AVCPIPAAGL
1127
DVTQPCGDCG
1137
TIQENWVCLS
1147
CYQVYCGRYI
1157

NGHMLQHHGN
1167
SGHPLVLSYI
1177
DLSAWCYYCQ
1187
AYVHHQALLD
1197
VKNIAHQNKF
1207

G
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .6T7 or .6T72 or .6T73 or :36T7;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.308
CYS1153
4.865
GLY1154
3.613
ARG1155
2.837
MET1161
4.274
Residue
Distance (Å)
LEU1162
3.854
VAL1173
4.296
TRP1182
3.286
TYR1184
2.612
TYR1189
2.721
Ligand Name: 3-(1,3-Benzothiazol-2-yl)propanoic acid Ligand Info
Structure Description Crystal structure of fragment 3-(1,3-Benzothiazol-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:6CEF
Method X-ray diffraction Resolution 1.80 Å Mutation No [2]
PDB Sequence
PLPWCPHLVA
1118
VCPIPAAGLD
1128
VTQPCGDCGT
1138
IQENWVCLSC
1148
YQVYCGRYIN
1158

GHMLQHHGNS
1168
GHPLVLSYID
1178
LSAWCYYCQA
1188
YVHHQALLDV
1198
KNIAHQNKFG
1208
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .EYJ or .EYJ2 or .EYJ3 or :3EYJ;style chemicals stick;color identity;select .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1161 or .A:1162 or .A:1173 or .A:1182 or .A:1184 or .A:1189; color #f3c393; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
TRP1143
3.379
CYS1153
4.850
GLY1154
3.514
ARG1155
2.878
MET1161
4.319
Residue
Distance (Å)
LEU1162
3.909
VAL1173
4.171
TRP1182
3.263
TYR1184
2.625
TYR1189
3.306
Ligand Name: 3-{3-[(Pyridin-2-Yl)methoxy]quinoxalin-2-Yl}propanoic Acid Ligand Info
Structure Description Crystal structure of fragment 3-(3-(pyridin-2-ylmethoxy)quinoxalin-2-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain PDB:5WPB
Method X-ray diffraction Resolution 1.55 Å Mutation No [1]
PDB Sequence
GSPLPWCPHL
1116
VAVCPIPAAG
1126
LDVTQPCGDC
1136
GTIQENWVCL
1146
SCYQVYCGRY
1156

INGHMLQHHG
1166
NSGHPLVLSY
1176
IDLSAWCYYC
1186
QAYVHHQALL
1196
DVKNIAHQNK
1206

FG
Click to Show 3D Structure of This Binding Site
set background white;style ions nothing; color 8e8e8e;style chemicals nothing; select .B8P or .B8P2 or .B8P3 or :3B8P;style chemicals stick;color identity;select .A:1141 or .A:1143 or .A:1153 or .A:1154 or .A:1155 or .A:1156 or .A:1161 or .A:1162 or .A:1173 or .A:1175 or .A:1177 or .A:1178 or .A:1180 or .A:1182 or .A:1184 or .A:1189; color #00ffc7; zoom selection;set surface opacity 0.5;set surface Van der Waals surface;set mode all
Residue
Distance (Å)
GLU1141
3.740
TRP1143
3.325
CYS1153
4.742
GLY1154
3.482
ARG1155
2.817
TYR1156
3.617
MET1161
4.328
LEU1162
3.903
Residue
Distance (Å)
VAL1173
4.741
SER1175
3.258
ILE1177
3.993
ASP1178
3.359
SER1180
3.464
TRP1182
3.689
TYR1184
2.576
TYR1189
2.703
References  Top
REF 1 Small Molecule Antagonists of the Interaction between the Histone Deacetylase 6 Zinc-Finger Domain and Ubiquitin. J Med Chem. 2017 Nov 9;60(21):9090-9096.
REF 2 Identification and Structure-Activity Relationship of HDAC6 Zinc-Finger Ubiquitin Binding Domain Inhibitors. J Med Chem. 2018 May 24;61(10):4517-4527.
REF 3 Crystal structure of fragment 3-(3-Benzyl-2-oxo-2H-[1,2,4]triazino[2,3-c]quinazolin-6-yl)propanoic acid bound in the ubiquitin binding pocket of the HDAC6 zinc-finger domain

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