Receptor
PDB id Resolution Class Description Source Keywords
5FCW 1.98 Å EC: 3.5.1.98 HDAC8 COMPLEXED WITH A HYDROXAMIC ACID HOMO SAPIENS HISTONE DEACETYLASE HDAC8 HYDROXAMIC ACID HYDROLASE
Ref.: STRUCTURE OF 'LINKERLESS' HYDROXAMIC ACID INHIBITOR COMPLEX CONFIRMS THE FORMATION OF AN ISOFORM-SPECIF SUBPOCKET. J.STRUCT.BIOL. V. 195 373 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:402;
B:402;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
GOL B:406;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
5YA B:404;
B:401;
B:405;
A:401;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 ic50 = 0.3 uM
263.291 C17 H13 N O2 c1ccc...
K B:403;
A:403;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
39.098 K [K+]
P6G A:404;
 Invalid;
 none;
 submit data
282.331 C12 H26 O7 C(COC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W22 2.5 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF INHIBITED HUMAN HDAC8 HOMO SAPIENS HYDROXAMIC ACID CHROMATIN DEACETYLATION HDAC HYDROLASE NUCLEAR PROTEIN REPRESSOR
Ref.: CRYSTAL STRUCTURE OF A EUKARYOTIC ZN-DEPENDENT HISTONE DEACETYLASE,HUMAN HDAC8,COMPLEXED WITH A HYDROXAMIC ACID INHIBITOR PROC.NATL.ACAD.SCI.USA V. 101 15064 2004
Members (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5THU - B3N C16 H25 N3 O3 CN(C)c1ccc....
2 5D1D - ACE ARG HIS ALY ALY MCM n/a n/a
3 5DC7 - ACE ARG HIS ALY ALY MCM n/a n/a
4 4QA4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 2V5X Kd = 220 nM V5X C36 H41 N5 O5 Cc1c(c2cc(....
6 4QA6 - ACE ARG HIS ALY ALY MCM n/a n/a
7 5THT - B3N C16 H25 N3 O3 CN(C)c1ccc....
8 4QA0 - SHH C14 H20 N2 O3 c1ccc(cc1)....
9 4QA2 - SHH C14 H20 N2 O3 c1ccc(cc1)....
10 3SFF ic50 = 200 nM 0DI C20 H20 Cl F2 N3 O2 c1cc(cc(c1....
11 7JVU - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
13 3RQD - 02G GLY BB9 03Y VAL n/a n/a
14 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
16 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
17 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
18 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
19 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
21 7JVW - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
23 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
24 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
25 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
26 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
27 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
28 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 7JVV - ACE ARG HIS ALY ALY MCM n/a n/a
30 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
32 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
33 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
34 5VI6 - PHE PHE CPI 5OM n/a n/a
35 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
36 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
37 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
38 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
39 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
70% Homology Family (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 5THU - B3N C16 H25 N3 O3 CN(C)c1ccc....
2 5D1D - ACE ARG HIS ALY ALY MCM n/a n/a
3 5DC7 - ACE ARG HIS ALY ALY MCM n/a n/a
4 4QA4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 2V5X Kd = 220 nM V5X C36 H41 N5 O5 Cc1c(c2cc(....
6 4QA6 - ACE ARG HIS ALY ALY MCM n/a n/a
7 5THT - B3N C16 H25 N3 O3 CN(C)c1ccc....
8 4QA0 - SHH C14 H20 N2 O3 c1ccc(cc1)....
9 4QA2 - SHH C14 H20 N2 O3 c1ccc(cc1)....
10 3SFF ic50 = 200 nM 0DI C20 H20 Cl F2 N3 O2 c1cc(cc(c1....
11 7JVU - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
13 3RQD - 02G GLY BB9 03Y VAL n/a n/a
14 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
16 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
17 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
18 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
19 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
21 7JVW - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
23 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
24 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
25 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
26 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
27 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
28 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 7JVV - ACE ARG HIS ALY ALY MCM n/a n/a
30 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
32 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
33 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
34 5VI6 - PHE PHE CPI 5OM n/a n/a
35 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
36 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
37 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
38 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
39 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
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 5THU - B3N C16 H25 N3 O3 CN(C)c1ccc....
2 5D1D - ACE ARG HIS ALY ALY MCM n/a n/a
3 5DC7 - ACE ARG HIS ALY ALY MCM n/a n/a
4 4QA4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
5 2V5X Kd = 220 nM V5X C36 H41 N5 O5 Cc1c(c2cc(....
6 4QA6 - ACE ARG HIS ALY ALY MCM n/a n/a
7 5THT - B3N C16 H25 N3 O3 CN(C)c1ccc....
8 4QA0 - SHH C14 H20 N2 O3 c1ccc(cc1)....
9 4QA2 - SHH C14 H20 N2 O3 c1ccc(cc1)....
10 3SFF ic50 = 200 nM 0DI C20 H20 Cl F2 N3 O2 c1cc(cc(c1....
11 7JVU - SHH C14 H20 N2 O3 c1ccc(cc1)....
12 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
13 3RQD - 02G GLY BB9 03Y VAL n/a n/a
14 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
16 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
17 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
18 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
19 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
21 7JVW - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
23 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
24 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
25 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
26 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
27 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
28 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 7JVV - ACE ARG HIS ALY ALY MCM n/a n/a
30 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
32 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
33 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
34 5VI6 - PHE PHE CPI 5OM n/a n/a
35 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
36 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
37 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
38 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
39 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
40 5IX0 Ki = 0.519 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
41 6XDM ic50 = 0.1 nM V1D C24 H30 F N5 O4 CN1CC(C1)C....
42 7KBG ic50 = 29 nM WBA C29 H26 F N5 O3 S c1ccc2cc(c....
43 6XEC - V1S C28 H38 F N5 O3 CCC(CCCCC[....
44 4LY1 Kd = 0.0552 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
45 4LXZ Kd = 0.182 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
46 6XEB - V1P C24 H35 N5 O4 CCC(CCCCC[....
47 6WBW - TV1 C27 H37 N5 O4 CCC(CCCCC[....
48 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
49 5IWG Ki = 0.346 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
50 6WBZ - TV7 C32 H45 N5 O4 CCC(CCCCC[....
51 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5YA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 5YA 1 1
2 8GK 0.436364 0.965517
Similar Ligands (3D)
Ligand no: 1; Ligand: 5YA; Similar ligands found: 255
No: Ligand Similarity coefficient
1 338 0.9453
2 JFS 0.9356
3 GVI 0.9333
4 2UV 0.9293
5 8UY 0.9291
6 TVZ 0.9286
7 A63 0.9255
8 6T5 0.9231
9 F08 0.9218
10 65W 0.9214
11 NPZ 0.9212
12 1UT 0.9210
13 A64 0.9208
14 5WW 0.9195
15 4K2 0.9188
16 1V0 0.9168
17 J45 0.9164
18 1UR 0.9155
19 73E 0.9155
20 PNW 0.9149
21 OJ7 0.9147
22 KVW 0.9125
23 40W 0.9123
24 SIJ 0.9117
25 6MY 0.9115
26 PNJ 0.9109
27 KVQ 0.9103
28 U4J 0.9102
29 LLG 0.9089
30 A5W 0.9083
31 FBC 0.9072
32 1UZ 0.9068
33 SNP 0.9067
34 S1C 0.9061
35 3TI 0.9059
36 NU3 0.9044
37 KVN 0.9035
38 147 0.9027
39 LU2 0.9018
40 KHP 0.9010
41 08C 0.9001
42 PNG 0.8998
43 Q5M 0.8998
44 KUQ 0.8993
45 UN4 0.8989
46 GF7 0.8988
47 XYP XIM 0.8987
48 6BK 0.8985
49 T5J 0.8985
50 J8D 0.8984
51 3WJ 0.8983
52 JFZ 0.8979
53 1Q1 0.8975
54 EZB 0.8975
55 GLA NPO 0.8974
56 NBZ GLA 0.8974
57 OSY 0.8973
58 LFK 0.8972
59 VIB 0.8971
60 GA6 0.8969
61 MHB 0.8967
62 EUN 0.8966
63 97K 0.8961
64 TVC 0.8958
65 AGI 0.8957
66 INI 0.8954
67 TH1 0.8953
68 3Q0 0.8950
69 W2E 0.8942
70 RNP 0.8938
71 5TU 0.8932
72 7ZO 0.8930
73 72G 0.8926
74 S13 0.8925
75 BO1 0.8923
76 NAR 0.8922
77 91F 0.8921
78 E9L 0.8921
79 O9Z 0.8918
80 F36 0.8917
81 0NH 0.8914
82 7VF 0.8913
83 WDW 0.8907
84 DL6 0.8903
85 LMZ 0.8900
86 B7H 0.8898
87 U55 0.8897
88 M16 0.8895
89 O53 0.8894
90 1FL 0.8893
91 H2W 0.8892
92 M08 0.8889
93 VT3 0.8888
94 FHI 0.8886
95 JTE 0.8885
96 D1L 0.8883
97 CDJ 0.8882
98 FT1 0.8881
99 XAV 0.8879
100 ECZ 0.8876
101 MZR 0.8876
102 27F 0.8875
103 W8L 0.8875
104 FT2 0.8872
105 20D 0.8870
106 FT3 0.8866
107 CMG 0.8865
108 FE5 0.8862
109 EEY 0.8855
110 BDE 0.8855
111 7DE 0.8854
112 J5Z 0.8853
113 9C8 0.8852
114 4YE 0.8851
115 1V1 0.8848
116 6UI 0.8844
117 IMK 0.8844
118 GAL PHB 0.8840
119 JTK 0.8835
120 121 0.8835
121 AUY 0.8832
122 AT2 0.8829
123 3CA 0.8827
124 KMP 0.8827
125 1NE 0.8825
126 B4L 0.8821
127 22M 0.8819
128 BNY 0.8819
129 6QX 0.8817
130 AYS 0.8815
131 4MP 0.8812
132 QDR 0.8811
133 CWE 0.8808
134 WCU 0.8807
135 4YF 0.8805
136 2ZI 0.8804
137 A73 0.8804
138 DFL 0.8798
139 CT7 0.8798
140 QC1 0.8796
141 2OX 0.8791
142 HGH 0.8790
143 QTK 0.8788
144 IY5 0.8787
145 7FZ 0.8787
146 KS5 0.8782
147 A45 0.8782
148 MBE 0.8781
149 JTN 0.8778
150 B1N 0.8776
151 OUA 0.8775
152 F1T 0.8774
153 JZ8 0.8773
154 9PP 0.8770
155 5CX 0.8770
156 KS2 0.8769
157 M07 0.8766
158 31F 0.8763
159 JRE 0.8760
160 XYP XYP 0.8759
161 IEE 0.8757
162 M3W 0.8754
163 Q92 0.8751
164 NKI 0.8749
165 8XY 0.8747
166 8BD 0.8747
167 9ME 0.8746
168 ZEA 0.8745
169 CMP 0.8742
170 RGK 0.8740
171 A7K 0.8738
172 AWE 0.8737
173 JD7 0.8733
174 BX4 0.8733
175 FSU 0.8732
176 OUG 0.8730
177 DFV 0.8729
178 26C 0.8729
179 FLF 0.8722
180 QTJ 0.8721
181 5GP 0.8713
182 GQZ 0.8712
183 5P7 0.8711
184 3WK 0.8710
185 UN9 0.8709
186 ELH 0.8707
187 SZ5 0.8702
188 LVY 0.8702
189 06R 0.8698
190 UX0 0.8696
191 3F4 0.8694
192 83D 0.8685
193 5R9 0.8684
194 KWK 0.8681
195 J47 0.8677
196 XYS XYS 0.8677
197 MEX 0.8675
198 QUE 0.8671
199 7FC 0.8668
200 Z8R 0.8667
201 1SF 0.8667
202 UV4 0.8666
203 25F 0.8665
204 L43 0.8664
205 NZ4 0.8663
206 205 0.8661
207 MRI 0.8658
208 4NR 0.8657
209 BGC BGC 0.8653
210 3G5 0.8652
211 TCL 0.8650
212 47X 0.8648
213 Q2S 0.8648
214 0HV 0.8648
215 26A 0.8645
216 SAK 0.8642
217 57D 0.8639
218 35G 0.8638
219 MTP 0.8637
220 3N0 0.8630
221 KVD 0.8628
222 NQE 0.8628
223 NW1 0.8627
224 MTA 0.8625
225 D7D 0.8625
226 QTD 0.8620
227 LZ7 0.8620
228 JSX 0.8619
229 3WL 0.8618
230 6X1 0.8617
231 WA2 0.8617
232 ADN 0.8614
233 5CJ 0.8614
234 41L 0.8614
235 H35 0.8608
236 GYZ 0.8604
237 5PK 0.8603
238 DQH 0.8600
239 SNV 0.8594
240 RPB 0.8587
241 72E 0.8581
242 9C6 0.8579
243 P34 0.8579
244 JA3 0.8578
245 NQK 0.8577
246 8OB 0.8576
247 361 0.8570
248 FB4 0.8568
249 G2V 0.8556
250 L3L 0.8553
251 STL 0.8550
252 2KR 0.8549
253 3JC 0.8546
254 4L2 0.8540
255 PCG 0.8534
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W22; Ligand: NHB; 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: 1w22.bio2) has 64 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1W22; Ligand: NHB; 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: 1w22.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
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