Receptor
PDB id Resolution Class Description Source Keywords
5THU 1.95 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF G304A HDAC8 IN COMPLEX WITH M344 HOMO SAPIENS ZINC HISTONE DEACETYLASE HYDROLASE
Ref.: STRUCTURAL AND FUNCTIONAL INFLUENCE OF THE GLYCINE-G302GGGY ON THE CATALYTIC TYROSINE OF HISTONE DEACE BIOCHEMISTRY V. 55 6718 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:402;
B:403;
A:403;
A:402;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
39.098 K [K+]
ZN A:401;
B:401;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
B3N A:404;
B:404;
 Valid;
Valid;
 none;
none;
 submit data
307.388 C16 H25 N3 O3 CN(C)...
GGG B:405;
 Valid;
 none;
 submit data
189.169 C6 H11 N3 O4 C(C(=...
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: B3N; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 B3N 1 1
2 AH4 0.513889 0.738462
Ligand no: 2; Ligand: GGG; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GGG 1 1
2 GLY GLY 0.454545 0.909091
3 4SQ 0.416667 0.727273
Similar Ligands (3D)
Ligand no: 1; Ligand: B3N; Similar ligands found: 6
No: Ligand Similarity coefficient
1 UFJ 0.9065
2 SHH 0.8989
3 EG2 0.8905
4 TSN 0.8870
5 2VZ 0.8602
6 BNI 0.8568
Ligand no: 2; Ligand: GGG; Similar ligands found: 173
No: Ligand Similarity coefficient
1 MGB 0.9281
2 GLY GLY GLY 0.9255
3 N8C 0.9199
4 6FG 0.9193
5 2J3 0.9191
6 GVA 0.9171
7 RES 0.9128
8 MKN 0.9122
9 PML 0.9113
10 N9M 0.9082
11 A5P 0.9081
12 9J6 0.9080
13 EGV 0.9078
14 R52 0.9068
15 HSA 0.9067
16 BGT 0.9066
17 HRG 0.9061
18 3S9 0.9054
19 1N5 0.9052
20 0OM 0.9044
21 S8G 0.9041
22 E8U 0.9032
23 NK5 0.9029
24 7XA 0.9028
25 JX7 0.9028
26 KNA 0.9023
27 BZM 0.9015
28 5RP 0.9014
29 ALY 0.9004
30 6C8 0.8999
31 ASF 0.8993
32 5SP 0.8985
33 CT0 0.8977
34 AHL 0.8963
35 HJD 0.8950
36 I58 0.8950
37 R5P 0.8949
38 DAR 0.8937
39 KAP 0.8937
40 5TO 0.8925
41 OCA 0.8921
42 CIR 0.8918
43 G6Q 0.8912
44 6C9 0.8912
45 REG 0.8910
46 ARG 0.8908
47 DMA 0.8906
48 F6R 0.8901
49 GPE 0.8900
50 HAR 0.8900
51 DKA 0.8896
52 M3L 0.8890
53 3CX 0.8889
54 ENV 0.8883
55 DI9 0.8882
56 RGP 0.8881
57 DEZ 0.8878
58 0QA 0.8874
59 LPA 0.8872
60 SPD 0.8870
61 DIA 0.8863
62 P93 0.8861
63 1AE 0.8853
64 SOR 0.8853
65 IAR 0.8852
66 NFZ 0.8850
67 6C4 0.8848
68 BSA 0.8843
69 OJM 0.8840
70 HPO 0.8838
71 T03 0.8835
72 4DI 0.8833
73 JGY 0.8829
74 4Z0 0.8829
75 HLP 0.8828
76 GHQ 0.8825
77 5KJ 0.8823
78 XOG 0.8820
79 6FR 0.8815
80 S0B 0.8814
81 PRO GLY 0.8812
82 TEG 0.8808
83 IPE 0.8808
84 LXP 0.8805
85 S8P 0.8805
86 PAN 0.8805
87 9VQ 0.8805
88 DX5 0.8802
89 PTB 0.8801
90 6C5 0.8800
91 27K 0.8788
92 DXP 0.8785
93 JF5 0.8784
94 CLT 0.8779
95 HL6 0.8779
96 8YH 0.8772
97 HPL 0.8771
98 TX4 0.8770
99 ENW 0.8769
100 8AC 0.8769
101 4JK 0.8769
102 LPB 0.8768
103 4AF 0.8759
104 D10 0.8755
105 5LD 0.8754
106 0F3 0.8751
107 ODI 0.8750
108 YI6 0.8750
109 3GZ 0.8744
110 MMN 0.8740
111 X1R 0.8740
112 D53 0.8739
113 API 0.8737
114 3S6 0.8737
115 3VR 0.8736
116 S6P 0.8732
117 ALA GLU 0.8730
118 64Z 0.8730
119 MN9 0.8728
120 D1G 0.8727
121 011 0.8726
122 R10 0.8726
123 NBB 0.8723
124 M1T 0.8720
125 STX 0.8715
126 SAZ 0.8715
127 ILO 0.8714
128 58X 0.8713
129 536 0.8710
130 D6P 0.8708
131 GGB 0.8706
132 VIO 0.8706
133 OHJ 0.8705
134 C26 0.8705
135 ZZU 0.8702
136 WT2 0.8702
137 DHJ 0.8697
138 PA5 0.8695
139 7UC 0.8694
140 0OO 0.8688
141 OJD 0.8685
142 AGP 0.8680
143 Q86 0.8675
144 531 0.8673
145 JAA 0.8656
146 NOT 0.8653
147 MYI 0.8649
148 6MW 0.8647
149 IPR 0.8645
150 463 0.8643
151 MFY 0.8642
152 3W6 0.8638
153 OYA 0.8636
154 3KJ 0.8635
155 SB7 0.8629
156 M3B 0.8629
157 M5B 0.8627
158 S7D 0.8624
159 DA2 0.8619
160 AHN 0.8608
161 3W3 0.8606
162 MVH 0.8605
163 HPK 0.8603
164 ALA GLN 0.8602
165 HPX 0.8598
166 ALA ZGL 0.8598
167 ALA ALA ALA 0.8595
168 G3M 0.8594
169 M28 0.8585
170 6PG 0.8571
171 U4G 0.8557
172 ATX 0.8535
173 DST 0.8524
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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