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Receptor
PDB id Resolution Class Description Source Keywords
3sff 2 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HUMAN HDAC8 INHIBITOR COMPLEX, AN AMINO DERIVED INHIBITOR HOMO SAPIENS DEACETYLASE NVP-LCI785 HYDROLASE-HYDROLASE INHIBITOR COMPL
Ref.: HUMAN HDAC ISOFORM SELECTIVITY ACHIEVED VIA EXPLOIT THE ACETATE RELEASE CHANNEL WITH STRUCTURALLY UNIQU MOLECULE INHIBITORS. BIOORG.MED.CHEM. V. 19 4626 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0DI A:378;
Valid;
none;
ic50 = 200 nM
407.842 C20 H20 Cl F2 N3 O2 c1cc(...
K A:401;
A:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
39.098 K [K+]
ZN A:403;
Part of Protein;
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: 0DI; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 0DI 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: 30
This union binding pocket(no: 1) in the query (biounit: 2v5x.bio1) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 4XFR CIT 1.54639
2 3T3Z 9PL 1.89076
3 4YSW URC 2.31959
4 3JQ9 AX1 2.77778
5 5GQX GLC GLC GLC GLC 2.83505
6 3IP6 PRO 3.37079
7 3R51 MMA 3.75
8 1UGY GLA GLC 3.7594
9 1WS5 MMA 3.7594
10 4H69 10Y 4.12371
11 2QS8 MET 4.12371
12 3BY8 MLT 4.22535
13 6FMC DUE 4.43038
14 4M3P HCS 4.63918
15 2OG2 MLI 4.73538
16 3CQO FUC 4.77816
17 6EWZ GTP 5.06329
18 6B2W AG2 5.1051
19 3B9Q MLI 5.62914
20 3N8K D1X 5.81395
21 3W6X HZP 6.11354
22 5TQZ GLC 7.33333
23 5X2N ALA 10.2222
24 5G10 6DK 30.8707
25 5G1C 9RB 37.2973
26 5G0H E1Z 38.9175
27 5G0G TSN 39.2105
28 5EF7 5OJ 42.5824
29 1C3R TSN 45.0667
30 6FYZ EBE 45.1031
Pocket No.: 2; Query (leader) PDB : 2V5X; Ligand: V5X; Similar sites found with APoc: 7
This union binding pocket(no: 2) in the query (biounit: 2v5x.bio2) has 64 residues
No: Leader PDB Ligand Sequence Similarity
1 1A78 TDG 2.23881
2 3JQB DX6 2.77778
3 2VAR AMP 2.8754
4 3OO6 GAL 3.09278
5 5AHO TLA 3.86905
6 2CYC TYR 5.06667
7 1KJ1 MAN 5.50459
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