Receptor
PDB id Resolution Class Description Source Keywords
6Q0Z 1.75 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATAL DOMAIN 2 COMPLEXED WITH JS28 DANIO RERIO HISTONE DEACETYLASE METALLOHYDROLASE HYDROLASE-HYDROLASE ICOMPLEX
Ref.: EXPLORING STRUCTURAL DETERMINANTS OF INHIBITOR AFFI SELECTIVITY IN COMPLEXES WITH HISTONE DEACETYLASE 6 J.MED.CHEM. V. 63 295 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:801;
A:801;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
K B:802;
B:803;
A:803;
A:802;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
39.098 K [K+]
P7V A:804;
B:804;
 Valid;
Valid;
 none;
none;
 submit data
283.078 C10 H7 Br N2 O3 c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5EF7 1.9 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATAL DOMAIN 2 IN COMPLEX WITH HPOB DANIO RERIO HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HISTONE DEACETYLASE 6 STRUCTURE AND MOLECULAR BASIS CATALYSIS AND INHIBITION. NAT.CHEM.BIOL. V. 12 741 2016
Members (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 6Q0Z - P7V C10 H7 Br N2 O3 c1cc(ccc1c....
4 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
5 6PZS - P7J C18 H26 N2 O2 CC1([C@@H]....
6 6PZU - A6I C25 H32 N4 O6 C[C@@H](C(....
7 6CSQ Kd = 410 nM F9P C7 H13 N O2 C1CCC(CC1)....
8 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
9 5EFN - ARG GLY 5OL MCM n/a n/a
10 6R0K ic50 = 12 nM JNN C13 H11 Cl2 N3 O4 c1cc(c(cc1....
11 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 6CSS Kd = 25 nM FBJ C6 H9 N O2 C1CC=C(C1)....
13 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
14 6V7A ic50 = 264.4 nM QQG C21 H25 N3 O2 CN1CC2(CCN....
15 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
16 6CSP Kd = 3 nM FBM C7 H11 N O2 C1CCC(=CC1....
17 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
18 6PZO - P6Y C15 H12 F3 N3 O3 c1cc(c(nc1....
19 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
20 6CSR Kd = 144 nM BHO C7 H7 N O2 c1ccc(cc1)....
21 5EFK - SER ASP ALY MCM n/a n/a
22 6PYE ic50 = 0.03 uM P5Y C25 H21 F3 N6 O3 c1ccc(cc1)....
23 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
24 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
25 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
26 6PZR - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
27 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
28 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
29 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
30 6VNR - R5G C17 H15 N3 O4 c1cc(ccc1C....
70% Homology Family (30)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 6Q0Z - P7V C10 H7 Br N2 O3 c1cc(ccc1c....
4 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
5 6PZS - P7J C18 H26 N2 O2 CC1([C@@H]....
6 6PZU - A6I C25 H32 N4 O6 C[C@@H](C(....
7 6CSQ Kd = 410 nM F9P C7 H13 N O2 C1CCC(CC1)....
8 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
9 5EFN - ARG GLY 5OL MCM n/a n/a
10 6R0K ic50 = 12 nM JNN C13 H11 Cl2 N3 O4 c1cc(c(cc1....
11 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 6CSS Kd = 25 nM FBJ C6 H9 N O2 C1CC=C(C1)....
13 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
14 6V7A ic50 = 264.4 nM QQG C21 H25 N3 O2 CN1CC2(CCN....
15 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
16 6CSP Kd = 3 nM FBM C7 H11 N O2 C1CCC(=CC1....
17 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
18 6PZO - P6Y C15 H12 F3 N3 O3 c1cc(c(nc1....
19 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
20 6CSR Kd = 144 nM BHO C7 H7 N O2 c1ccc(cc1)....
21 5EFK - SER ASP ALY MCM n/a n/a
22 6PYE ic50 = 0.03 uM P5Y C25 H21 F3 N6 O3 c1ccc(cc1)....
23 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
24 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
25 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
26 6PZR - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
27 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
28 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
29 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
30 6VNR - R5G C17 H15 N3 O4 c1cc(ccc1C....
50% Homology Family (51)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5EEN - 5OG C15 H14 N2 O4 S c1ccc(cc1)....
2 5EFH Ki = 0.8 uM FKS C10 H21 F3 N2 O2 C(CCC(C(F)....
3 6Q0Z - P7V C10 H7 Br N2 O3 c1cc(ccc1c....
4 5EEK - TSN C17 H22 N2 O3 C[C@H](C=C....
5 6PZS - P7J C18 H26 N2 O2 CC1([C@@H]....
6 6PZU - A6I C25 H32 N4 O6 C[C@@H](C(....
7 6CSQ Kd = 410 nM F9P C7 H13 N O2 C1CCC(CC1)....
8 5WGK - AGJ C18 H20 N2 O4 c1ccc(cc1)....
9 5EFN - ARG GLY 5OL MCM n/a n/a
10 6R0K ic50 = 12 nM JNN C13 H11 Cl2 N3 O4 c1cc(c(cc1....
11 5EEI - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 6CSS Kd = 25 nM FBJ C6 H9 N O2 C1CC=C(C1)....
13 6CGP ic50 = 0.058 uM F1Y C17 H18 N4 O2 CCCc1c(n2c....
14 6V7A ic50 = 264.4 nM QQG C21 H25 N3 O2 CN1CC2(CCN....
15 5WGL - AH4 C24 H27 N5 O3 c1ccc(cc1)....
16 6CSP Kd = 3 nM FBM C7 H11 N O2 C1CCC(=CC1....
17 5WGI - TSN C17 H22 N2 O3 C[C@H](C=C....
18 6PZO - P6Y C15 H12 F3 N3 O3 c1cc(c(nc1....
19 6DVM ic50 = 3 nM HBJ C26 H28 N4 O4 Cc1ccc(cc1....
20 6CSR Kd = 144 nM BHO C7 H7 N O2 c1ccc(cc1)....
21 5EFK - SER ASP ALY MCM n/a n/a
22 6PYE ic50 = 0.03 uM P5Y C25 H21 F3 N6 O3 c1ccc(cc1)....
23 6DVO ic50 = 60 nM HBV C20 H27 F N2 O2 CN(Cc1ccc(....
24 6DVL ic50 = 11 nM HBG C25 H31 N3 O4 Cc1cc(cc(c....
25 5EFJ Ki = 0.35 uM 5OM DPR ALA DAL n/a n/a
26 6PZR - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
27 6DVN ic50 = 14 nM HB7 C26 H28 N4 O4 CN(C)c1ccc....
28 5EF7 Ki = 1 nM 5OJ C17 H18 N2 O4 c1ccc(cc1)....
29 5WGM - AH7 C17 H18 F2 N4 O2 c1ccc(cc1)....
30 6VNR - R5G C17 H15 N3 O4 c1cc(ccc1C....
31 6UO5 - QCP C18 H20 N2 O3 CC(C)[C@@H....
32 6UO2 - TSN C17 H22 N2 O3 C[C@H](C=C....
33 6UO7 - QCP C18 H20 N2 O3 CC(C)[C@@H....
34 6UO4 - TSN C17 H22 N2 O3 C[C@H](C=C....
35 6UOC - QCM C24 H27 N3 O4 CCN(CC)Cc1....
36 6UOB - P7D C16 H19 N3 O4 S CN(C)Cc1cc....
37 5G0G ic50 = 5.45 nM TSN C17 H22 N2 O3 C[C@H](C=C....
38 5EEF - TSN C17 H22 N2 O3 C[C@H](C=C....
39 6WYQ - UFJ C14 H19 I N2 O3 c1cc(ccc1N....
40 6UO3 - QCP C18 H20 N2 O3 CC(C)[C@@H....
41 6WYP - UFS C27 H31 N3 O5 C#CCCCC(=O....
42 6WYO - TSN C17 H22 N2 O3 C[C@H](C=C....
43 3ZNS Ki = 0.039 uM NU7 C26 H24 F3 N5 O2 S CN1CCC(CC1....
44 3C0Z ic50 = 113 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
45 3C10 ic50 = 0.3 uM TSN C17 H22 N2 O3 C[C@H](C=C....
46 3ZNR Ki = 0.036 uM NU9 C25 H21 F3 N4 O3 S c1ccc(cc1)....
47 2VQM ic50 = 978 nM HA3 C18 H16 N4 O3 S c1ccc(cc1)....
48 6FYZ Kd = 0.039 uM EBE C19 H16 F N3 O2 Cc1ncc(cn1....
49 2VQQ ic50 = 367 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
50 2VQJ - TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
51 2VQO ic50 = 317 nM TFG C19 H16 F3 N3 O3 S c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P7V; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 P7V 1 1
2 IKY 0.421875 0.843137
Similar Ligands (3D)
Ligand no: 1; Ligand: P7V; Similar ligands found: 321
No: Ligand Similarity coefficient
1 A9B 1.0000
2 M4N 0.9607
3 G14 0.9570
4 ZZA 0.9526
5 7G2 0.9489
6 7KE 0.9488
7 3VQ 0.9477
8 8CC 0.9461
9 YE6 0.9439
10 NK5 0.9432
11 5H6 0.9410
12 RF2 0.9401
13 1XS 0.9361
14 KLE 0.9342
15 5C1 0.9339
16 NKI 0.9339
17 D1G 0.9337
18 7FU 0.9336
19 5VU 0.9335
20 JMG 0.9334
21 ODK 0.9334
22 D2G 0.9323
23 D25 0.9319
24 5TT 0.9315
25 L03 0.9308
26 0UL 0.9278
27 A6W 0.9276
28 27K 0.9269
29 6MW 0.9257
30 FHV 0.9253
31 90G 0.9249
32 KWV 0.9247
33 397 0.9247
34 8YH 0.9242
35 D26 0.9241
36 MKN 0.9235
37 0NX 0.9235
38 0K7 0.9231
39 A73 0.9222
40 AJ1 0.9203
41 4FF 0.9202
42 BVS 0.9196
43 L1T 0.9196
44 S0D 0.9196
45 X6W 0.9190
46 MMJ 0.9183
47 B1J 0.9175
48 4AU 0.9174
49 8D6 0.9168
50 RGK 0.9162
51 KLS 0.9159
52 E3X 0.9150
53 PUE 0.9141
54 272 0.9135
55 HH6 0.9132
56 20D 0.9128
57 EES 0.9118
58 G2V 0.9113
59 6H2 0.9109
60 4HB 0.9109
61 S45 0.9107
62 5TO 0.9106
63 78Y 0.9097
64 AD6 0.9095
65 08C 0.9087
66 2D2 0.9085
67 1UZ 0.9083
68 20N 0.9079
69 WLH 0.9074
70 TCR 0.9072
71 27F 0.9071
72 RA7 0.9066
73 J38 0.9063
74 A5H 0.9054
75 47V 0.9051
76 LR8 0.9050
77 C4E 0.9049
78 RKV 0.9048
79 7O4 0.9048
80 6C5 0.9045
81 0ON 0.9040
82 28A 0.9035
83 FCD 0.9035
84 2PK 0.9034
85 JF5 0.9031
86 YZ9 0.9026
87 JCZ 0.9026
88 6P3 0.9024
89 M78 0.9024
90 9NB 0.9023
91 A63 0.9022
92 CR4 0.9022
93 1V1 0.9020
94 CIU 0.9018
95 YE7 0.9018
96 2PV 0.9018
97 5WK 0.9017
98 BMZ 0.9011
99 613 0.9007
100 HHB 0.9005
101 HRD 0.9004
102 IPJ 0.9003
103 5E5 0.8998
104 SJR 0.8993
105 EV2 0.8990
106 25F 0.8988
107 DFL 0.8987
108 II4 0.8986
109 UN3 0.8981
110 2FX 0.8975
111 0DF 0.8975
112 SNJ 0.8972
113 4UM 0.8970
114 DBE 0.8970
115 60L 0.8966
116 QIV 0.8964
117 AJG 0.8963
118 120 0.8961
119 7MW 0.8960
120 D8Q 0.8958
121 SSY 0.8957
122 PIQ 0.8954
123 1Q2 0.8952
124 LIG 0.8951
125 363 0.8951
126 LL1 0.8951
127 NIF 0.8949
128 6FG 0.8947
129 J1K 0.8945
130 801 0.8944
131 2JX 0.8944
132 HDI 0.8942
133 SWX 0.8941
134 A9E 0.8941
135 6C8 0.8937
136 XCG 0.8936
137 9JT 0.8935
138 Y3L 0.8931
139 VC3 0.8928
140 TID 0.8927
141 5F8 0.8922
142 135 0.8917
143 4FC 0.8913
144 L02 0.8909
145 D9Z 0.8906
146 GVY 0.8904
147 1Q1 0.8901
148 39R 0.8901
149 NDD 0.8901
150 1EB 0.8901
151 PRL 0.8900
152 LZ5 0.8899
153 5TZ 0.8899
154 IDZ 0.8898
155 PQM 0.8897
156 795 0.8896
157 D3G 0.8895
158 SZ5 0.8893
159 122 0.8893
160 F40 0.8892
161 52F 0.8892
162 LR2 0.8890
163 3F4 0.8889
164 GO2 0.8888
165 A8D 0.8887
166 VGS 0.8885
167 K7H 0.8880
168 FZM 0.8876
169 5FL 0.8875
170 EAE 0.8873
171 1AJ 0.8873
172 HNT 0.8872
173 VFJ 0.8868
174 ESJ 0.8865
175 2P3 0.8858
176 LC1 0.8857
177 SO7 0.8856
178 SX2 0.8855
179 HRM 0.8853
180 MD6 0.8852
181 FZ0 0.8852
182 NVS 0.8850
183 6FB 0.8850
184 124 0.8849
185 CT0 0.8848
186 833 0.8848
187 S7S 0.8847
188 Z3R 0.8845
189 JA5 0.8844
190 MBT 0.8840
191 J84 0.8838
192 49P 0.8835
193 PZX 0.8834
194 6SD 0.8831
195 TRP 0.8831
196 XI7 0.8829
197 A7H 0.8826
198 1HP 0.8825
199 C0V 0.8823
200 CBE 0.8823
201 3C5 0.8820
202 121 0.8820
203 JGY 0.8818
204 5O6 0.8817
205 1OT 0.8815
206 2J1 0.8808
207 4I8 0.8808
208 VFM 0.8805
209 0NJ 0.8805
210 J3B 0.8803
211 U4J 0.8803
212 8V8 0.8796
213 LWA 0.8793
214 2L1 0.8786
215 ERZ 0.8786
216 FMH 0.8785
217 JVD 0.8781
218 PQV 0.8781
219 1FE 0.8778
220 9FH 0.8778
221 SQG 0.8777
222 492 0.8776
223 JAH 0.8773
224 I2E 0.8772
225 A05 0.8771
226 0MB 0.8771
227 D1Y 0.8770
228 FMQ 0.8763
229 TJM 0.8762
230 ZEA 0.8762
231 2OX 0.8759
232 1R5 0.8756
233 LJ5 0.8755
234 62D 0.8754
235 NAL 0.8746
236 NPX 0.8745
237 0LO 0.8745
238 HL6 0.8742
239 GHQ 0.8737
240 OLU 0.8736
241 ITE 0.8732
242 VM1 0.8731
243 4G2 0.8730
244 SOJ 0.8729
245 J2N 0.8727
246 P4L 0.8724
247 90M 0.8721
248 VFG 0.8720
249 A5Q 0.8717
250 GB5 0.8711
251 0XR 0.8709
252 4CN 0.8709
253 BXS 0.8706
254 80G 0.8701
255 PQS 0.8701
256 5SJ 0.8699
257 N4E 0.8697
258 NY4 0.8695
259 5ZM 0.8693
260 3SU 0.8691
261 5OR 0.8689
262 AO 0.8685
263 5M2 0.8683
264 IOP 0.8683
265 EQW 0.8683
266 EWG 0.8683
267 V2Z 0.8683
268 7EH 0.8680
269 5B2 0.8680
270 Q9T 0.8679
271 KWD 0.8673
272 SNV 0.8664
273 TEF 0.8664
274 NPS 0.8663
275 6ZX 0.8661
276 EZL 0.8659
277 3CX 0.8654
278 OJD 0.8652
279 S0A 0.8650
280 OQC 0.8647
281 2QC 0.8643
282 S8G 0.8642
283 JCQ 0.8641
284 GB4 0.8641
285 22T 0.8636
286 11X 0.8634
287 E42 0.8632
288 SU9 0.8631
289 S98 0.8629
290 WF4 0.8627
291 2GQ 0.8626
292 LFQ 0.8622
293 92G 0.8619
294 MGB 0.8618
295 RCV 0.8618
296 AZM 0.8608
297 KYN 0.8606
298 IWT 0.8600
299 AWE 0.8599
300 4ZF 0.8599
301 S62 0.8597
302 5ER 0.8595
303 A6Z 0.8592
304 3XH 0.8591
305 U55 0.8590
306 YIP 0.8588
307 E9S 0.8587
308 U7E 0.8580
309 1PS 0.8577
310 S60 0.8577
311 KW7 0.8570
312 BZQ 0.8567
313 OA1 0.8558
314 FT6 0.8550
315 CX4 0.8547
316 JVB 0.8547
317 3S9 0.8541
318 BVA 0.8536
319 EQA 0.8534
320 LEL 0.8528
321 BZM 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5EF7; Ligand: 5OJ; 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: 5ef7.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5EF7; Ligand: 5OJ; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5ef7.bio2) has 41 residues
No: Leader PDB Ligand Sequence Similarity
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