Receptor
PDB id Resolution Class Description Source Keywords
2V5X 2.25 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HDAC8-INHIBITOR COMPLEX HOMO SAPIENS HYDROXAMATE INHIBITOR CHROMATIN REGULATOR HISTONE DEACETYLP53 HDAC HDAC8 NUCLEUS HYDROLASE REPRESSOR CHROMATINDESIGN DEACETYLATION TRANSCRIPTION TRANSCRIPTION REGULATNUCLEAR PROTEIN PEPTIDIC SUBSTRATE
Ref.: SUBSTRATE BINDING TO HISTONE DEACETYLASES AS REVEAL CRYSTAL STRUCTURE OF HDAC8-SUBSTRATE COMPLEX EMBO REP. V. 8 879 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K A:1378;
A:1379;
B:1378;
B:1379;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
39.098 K [K+]
V5X A:1380;
B:1380;
 Valid;
Valid;
 none;
none;
 ic50 = 100 nM
623.741 C36 H41 N5 O5 Cc1c(...
ZN A:1377;
B:1377;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2V5X 2.25 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HDAC8-INHIBITOR COMPLEX HOMO SAPIENS HYDROXAMATE INHIBITOR CHROMATIN REGULATOR HISTONE DEACETYLP53 HDAC HDAC8 NUCLEUS HYDROLASE REPRESSOR CHROMATINDESIGN DEACETYLATION TRANSCRIPTION TRANSCRIPTION REGULATNUCLEAR PROTEIN PEPTIDIC SUBSTRATE
Ref.: SUBSTRATE BINDING TO HISTONE DEACETYLASES AS REVEAL CRYSTAL STRUCTURE OF HDAC8-SUBSTRATE COMPLEX EMBO REP. V. 8 879 2007
Members (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 ic50 = 100 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 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
12 3RQD - 02G GLY BB9 03Y VAL n/a n/a
13 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
14 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
16 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
17 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
18 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
19 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
21 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
23 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
24 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
25 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
26 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
27 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
28 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
29 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
30 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 5VI6 - PHE PHE CPI 5OM n/a n/a
32 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
33 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
34 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
35 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
36 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
70% Homology Family (36)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 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 ic50 = 100 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 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
12 3RQD - 02G GLY BB9 03Y VAL n/a n/a
13 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
14 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
16 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
17 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
18 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
19 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
21 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
23 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
24 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
25 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
26 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
27 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
28 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
29 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
30 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 5VI6 - PHE PHE CPI 5OM n/a n/a
32 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
33 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
34 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
35 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
36 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
50% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 ic50 = 100 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 1W22 ic50 = 175.5 nM NHB C17 H15 N3 O4 S2 CN(c1ccc(c....
12 3RQD - 02G GLY BB9 03Y VAL n/a n/a
13 3MZ4 - B3N C16 H25 N3 O3 CN(C)c1ccc....
14 5THV - B3N C16 H25 N3 O3 CN(C)c1ccc....
15 5DC6 - ACE ARG HIS ALY ALY MCM n/a n/a
16 3EW8 - B3N C16 H25 N3 O3 CN(C)c1ccc....
17 1VKG - CRI C24 H23 N3 O4 Cc1ccc(cc1....
18 3MZ6 - B3N C16 H25 N3 O3 CN(C)c1ccc....
19 5THS - B3N C16 H25 N3 O3 CN(C)c1ccc....
20 3EWF - ACE ARG HIS ALY ALY MCM n/a n/a
21 3MZ7 - B3N C16 H25 N3 O3 CN(C)c1ccc....
22 5DC5 - B3N C16 H25 N3 O3 CN(C)c1ccc....
23 4QA5 - ACE ARG HIS ALY ALY MCM n/a n/a
24 1T64 - TSN C17 H22 N2 O3 C[C@H](C=C....
25 4QA7 - ACE ARG HIS ALY ALY MCM n/a n/a
26 4RN2 ic50 = 1500 nM L7G C23 H31 N5 O3 S2 CC(C)[C@H]....
27 1T67 - B3N C16 H25 N3 O3 CN(C)c1ccc....
28 6HSK - GOK C21 H26 N6 O2 Cn1cc(c2c1....
29 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
30 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
31 5VI6 - PHE PHE CPI 5OM n/a n/a
32 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
33 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
34 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
35 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
36 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
37 5IX0 ic50 = 0.168 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
38 4LY1 ic50 = 0.0563 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
39 4LXZ ic50 = 0.251 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
40 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
41 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
42 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: V5X; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 V5X 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2V5X; Ligand: V5X; 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: 2v5x.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2V5X; Ligand: V5X; 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: 2v5x.bio2) has 64 residues
No: Leader PDB Ligand Sequence Similarity
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