Receptor
PDB id Resolution Class Description Source Keywords
6HQY 2.5 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI HDAC8 COMPLEXED WIT 34051 SCHISTOSOMA MANSONI EPIGENETICS HISTONE DEACETYLASE HDAC8 SELECTIVE INHIBITORPATHOGEN HYDROLASE
Ref.: CHARACTERIZATION OF HISTONE DEACETYLASE 8 (HDAC8) S INHIBITION REVEALS SPECIFIC ACTIVE SITE STRUCTURAL FUNCTIONAL DETERMINANTS. J. MED. CHEM. V. 61 10000 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K B:503;
A:502;
A:503;
C:503;
D:503;
D:502;
C:502;
B:502;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
39.098 K [K+]
GOL A:506;
D:505;
A:507;
B:505;
C:505;
A:505;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
GKW A:504;
C:504;
B:504;
D:504;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Kd = 367 nM
296.321 C17 H16 N2 O3 COc1c...
ZN C:501;
D:501;
B:501;
A:501;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6GXA 2.1 Å EC: 7.-.-.- CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI HDAC8 COMPLEXED WIT HYDROXAMATE 2 SCHISTOSOMA MANSONI EPIGENETICS HISTONE DEACETYLASE HDAC8 SELECTIVE INHIBITORPATHOGEN HYDROLASE
Ref.: SYNTHESIS, CRYSTALLIZATION STUDIES, AND IN VITRO CHARACTERIZATION OF CINNAMIC ACID DERIVATIVES AS SM INHIBITORS FOR THE TREATMENT OF SCHISTOSOMIASIS. CHEMMEDCHEM V. 13 1517 2018
Members (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 4BZ8 - J38 C10 H10 N2 O3 S C[C@@H]1C(....
2 6HQY Kd = 367 nM GKW C17 H16 N2 O3 COc1ccc(cc....
3 4BZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
4 6HU2 ic50 = 1260 nM T34 C15 H16 N2 O2 Cc1ccc(cc1....
5 6HU0 ic50 = 122 nM T86 C15 H12 Cl2 N2 O4 COc1ccc(cc....
6 4CQF - 9Z8 C14 H20 N2 O2 S c1ccc(cc1)....
7 6HTG ic50 = 67 nM T61 C14 H11 Cl N2 O3 c1ccc(cc1)....
8 6GX3 ic50 = 250 nM FF2 C9 H6 Cl N O2 S c1cc2c(cc(....
9 6GXU ic50 = 180 nM FG8 C15 H12 Cl N O2 S c1ccc(c(c1....
10 6HTI ic50 = 97 nM GQW C16 H11 Cl N2 O3 S c1cc2ccsc2....
11 6HSG - GM5 C16 H14 N4 O2 S c1ccc(cc1)....
12 6TLD Kd = 4.4 uM NK5 C9 H8 N4 O2 c1ccc(cc1)....
13 6HT8 ic50 = 190 nM GQE C15 H14 N2 O4 COc1ccc(cc....
14 6HU1 ic50 = 191 nM GT2 C14 H9 Cl3 N2 O3 c1cc(c(cc1....
15 6HRQ Kd = 81.7 nM GM5 C16 H14 N4 O2 S c1ccc(cc1)....
16 6HSF - GKW C17 H16 N2 O3 COc1ccc(cc....
17 4BZ9 - KMY C9 H6 Cl N O2 S c1ccc2c(c1....
18 6HSZ ic50 = 116 nM GOW C15 H14 N2 O3 Cc1ccc(cc1....
19 6GXW ic50 = 440 nM FGN C16 H13 Cl2 N O3 c1ccc(c(c1....
20 6FU1 ic50 = 4.4 uM E7Q C16 H19 Cl N2 O4 CCCCCC(=O)....
21 6GXA ic50 = 60 nM TB8 C9 H8 Cl N O2 c1ccc(c(c1....
22 5FUE ic50 = 468.2 nM UV4 C14 H10 N2 O3 c1ccc(cc1)....
23 6HSH Kd = 28.4 nM GOK C21 H26 N6 O2 Cn1cc(c2c1....
24 6HU3 ic50 = 504 nM GRZ C15 H10 Cl F N4 O3 c1cc(ccc1O....
25 6HTT ic50 = 220 nM GQZ C14 H12 N2 O3 c1ccc(cc1)....
26 4BZ6 - SHH C14 H20 N2 O3 c1ccc(cc1)....
27 4BZ5 - TLA C4 H6 O6 [C@@H]([C@....
28 6HTZ ic50 = 183 nM GRK C16 H16 N2 O4 COc1ccc(cc....
29 6HTH ic50 = 75 nM GQN C21 H18 N2 O4 COc1ccc(cc....
70% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 271 families.
1 4BZ8 - J38 C10 H10 N2 O3 S C[C@@H]1C(....
2 6HQY Kd = 367 nM GKW C17 H16 N2 O3 COc1ccc(cc....
3 4BZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
4 6HU2 ic50 = 1260 nM T34 C15 H16 N2 O2 Cc1ccc(cc1....
5 6HU0 ic50 = 122 nM T86 C15 H12 Cl2 N2 O4 COc1ccc(cc....
6 4CQF - 9Z8 C14 H20 N2 O2 S c1ccc(cc1)....
7 6HTG ic50 = 67 nM T61 C14 H11 Cl N2 O3 c1ccc(cc1)....
8 6GX3 ic50 = 250 nM FF2 C9 H6 Cl N O2 S c1cc2c(cc(....
9 6GXU ic50 = 180 nM FG8 C15 H12 Cl N O2 S c1ccc(c(c1....
10 6HTI ic50 = 97 nM GQW C16 H11 Cl N2 O3 S c1cc2ccsc2....
11 6HSG - GM5 C16 H14 N4 O2 S c1ccc(cc1)....
12 6TLD Kd = 4.4 uM NK5 C9 H8 N4 O2 c1ccc(cc1)....
13 6HT8 ic50 = 190 nM GQE C15 H14 N2 O4 COc1ccc(cc....
14 6HU1 ic50 = 191 nM GT2 C14 H9 Cl3 N2 O3 c1cc(c(cc1....
15 6HRQ Kd = 81.7 nM GM5 C16 H14 N4 O2 S c1ccc(cc1)....
16 6HSF - GKW C17 H16 N2 O3 COc1ccc(cc....
17 4BZ9 - KMY C9 H6 Cl N O2 S c1ccc2c(c1....
18 6HSZ ic50 = 116 nM GOW C15 H14 N2 O3 Cc1ccc(cc1....
19 6GXW ic50 = 440 nM FGN C16 H13 Cl2 N O3 c1ccc(c(c1....
20 6FU1 ic50 = 4.4 uM E7Q C16 H19 Cl N2 O4 CCCCCC(=O)....
21 6GXA ic50 = 60 nM TB8 C9 H8 Cl N O2 c1ccc(c(c1....
22 5FUE ic50 = 468.2 nM UV4 C14 H10 N2 O3 c1ccc(cc1)....
23 6HSH Kd = 28.4 nM GOK C21 H26 N6 O2 Cn1cc(c2c1....
24 6HU3 ic50 = 504 nM GRZ C15 H10 Cl F N4 O3 c1cc(ccc1O....
25 6HTT ic50 = 220 nM GQZ C14 H12 N2 O3 c1ccc(cc1)....
26 4BZ6 - SHH C14 H20 N2 O3 c1ccc(cc1)....
27 4BZ5 - TLA C4 H6 O6 [C@@H]([C@....
28 6HTZ ic50 = 183 nM GRK C16 H16 N2 O4 COc1ccc(cc....
29 6HTH ic50 = 75 nM GQN C21 H18 N2 O4 COc1ccc(cc....
50% Homology Family (29)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 4BZ8 - J38 C10 H10 N2 O3 S C[C@@H]1C(....
2 6HQY Kd = 367 nM GKW C17 H16 N2 O3 COc1ccc(cc....
3 4BZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
4 6HU2 ic50 = 1260 nM T34 C15 H16 N2 O2 Cc1ccc(cc1....
5 6HU0 ic50 = 122 nM T86 C15 H12 Cl2 N2 O4 COc1ccc(cc....
6 4CQF - 9Z8 C14 H20 N2 O2 S c1ccc(cc1)....
7 6HTG ic50 = 67 nM T61 C14 H11 Cl N2 O3 c1ccc(cc1)....
8 6GX3 ic50 = 250 nM FF2 C9 H6 Cl N O2 S c1cc2c(cc(....
9 6GXU ic50 = 180 nM FG8 C15 H12 Cl N O2 S c1ccc(c(c1....
10 6HTI ic50 = 97 nM GQW C16 H11 Cl N2 O3 S c1cc2ccsc2....
11 6HSG - GM5 C16 H14 N4 O2 S c1ccc(cc1)....
12 6TLD Kd = 4.4 uM NK5 C9 H8 N4 O2 c1ccc(cc1)....
13 6HT8 ic50 = 190 nM GQE C15 H14 N2 O4 COc1ccc(cc....
14 6HU1 ic50 = 191 nM GT2 C14 H9 Cl3 N2 O3 c1cc(c(cc1....
15 6HRQ Kd = 81.7 nM GM5 C16 H14 N4 O2 S c1ccc(cc1)....
16 6HSF - GKW C17 H16 N2 O3 COc1ccc(cc....
17 4BZ9 - KMY C9 H6 Cl N O2 S c1ccc2c(c1....
18 6HSZ ic50 = 116 nM GOW C15 H14 N2 O3 Cc1ccc(cc1....
19 6GXW ic50 = 440 nM FGN C16 H13 Cl2 N O3 c1ccc(c(c1....
20 6FU1 ic50 = 4.4 uM E7Q C16 H19 Cl N2 O4 CCCCCC(=O)....
21 6GXA ic50 = 60 nM TB8 C9 H8 Cl N O2 c1ccc(c(c1....
22 5FUE ic50 = 468.2 nM UV4 C14 H10 N2 O3 c1ccc(cc1)....
23 6HSH Kd = 28.4 nM GOK C21 H26 N6 O2 Cn1cc(c2c1....
24 6HU3 ic50 = 504 nM GRZ C15 H10 Cl F N4 O3 c1cc(ccc1O....
25 6HTT ic50 = 220 nM GQZ C14 H12 N2 O3 c1ccc(cc1)....
26 4BZ6 - SHH C14 H20 N2 O3 c1ccc(cc1)....
27 4BZ5 - TLA C4 H6 O6 [C@@H]([C@....
28 6HTZ ic50 = 183 nM GRK C16 H16 N2 O4 COc1ccc(cc....
29 6HTH ic50 = 75 nM GQN C21 H18 N2 O4 COc1ccc(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GKW; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 GKW 1 1
2 R5G 0.766667 0.811321
3 JCH 0.480519 0.629032
Similar Ligands (3D)
Ligand no: 1; Ligand: GKW; Similar ligands found: 82
No: Ligand Similarity coefficient
1 LKG 0.9441
2 50R 0.9276
3 JDQ 0.9127
4 V0L 0.9123
5 FG8 0.9075
6 SAK 0.9074
7 5TF 0.9067
8 F47 0.9064
9 3U5 0.9061
10 J8G 0.9033
11 3TI 0.9030
12 B5T 0.9021
13 SX8 0.9020
14 LJV 0.9018
15 3QT 0.9009
16 W9Z 0.9006
17 499 0.8959
18 6QX 0.8945
19 7SB 0.8924
20 0H5 0.8883
21 HHW 0.8870
22 8IP 0.8862
23 76P 0.8857
24 T86 0.8851
25 UI2 0.8848
26 AZ5 0.8841
27 T34 0.8841
28 0JK 0.8832
29 2WF 0.8826
30 78Z 0.8822
31 1BJ 0.8818
32 HY7 0.8816
33 FYB 0.8802
34 O9T 0.8801
35 5SZ 0.8794
36 21X 0.8793
37 TJ3 0.8788
38 O9Z 0.8783
39 GQE 0.8769
40 26K 0.8765
41 JYM 0.8755
42 6XE 0.8755
43 2J6 0.8753
44 GRK 0.8749
45 LU2 0.8744
46 NAR 0.8743
47 WUL 0.8741
48 QLV 0.8741
49 J8D 0.8738
50 QUE 0.8738
51 M16 0.8721
52 3XL 0.8721
53 GQZ 0.8707
54 GOW 0.8695
55 JET 0.8684
56 PZB 0.8678
57 DN8 0.8676
58 DZJ 0.8671
59 MYC 0.8660
60 GZT 0.8657
61 9N2 0.8655
62 3E1 0.8654
63 T61 0.8654
64 0J6 0.8638
65 36C 0.8636
66 47D 0.8629
67 DQH 0.8626
68 DFV 0.8626
69 OSY 0.8623
70 ML1 0.8621
71 QI9 0.8616
72 LZ7 0.8592
73 5TQ 0.8587
74 9X0 0.8570
75 340 0.8569
76 49D 0.8563
77 F45 0.8560
78 FO2 0.8542
79 M62 0.8541
80 7WH 0.8528
81 NX2 0.8522
82 JE8 0.8520
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6GXA; Ligand: TB8; 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: 6gxa.bio4) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6GXA; Ligand: TB8; 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: 6gxa.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6GXA; Ligand: TB8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6gxa.bio2) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6GXA; Ligand: TB8; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6gxa.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback