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 (35)
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 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 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
30 5VI6 - PHE PHE CPI 5OM n/a n/a
31 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
32 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
33 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
34 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
35 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
70% Homology Family (35)
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 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 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
30 5VI6 - PHE PHE CPI 5OM n/a n/a
31 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
32 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
33 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
34 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
35 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
50% Homology Family (40)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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 4RN1 - L8G C23 H31 N5 O3 S2 CC(C)[C@H]....
29 4QA1 - B3N C16 H25 N3 O3 CN(C)c1ccc....
30 5VI6 - PHE PHE CPI 5OM n/a n/a
31 5FCW ic50 = 0.3 uM 5YA C17 H13 N O2 c1ccc2c(c1....
32 5D1C - ACE ARG HIS ALY ALY MCM n/a n/a
33 5DC8 - ACE ARG HIS ALY ALY MCM n/a n/a
34 2V5W - ACE ARG HIS ALY ALY MCM n/a n/a
35 4RN0 ic50 = 255 nM L6G C21 H29 N5 O3 S3 CC(C)[C@H]....
36 5IX0 ic50 = 0.168 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
37 4LY1 ic50 = 0.0563 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
38 4LXZ ic50 = 0.251 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
39 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
40 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: 9
This union binding pocket(no: 1) in the query (biounit: 2v5x.bio1) has 64 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4YSW URC 0.03578 0.40986 2.31959
2 3IP5 ALA 0.04021 0.40623 3.37079
3 1WS5 MMA 0.01987 0.40739 3.7594
4 4ZUR 7XA 0.0000002556 0.49601 29.0323
5 2VQO TFG 0.0000001102 0.43612 37.6289
6 5G0H E1Z 0.00000008442 0.47122 38.9175
7 5G0G TSN 0.0000001503 0.68291 39.2105
8 5EF7 5OJ 0.0000002497 0.49737 42.5824
9 1C3R TSN 0.0000008347 0.43609 45.0667
Pocket No.: 2; Query (leader) PDB : 2V5X; Ligand: V5X; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 2v5x.bio2) has 64 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1A78 TDG 0.04979 0.40328 2.23881
2 2CYC TYR 0.04756 0.40201 5.06667
3 1KJ1 MAN 0.0286 0.41287 5.50459
4 3N8K D1X 0.03199 0.40258 5.81395
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