Receptor
PDB id Resolution Class Description Source Keywords
2V5W 2 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HDAC8-SUBSTRATE COMPLEX HOMO SAPIENS HISTONE DEACETYLASE CHROMATIN REGULATOR P53 HDAC HDAC8 REPRESSOR HYDROLASE NUCLEAR PROTEIN PEPTIDIC SUBSTRATE TRANSCRIPTION REGULATION CHROMATIN TRANSCRIPTION DEACETYHYDROLASE-HYDROLASE SUBSTRATE COMPLEX
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
ACE ARG HIS ALY ALY MCM I:1;
L:1;
Valid;
Valid;
none;
none;
submit data
851.987 n/a O=C(N...
GLY GLY GLY G:1;
Invalid;
none;
submit data
174.18 n/a O=C(N...
K A:1378;
A:1379;
B:1377;
B:1378;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
39.098 K [K+]
ZN A:1380;
B:1379;
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: ACE ARG HIS ALY ALY MCM; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 ACE ARG HIS ALY ALY MCM 1 1
2 ARG HIS LYS FDL 0.813559 1
3 ACE ARG HIS LYS ALY MCM 0.643939 0.958904
4 SER ASP ALY MCM 0.619469 0.791667
5 LYS GLY GLY ALA ALY ARG HIS ARG LYS VAL 0.51145 0.726027
6 LYS GLY GLY ALA ALY ARG HIS ARG 0.479167 0.743243
7 ALA LYS PHE ARG HIS ASP 0.459854 0.763889
8 LYS GLY GLY ALA ALY ARG HIS ARG LYS ILE 0.456376 0.716216
9 THR SER ARG HIS LYS ALY LEU MET ALA 0.450331 0.703704
10 ARG ARG LYS TRP ARG ARG TRP HIS LEU 0.42 0.77027
11 ARG HIS LYS ALY LEU MET PHE LYS 0.419355 0.723684
12 ARG ARG LYS TRP CIR ARG TRP HIS LEU 0.418301 0.76
13 ALA ILE LEU HIS ARG LEU LEU GLN 0.416667 0.666667
14 ARG ARG ARG TRP HIS ARG TRP ARG LEU 0.413793 0.756757
15 ILE LEU GLY LYS PHE LEU HIS ARG LEU 0.409091 0.723684
16 GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 0.406667 0.710526
17 ARG GLY 5OL MCM 0.402985 0.789474
18 GLY ALA ARG ALA HIS SER SER 0.40146 0.701299
19 ALA LYS ARG HIS ARG LYS VAL LEU ARG ASP 0.401361 0.69863
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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