Receptor
PDB id Resolution Class Description Source Keywords
6cee 1.55 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF FRAGMENT 3-(1-METHYL-2-OXO-1,2-DIHYDROQ 3-YL)PROPIONIC ACID BOUND IN THE UBIQUITIN BINDING POCKET OH DAC6 ZINC-FINGER DOMAIN HOMO SAPIENS HISTONE DEACETYLASE HDAC HDAC6 UBIQUITIN STRUCTURAL GENOCONSORTIUM SGC HYDROLASE
Ref.: IDENTIFICATION AND STRUCTURE-ACTIVITY RELATIONSHIP ZINC-FINGER UBIQUITIN BINDING DOMAIN INHIBITORS. J. MED. CHEM. V. 61 4517 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:1301;
A:1303;
A:1302;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
EYM A:1304;
 Valid;
 none;
 ic50 = 65 uM
232.235 C12 H12 N2 O3 CN1c2...
UNX A:1305;
A:1306;
A:1308;
A:1307;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
n/a X *
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CED 1.7 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF FRAGMENT 3-(3-METHYL-4-OXO-3,4-DIHYDROQ 2-YL)PROPANOIC ACID BOUND IN THE UBIQUITIN BINDING POCKET OH DAC6 ZINC-FINGER DOMAIN HOMO SAPIENS HISTONE DEACETYLASE HDAC HDAC6 UBIQUITIN STRUCTURAL GENOCONSORTIUM SGC HYDROLASE
Ref.: IDENTIFICATION AND STRUCTURE-ACTIVITY RELATIONSHIP ZINC-FINGER UBIQUITIN BINDING DOMAIN INHIBITORS. J. MED. CHEM. V. 61 4517 2018
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6CEF ic50 = 180 uM EYJ C10 H9 N O2 S c1ccc2c(c1....
2 6CE8 ic50 = 390 uM EYV C9 H7 N O2 S c1ccc2c(c1....
3 6CEC ic50 = 45 uM EY7 C12 H12 N2 O3 COc1c(nc2c....
4 6CED Kd = 1.5 uM EYA C12 H12 N2 O3 CN1C(=Nc2c....
5 6CE6 ic50 = 5.1 uM EYP C14 H12 N2 O4 S2 c1c2c(cc3c....
6 6CEA - EYY C12 H11 N O2 c1ccc2c(c1....
7 6CEE ic50 = 65 uM EYM C12 H12 N2 O3 CN1c2ccccc....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 6CEF ic50 = 180 uM EYJ C10 H9 N O2 S c1ccc2c(c1....
2 6CE8 ic50 = 390 uM EYV C9 H7 N O2 S c1ccc2c(c1....
3 6CEC ic50 = 45 uM EY7 C12 H12 N2 O3 COc1c(nc2c....
4 6CED Kd = 1.5 uM EYA C12 H12 N2 O3 CN1C(=Nc2c....
5 6CE6 ic50 = 5.1 uM EYP C14 H12 N2 O4 S2 c1c2c(cc3c....
6 6CEA - EYY C12 H11 N O2 c1ccc2c(c1....
7 6CEE ic50 = 65 uM EYM C12 H12 N2 O3 CN1c2ccccc....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 6CEF ic50 = 180 uM EYJ C10 H9 N O2 S c1ccc2c(c1....
2 6CE8 ic50 = 390 uM EYV C9 H7 N O2 S c1ccc2c(c1....
3 6CEC ic50 = 45 uM EY7 C12 H12 N2 O3 COc1c(nc2c....
4 6CED Kd = 1.5 uM EYA C12 H12 N2 O3 CN1C(=Nc2c....
5 6CE6 ic50 = 5.1 uM EYP C14 H12 N2 O4 S2 c1c2c(cc3c....
6 6CEA - EYY C12 H11 N O2 c1ccc2c(c1....
7 6CEE ic50 = 65 uM EYM C12 H12 N2 O3 CN1c2ccccc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: EYM; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 EYM 1 1
2 EYA 0.424242 0.851852
3 52F 0.415385 0.784314
Similar Ligands (3D)
Ligand no: 1; Ligand: EYM; Similar ligands found: 348
No: Ligand Similarity coefficient
1 EY7 0.9541
2 T6Z 0.9442
3 CX4 0.9417
4 64C 0.9400
5 TQU 0.9346
6 64E 0.9293
7 6HP 0.9242
8 KED 0.9238
9 Q5M 0.9235
10 96R 0.9224
11 5WT 0.9223
12 3AK 0.9221
13 D80 0.9217
14 EV2 0.9215
15 HA6 0.9202
16 LP8 0.9188
17 IOP 0.9177
18 QUB 0.9174
19 7FF 0.9168
20 NAL 0.9167
21 F5C 0.9165
22 ZIP 0.9162
23 M9N 0.9156
24 F95 0.9155
25 5V5 0.9150
26 5V6 0.9150
27 R4E 0.9148
28 TRP 0.9141
29 QMS 0.9123
30 8RK 0.9123
31 M3Q 0.9122
32 ITW 0.9121
33 JHY 0.9119
34 JYK 0.9106
35 VYM 0.9105
36 2JK 0.9099
37 NIY 0.9092
38 34L 0.9090
39 JTF 0.9082
40 4XY 0.9082
41 22T 0.9075
42 5OF 0.9072
43 IBM 0.9071
44 XG1 0.9067
45 5WS 0.9062
46 C09 0.9061
47 BB4 0.9058
48 9F8 0.9057
49 DTR 0.9057
50 EV3 0.9054
51 S3P 0.9054
52 AO6 0.9051
53 6XC 0.9050
54 FSU 0.9047
55 NLA 0.9045
56 TXW 0.9042
57 7I2 0.9039
58 7M5 0.9038
59 1QP 0.9036
60 39Z 0.9030
61 9BF 0.9028
62 EYY 0.9021
63 5WN 0.9021
64 G6P 0.9017
65 SYE 0.9009
66 3N4 0.9009
67 5V7 0.9008
68 AC2 0.9008
69 774 0.9006
70 L07 0.9006
71 TWB 0.9005
72 25O 0.9001
73 XJ2 0.8995
74 FUZ 0.8993
75 SRO 0.8992
76 78P 0.8991
77 MYI 0.8990
78 535 0.8989
79 NPA 0.8988
80 X0T 0.8986
81 64F 0.8985
82 GNR 0.8977
83 ONZ 0.8976
84 XFE 0.8968
85 NWD 0.8967
86 ELH 0.8962
87 3EB 0.8954
88 772 0.8954
89 790 0.8952
90 HBI 0.8949
91 G1P 0.8947
92 28S 0.8947
93 EYJ 0.8945
94 EXG 0.8938
95 P9T 0.8937
96 YKG 0.8937
97 1Q4 0.8931
98 D87 0.8931
99 3D8 0.8930
100 7ZC 0.8930
101 PW1 0.8924
102 CUT 0.8924
103 GTV 0.8922
104 RVE 0.8920
105 R8Y 0.8916
106 1YE 0.8916
107 OX2 0.8915
108 30G 0.8915
109 IAC 0.8914
110 P83 0.8912
111 L21 0.8912
112 1CE 0.8911
113 KFN 0.8910
114 JXW 0.8908
115 B23 0.8907
116 ZME 0.8905
117 LF5 0.8903
118 1X8 0.8903
119 7SX 0.8902
120 8WZ 0.8900
121 XEN 0.8899
122 5WM 0.8898
123 B61 0.8895
124 AZY 0.8893
125 BDI 0.8887
126 Z25 0.8886
127 JAK 0.8886
128 JY2 0.8885
129 JWW 0.8884
130 JXK 0.8884
131 1AJ 0.8883
132 E7R 0.8883
133 9UG 0.8882
134 3SU 0.8880
135 VJJ 0.8877
136 9E3 0.8877
137 67X 0.8876
138 ISJ 0.8875
139 YE6 0.8875
140 7CT 0.8874
141 JR2 0.8874
142 VKE 0.8873
143 8GK 0.8872
144 MQB 0.8871
145 B4L 0.8871
146 L8J 0.8869
147 6DP 0.8869
148 I46 0.8867
149 96U 0.8866
150 DYZ 0.8864
151 MUX 0.8863
152 JYW 0.8861
153 FXH 0.8858
154 55D 0.8855
155 ASE 0.8855
156 0J2 0.8854
157 4R1 0.8853
158 NPL 0.8850
159 C4E 0.8849
160 F91 0.8848
161 PLP 0.8846
162 S0I 0.8846
163 4KL 0.8846
164 BG6 0.8842
165 ZYW 0.8841
166 LI7 0.8840
167 FNA 0.8839
168 3IL 0.8838
169 TQL 0.8838
170 ZON 0.8838
171 536 0.8835
172 3IB 0.8834
173 I2E 0.8833
174 ML1 0.8832
175 OSB 0.8832
176 C9E 0.8830
177 0J4 0.8830
178 7M6 0.8829
179 2J9 0.8827
180 EVO 0.8826
181 54X 0.8825
182 EUH 0.8824
183 0SX 0.8824
184 9AP 0.8821
185 NAR 0.8821
186 ZEZ 0.8821
187 CSN 0.8819
188 4Z9 0.8817
189 AJD 0.8812
190 IPT 0.8810
191 RKY 0.8809
192 X2M 0.8809
193 2UD 0.8807
194 KDN 0.8804
195 LDR 0.8804
196 O82 0.8803
197 DK1 0.8803
198 BK9 0.8801
199 5PX 0.8801
200 57O 0.8800
201 HWH 0.8799
202 CR1 0.8794
203 ET0 0.8794
204 K68 0.8789
205 8Y7 0.8788
206 XM5 0.8786
207 9KZ 0.8786
208 NIP 0.8783
209 IAG 0.8782
210 MNP 0.8782
211 WA2 0.8780
212 DTE 0.8780
213 MS0 0.8779
214 NFZ 0.8779
215 531 0.8778
216 982 0.8773
217 32V 0.8767
218 M5H 0.8766
219 CG8 0.8766
220 TSR 0.8763
221 4B0 0.8763
222 KOM 0.8763
223 3TV 0.8761
224 7MX 0.8760
225 FUJ 0.8759
226 GRX 0.8757
227 FCW 0.8754
228 6J9 0.8751
229 CMG 0.8745
230 QTS 0.8742
231 MUR 0.8741
232 APS 0.8741
233 YO5 0.8740
234 I6G 0.8740
235 5WU 0.8738
236 BIE 0.8738
237 IOS 0.8737
238 FWB 0.8736
239 5O5 0.8736
240 1U7 0.8733
241 108 0.8733
242 2T4 0.8730
243 2SX 0.8728
244 AOJ 0.8725
245 226 0.8724
246 2KU 0.8724
247 ALR 0.8722
248 CPW 0.8722
249 NVU 0.8722
250 LIP 0.8720
251 NBG 0.8719
252 X04 0.8716
253 CGW 0.8708
254 C8O 0.8708
255 LNN 0.8703
256 D1G 0.8701
257 MBP 0.8701
258 29B 0.8700
259 MPP 0.8698
260 60L 0.8698
261 B0K 0.8698
262 A0O 0.8697
263 II4 0.8696
264 GG5 0.8691
265 BC3 0.8691
266 H2B 0.8686
267 3Y7 0.8686
268 22L 0.8683
269 KWB 0.8681
270 JXT 0.8680
271 9UL 0.8679
272 GSY 0.8676
273 0GA 0.8674
274 S7P 0.8674
275 ZYV 0.8672
276 8DA 0.8672
277 3D1 0.8671
278 UFO 0.8671
279 A1Y 0.8669
280 7AP 0.8668
281 3NM 0.8667
282 PVK 0.8667
283 MDR 0.8663
284 0H5 0.8662
285 JYT 0.8661
286 YM6 0.8661
287 PXP 0.8660
288 14W 0.8658
289 74Z 0.8657
290 HLP 0.8657
291 F52 0.8654
292 9X5 0.8654
293 5OU 0.8652
294 MPU 0.8651
295 0Q2 0.8645
296 SBK 0.8645
297 ETV 0.8643
298 PVQ 0.8642
299 2N0 0.8642
300 AVR 0.8641
301 LL1 0.8641
302 JAA 0.8640
303 CHQ 0.8636
304 THM 0.8636
305 7Z9 0.8636
306 QIF 0.8636
307 CRB 0.8635
308 B52 0.8635
309 B4O 0.8633
310 3B4 0.8633
311 OUB 0.8632
312 CFA 0.8628
313 JYE 0.8623
314 MYT 0.8618
315 4VT 0.8617
316 DE7 0.8616
317 NBV 0.8615
318 5JT 0.8612
319 MN QAY 0.8611
320 327 0.8611
321 EXL 0.8610
322 61M 0.8608
323 6VD 0.8607
324 27K 0.8603
325 FWD 0.8597
326 AKD 0.8594
327 I4D 0.8592
328 ER6 0.8591
329 LLT 0.8586
330 XY2 0.8586
331 B5A 0.8586
332 I59 0.8585
333 8HG 0.8584
334 ML2 0.8583
335 ARP 0.8579
336 GA2 0.8572
337 MEX 0.8561
338 GO8 0.8560
339 O2Y 0.8560
340 3D3 0.8560
341 OKM 0.8553
342 4VS 0.8545
343 0LH 0.8545
344 GI4 0.8542
345 2H4 0.8540
346 56N 0.8539
347 BGP 0.8533
348 T34 0.8523
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6CED; Ligand: EYA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6ced.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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