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Receptor
PDB id Resolution Class Description Source Keywords
4LY1 1.57 Å EC: 3.5.1.98 STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH INHIBITOR 4-(ACETYL [2-AMINO-5-(THIOPHEN-2-YL)PHENYL]BENZAMIDE HOMO SAPIENS DEACETYLASE HISTONE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: HISTONE DEACETYLASE (HDAC) INHIBITOR KINETIC RATE C CORRELATE WITH CELLULAR HISTONE ACETYLATION BUT NOT TRANSCRIPTION AND CELL VIABILITY. J.BIOL.CHEM. V. 288 26926 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
20Y C:406;
B:408;
A:407;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 0.0563 uM
351.422 C19 H17 N3 O2 S CC(=O...
NA B:403;
C:403;
A:403;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
CA C:402;
A:402;
B:402;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
PG4 A:404;
B:407;
A:405;
C:404;
B:406;
A:406;
C:405;
B:405;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
194.226 C8 H18 O5 C(COC...
ZN B:401;
C:401;
A:401;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
NHE B:404;
Invalid;
none;
submit data
207.29 C8 H17 N O3 S C1CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MAX 2.05 Å EC: 3.5.1.98 CRYSTAL STRUCTURE OF HUMAN HDAC2 COMPLEXED WITH AN N-(2-AMIN BENZAMIDE HOMO SAPIENS CLASS 2 HDAC FOOT POCKET HYDROLASE
Ref.: EXPLORATION OF THE HDAC2 FOOT POCKET: SYNTHESIS AND SUBSTITUTED N-(2-AMINOPHENYL)BENZAMIDES. BIOORG.MED.CHEM.LETT. V. 20 3142 2010
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5IX0 ic50 = 0.168 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
2 4LY1 ic50 = 0.0563 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
3 4LXZ ic50 = 0.251 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
4 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
5 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
6 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5IX0 ic50 = 0.168 uM 6EZ C20 H21 F N2 O2 c1cc(ccc1c....
2 4LY1 ic50 = 0.0563 uM 20Y C19 H17 N3 O2 S CC(=O)Nc1c....
3 4LXZ ic50 = 0.251 uM SHH C14 H20 N2 O3 c1ccc(cc1)....
4 6G3O - EL8 C18 H20 F3 N3 O5 C[C@H](CCC....
5 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
6 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
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: 20Y; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 20Y 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MAX; Ligand: LLX; Similar sites found with APoc: 66
This union binding pocket(no: 1) in the query (biounit: 3max.bio2) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1WUW TSU None
2 2IMP LAC 1.3624
3 4HNN LYS 1.44509
4 5AHO TLA 2.08333
5 6EWZ GTP 2.1097
6 5U83 ZN8 2.35849
7 2HHP FLC 2.7248
8 3JQG AX6 2.77778
9 2WT9 NIO 2.97872
10 2JHP GUN 2.99728
11 3T3Z 9PL 2.99728
12 2CE7 ADP 3.36134
13 5GLN XYP XYP XYP 3.48837
14 2B4B B33 3.50877
15 3SCH TB6 3.53535
16 3AVR OGA 3.54223
17 4C01 QY9 3.5461
18 6CI9 F3V 3.861
19 3TUR 6CL 4.35967
20 1G2O IMH 4.47761
21 1UGY GLA BGC 4.51128
22 3N8K D1X 4.65116
23 2DC1 CIT 4.66102
24 2GWH PCI 4.69799
25 3B8I OXL 4.90463
26 3N2O AG2 4.90463
27 4K6B GLU 4.96894
28 2GNM MAN 5.15873
29 1UKG MMA 5.15873
30 1Q8V MAN MAN 5.15873
31 2PHU MAN MAN 5.15873
32 2GNB MAN 5.15873
33 1Q8Q MAN MMA 5.15873
34 2GND MAN 5.15873
35 2GN3 MAN 5.15873
36 2PHT MAN MAN MAN 5.15873
37 2GND MAN MMA 5.15873
38 2PHR MAN MAN 5.15873
39 2PHF MAN MAN 5.15873
40 2PHW MAN MAN 5.15873
41 1Q8O MAN MMA 5.15873
42 1Q8P MAN MMA 5.15873
43 4AZC NGW 5.17711
44 2OG2 MLI 5.57103
45 3R51 MMA 5.625
46 5KBE IPH 5.67686
47 5TVM PUT 5.84615
48 2F6U CIT 5.99455
49 5GQX GLC GLC GLC GLC 6.53951
50 3KIF GDL 6.60377
51 3B9Q MLI 6.62252
52 2HIM ASN 6.70391
53 2X2T GAL NGA 7.18954
54 3VOZ 04A 7.30159
55 4XFR CIT 8.44687
56 3BY8 MLT 8.4507
57 3GXO SAH 8.71935
58 1UY4 XYP XYP XYP XYP 8.96552
59 5X2N ALA 12
60 5G1C 9RB 31.0627
61 5G10 6DK 33.7875
62 6FYZ EBE 35.6948
63 5G0G TSN 37.3297
64 5EF7 5OJ 39.5095
65 5G0H E1Z 44.6866
66 1C3R TSN 47.9564
Pocket No.: 2; Query (leader) PDB : 3MAX; Ligand: LLX; Similar sites found with APoc: 16
This union binding pocket(no: 2) in the query (biounit: 3max.bio3) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1SWG BTN 1.5625
2 1DMH MCT 2.89389
3 4XAR 40F 2.99728
4 6FTB M0E 3.33333
5 4M3P HCS 3.81471
6 1FDJ 2FP 3.85675
7 3E7S AT2 4.08719
8 1WUU GLA 4.35967
9 1WS5 MMA 4.51128
10 1KKR 2AS 4.90463
11 2PHX MAN MAN 5.15873
12 2GN3 MMA 5.15873
13 4UYF 73B 6.49351
14 2P1E LAC 6.75241
15 1GPJ CIT 13.3515
16 3K0T BGC 15.3846
Pocket No.: 3; Query (leader) PDB : 3MAX; Ligand: LLX; Similar sites found with APoc: 20
This union binding pocket(no: 3) in the query (biounit: 3max.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 3JQM GTP 1.91083
2 4CCO OGA 2.45232
3 1P4V GLY 2.71186
4 2WZF UDP 2.7248
5 3V1S 0LH 3.10559
6 6F5W KG1 3.54223
7 4USI AKG 3.8961
8 4OUE IPT 4.08719
9 4A59 AMP 4.25532
10 2ZUX RAM 4.35967
11 1JAC AMG 4.51128
12 1M26 GAL A2G 4.51128
13 6GYT GLY LEU GLY ALY GLY GLY ALA ALY ALA 4.96894
14 1Q8S MAN MMA 5.15873
15 5O2J 2PO 5.44959
16 4BJX 73B 5.88235
17 4FLP JQ1 8.40336
18 2Y69 CHD 11.6279
19 5W97 CHD 11.7647
20 5M6N 7H9 16.1017
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