Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:380;
B:380;
C:380;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
LLX A:400;
B:400;
C:400;
Valid;
Valid;
Valid;
none;
none;
none;
ic50 = 0.027 uM
288.343 C19 H16 N2 O c1ccc...
NA A:381;
B:381;
C:381;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
NHE A:383;
Invalid;
none;
submit data
207.29 C8 H17 N O3 S C1CCC...
ZN A:379;
B:379;
C:379;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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 (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
5 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 5IWG ic50 = 0.062 uM IWX C18 H19 F N2 O2 c1cc(ccc1c....
5 3MAX ic50 = 0.027 uM LLX C19 H16 N2 O c1ccc(cc1)....
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: LLX; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LLX 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: 34
This union binding pocket(no: 1) in the query (biounit: 3max.bio2) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5U83 ZN8 0.03562 0.4003 2.35849
2 2JHP GUN 0.007707 0.42713 2.99728
3 2B4B B33 0.01982 0.40886 3.50877
4 3AVR OGA 0.03647 0.40005 3.54223
5 4L6H HCS 0.02714 0.40709 4.35967
6 1G2O IMH 0.008339 0.41227 4.47761
7 1UGY GLA BGC 0.0146 0.40395 4.51128
8 3N8K D1X 0.01611 0.40995 4.65116
9 2GNB MAN 0.01393 0.4212 5.15873
10 1Q8Q MAN MMA 0.01737 0.41652 5.15873
11 2GND MAN 0.02064 0.41422 5.15873
12 2GN3 MAN 0.01503 0.4116 5.15873
13 2PHT MAN MAN MAN 0.027 0.40764 5.15873
14 2GND MAN MMA 0.02623 0.40732 5.15873
15 2PHR MAN MAN 0.02763 0.40613 5.15873
16 2PHF MAN MAN 0.02922 0.40485 5.15873
17 2PHW MAN MAN 0.02971 0.40447 5.15873
18 2GN3 MMA 0.0211 0.40295 5.15873
19 2OG2 MLI 0.009666 0.41733 5.57103
20 5KBE IPH 0.03395 0.4014 5.67686
21 5TVM PUT 0.03382 0.40127 5.84615
22 3B9Q MLI 0.01602 0.41529 6.62252
23 3IP5 ALA 0.03381 0.40228 6.81199
24 2X2T GAL NGA 0.01555 0.4044 7.18954
25 1OW4 2AN 0.02342 0.40184 7.75194
26 4XFR CIT 0.02257 0.41245 8.44687
27 3BY8 MLT 0.02713 0.40674 8.4507
28 1UY4 XYP XYP XYP XYP 0.02432 0.40772 8.96552
29 4ZUR 7XA 0.0000001372 0.60189 21.5259
30 2VQO TFG 0.00000003451 0.70138 35.6948
31 5G0G TSN 0.00000001265 0.72346 37.3297
32 5EF7 5OJ 0.00000002842 0.58431 39.5095
33 5G0H E1Z 0.00000000219 0.72621 44.6866
34 1C3R TSN 0.000000001286 0.56458 47.9564
Pocket No.: 2; Query (leader) PDB : 3MAX; Ligand: LLX; Similar sites found: 6
This union binding pocket(no: 2) in the query (biounit: 3max.bio3) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WZF UDP 0.01718 0.40113 2.7248
2 2ET1 GLV 0.03629 0.40026 3.81471
3 1APZ ASP 0.0219 0.41144 4.25532
4 3BF8 MLA 0.02242 0.40591 5.88235
5 4UYF 73B 0.03055 0.40383 6.49351
6 2P1E LAC 0.00466 0.43889 6.75241
Pocket No.: 3; Query (leader) PDB : 3MAX; Ligand: LLX; Similar sites found: 7
This union binding pocket(no: 3) in the query (biounit: 3max.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CCO OGA 0.03547 0.40175 2.45232
2 3V1S 0LH 0.02558 0.40612 3.10559
3 4K6B GLU 0.02736 0.40774 4.96894
4 1Q8S MAN MMA 0.02397 0.41019 5.15873
5 4FLP JQ1 0.02698 0.40989 8.40336
6 2Y69 CHD 0.03107 0.40831 11.6279
7 5M6N 7H9 0.0279 0.40905 16.1017
Feedback