Receptor
PDB id Resolution Class Description Source Keywords
6TOF 1.67 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF HUMAN BCL6 BTB DOMAIN IN COMPLEX WITH C HOMO SAPIENS CANCER LYMPHOMA INHIBITOR DEGRADER TRANSCRIPTION
Ref.: ACHIEVINGIN VIVOTARGET DEPLETION THROUGH THE DISCOV OPTIMIZATION OF BENZIMIDAZOLONE BCL6 DEGRADERS. J.MED.CHEM. V. 63 4047 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NQE A:201;
 Valid;
 none;
 ic50 = 86 uM
279.297 C15 H13 N5 O CN1c2...
ALA TRP VAL ILE PRO ALA B:0;
 Valid;
 Atoms found LESS than expected: % Diff = 0.149;
 submit data
555.7 n/a O=C(N...
EDO A:202;
A:205;
A:203;
A:204;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5MW2 2.35 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF BCL-6 BTB-DOMAIN WITH BI-3802 HOMO SAPIENS TRANSCRIPTION INHIBITOR
Ref.: CHEMICALLY INDUCED DEGRADATION OF THE ONCOGENIC TRANSCRIPTION FACTOR BCL6. CELL REP V. 20 2860 2017
Members (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 5MW6 ic50 = 18648 nM RC0 C15 H13 Cl2 N5 Cc1cc(n(n1....
2 5N20 ic50 = 61 uM 8GN C24 H29 N9 O CC(=O)Nc1c....
3 3LBZ Kd = 138 uM Z89 C15 H9 Br N2 O6 S2 c1cc2c(cc1....
4 6TOG ic50 = 207 uM NQH C10 H10 Cl N3 c1cnc(c(c1....
5 6CQ1 Kd = 219 uM F8J C30 H39 N7 O S CC(C)NC(=O....
6 4CP3 - RBT C46 H62 N4 O11 Cc1c(c2c3c....
7 6TOH ic50 = 10.5 uM NQK C15 H12 Cl N5 O CN1c2ccc(c....
8 6TOI ic50 = 1.7 uM NQN C18 H18 Cl N5 O2 C[C@H](CCN....
9 5MW2 ic50 < 3 nM U52 C24 H29 Cl N6 O3 C[C@@H]1C[....
10 6EW6 Kd > 829 uM C0H C9 H8 Cl N5 c1ccc(c(c1....
11 6C3L Kd = 44 uM EGP C31 H39 N7 O2 S CN1CCN(CC1....
12 6TOF ic50 = 86 uM NQE C15 H13 N5 O CN1c2ccc(c....
13 6TON ic50 = 0.097 uM NR5 C25 H35 Cl N6 O3 CC1(CN(CC(....
14 6EW8 - C0Q C21 H25 Cl N6 O3 CN1c2c(cc3....
15 6TOK ic50 = 0.26 uM NQT C22 H26 Cl N7 O2 Cc1cc(n(n1....
16 5N21 Kd = 1.1 uM 8HN C22 H21 N7 O3 c1cc2c(cc1....
17 5MWD ic50 = 632 nM TJ3 C17 H15 Cl N6 O Cc1cc(n(n1....
18 6EW7 ic50 = 2.9 uM C1W C17 H11 Cl2 F N4 O2 c1cc(ccc1N....
19 6TOO ic50 = 5.4 uM NR8 C18 H18 Cl N5 O2 CC[C@@H](C....
20 5N1Z Kd = 0.0065 uM 8GQ C25 H25 N7 O4 c1c2cc(c3c....
70% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6TOM ic50 = 0.52 uM NQZ C24 H31 Cl F2 N6 O2 C[C@@H]1CN....
2 6TOJ ic50 = 0.86 uM NQQ C19 H20 Cl N5 O2 CC(C)(CCN1....
3 5X9O Kd = 5 uM 80R C13 H9 Cl N4 O3 c1cc2c(cc1....
4 5X4P Kd = 9.3 uM 7ZO C12 H9 Cl N4 O c1cc2c(cc1....
5 5X4O Kd = 88 uM YAM C21 H20 F3 N7 O3 S CN(c1c(ccc....
6 5H7H ic50 = 170 uM ACE TRP ARG VAL PRO n/a n/a
7 5X4N Kd = 68 uM 7ZL C10 H9 Cl N4 c1ccc(cc1)....
8 5X4M Kd = 1200 uM 7ZF C9 H9 N5 c1ccc(cc1)....
9 5X4Q Kd = 0.078 uM 7Z6 C18 H15 Cl N6 O c1cc(cnc1)....
10 5X9P ic50 = 0.13 uM 80L C16 H14 Cl N5 O5 c1cc2c(cc1....
11 6TOL ic50 = 0.15 uM NQW C23 H31 Cl N6 O3 C[C@@H]1CN....
12 5MW6 ic50 = 18648 nM RC0 C15 H13 Cl2 N5 Cc1cc(n(n1....
13 5N20 ic50 = 61 uM 8GN C24 H29 N9 O CC(=O)Nc1c....
14 3LBZ Kd = 138 uM Z89 C15 H9 Br N2 O6 S2 c1cc2c(cc1....
15 6TOG ic50 = 207 uM NQH C10 H10 Cl N3 c1cnc(c(c1....
16 6CQ1 Kd = 219 uM F8J C30 H39 N7 O S CC(C)NC(=O....
17 4CP3 - RBT C46 H62 N4 O11 Cc1c(c2c3c....
18 6TOH ic50 = 10.5 uM NQK C15 H12 Cl N5 O CN1c2ccc(c....
19 6TOI ic50 = 1.7 uM NQN C18 H18 Cl N5 O2 C[C@H](CCN....
20 5MW2 ic50 < 3 nM U52 C24 H29 Cl N6 O3 C[C@@H]1C[....
21 6EW6 Kd > 829 uM C0H C9 H8 Cl N5 c1ccc(c(c1....
22 6C3L Kd = 44 uM EGP C31 H39 N7 O2 S CN1CCN(CC1....
23 6TOF ic50 = 86 uM NQE C15 H13 N5 O CN1c2ccc(c....
24 6TON ic50 = 0.097 uM NR5 C25 H35 Cl N6 O3 CC1(CN(CC(....
25 6EW8 - C0Q C21 H25 Cl N6 O3 CN1c2c(cc3....
26 6TOK ic50 = 0.26 uM NQT C22 H26 Cl N7 O2 Cc1cc(n(n1....
27 5N21 Kd = 1.1 uM 8HN C22 H21 N7 O3 c1cc2c(cc1....
28 5MWD ic50 = 632 nM TJ3 C17 H15 Cl N6 O Cc1cc(n(n1....
29 6EW7 ic50 = 2.9 uM C1W C17 H11 Cl2 F N4 O2 c1cc(ccc1N....
30 6TOO ic50 = 5.4 uM NR8 C18 H18 Cl N5 O2 CC[C@@H](C....
31 5N1Z Kd = 0.0065 uM 8GQ C25 H25 N7 O4 c1c2cc(c3c....
50% Homology Family (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6TOM ic50 = 0.52 uM NQZ C24 H31 Cl F2 N6 O2 C[C@@H]1CN....
2 6TOJ ic50 = 0.86 uM NQQ C19 H20 Cl N5 O2 CC(C)(CCN1....
3 5X9O Kd = 5 uM 80R C13 H9 Cl N4 O3 c1cc2c(cc1....
4 5X4P Kd = 9.3 uM 7ZO C12 H9 Cl N4 O c1cc2c(cc1....
5 5X4O Kd = 88 uM YAM C21 H20 F3 N7 O3 S CN(c1c(ccc....
6 5H7H ic50 = 170 uM ACE TRP ARG VAL PRO n/a n/a
7 5X4N Kd = 68 uM 7ZL C10 H9 Cl N4 c1ccc(cc1)....
8 5X4M Kd = 1200 uM 7ZF C9 H9 N5 c1ccc(cc1)....
9 5X4Q Kd = 0.078 uM 7Z6 C18 H15 Cl N6 O c1cc(cnc1)....
10 5X9P ic50 = 0.13 uM 80L C16 H14 Cl N5 O5 c1cc2c(cc1....
11 6TOL ic50 = 0.15 uM NQW C23 H31 Cl N6 O3 C[C@@H]1CN....
12 5MW6 ic50 = 18648 nM RC0 C15 H13 Cl2 N5 Cc1cc(n(n1....
13 5N20 ic50 = 61 uM 8GN C24 H29 N9 O CC(=O)Nc1c....
14 3LBZ Kd = 138 uM Z89 C15 H9 Br N2 O6 S2 c1cc2c(cc1....
15 6TOG ic50 = 207 uM NQH C10 H10 Cl N3 c1cnc(c(c1....
16 6CQ1 Kd = 219 uM F8J C30 H39 N7 O S CC(C)NC(=O....
17 4CP3 - RBT C46 H62 N4 O11 Cc1c(c2c3c....
18 6TOH ic50 = 10.5 uM NQK C15 H12 Cl N5 O CN1c2ccc(c....
19 6TOI ic50 = 1.7 uM NQN C18 H18 Cl N5 O2 C[C@H](CCN....
20 5MW2 ic50 < 3 nM U52 C24 H29 Cl N6 O3 C[C@@H]1C[....
21 6EW6 Kd > 829 uM C0H C9 H8 Cl N5 c1ccc(c(c1....
22 6C3L Kd = 44 uM EGP C31 H39 N7 O2 S CN1CCN(CC1....
23 6TOF ic50 = 86 uM NQE C15 H13 N5 O CN1c2ccc(c....
24 6TON ic50 = 0.097 uM NR5 C25 H35 Cl N6 O3 CC1(CN(CC(....
25 6EW8 - C0Q C21 H25 Cl N6 O3 CN1c2c(cc3....
26 6TOK ic50 = 0.26 uM NQT C22 H26 Cl N7 O2 Cc1cc(n(n1....
27 5N21 Kd = 1.1 uM 8HN C22 H21 N7 O3 c1cc2c(cc1....
28 5MWD ic50 = 632 nM TJ3 C17 H15 Cl N6 O Cc1cc(n(n1....
29 6EW7 ic50 = 2.9 uM C1W C17 H11 Cl2 F N4 O2 c1cc(ccc1N....
30 6TOO ic50 = 5.4 uM NR8 C18 H18 Cl N5 O2 CC[C@@H](C....
31 5N1Z Kd = 0.0065 uM 8GQ C25 H25 N7 O4 c1c2cc(c3c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NQE; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 NQE 1 1
2 NQK 0.52 0.903846
Ligand no: 2; Ligand: ALA TRP VAL ILE PRO ALA; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 ALA TRP VAL ILE PRO ALA 1 1
2 ACE TRP ARG VAL PRO 0.565574 0.833333
3 IPF 0.53125 0.828125
4 ALA VAL PRO TRP 0.521739 0.915254
5 SER PRO LEU ASP SER LEU TRP TRP ILE 0.482269 0.823529
6 TRP GLU TYR ILE PRO ASN VAL 0.47973 0.823529
7 SER TRP PHE PRO 0.471545 0.772727
8 GLY GLU GLU TRP GLY PRO TRP VAL NH2 0.466667 0.870968
9 TRP PRO TRP 0.464912 0.833333
10 PRO ARG PRO ILE LEU LEU PRO TRP ARG NH2 0.452703 0.861538
11 ASN GLN DPR TRP GLN 0.443609 0.836066
12 LEU LEU TRP ASN GLY PRO ILE ALA VAL 0.442953 0.875
13 ALA LEU TRP GLY PHE VAL PRO VAL LEU 0.440789 0.887097
14 MET TYR TRP TYR PRO TYR 0.439716 0.779412
15 ACE TRP HIS THR ALA NH2 NH2 0.435484 0.646154
16 ASP TRP GLU ILE VAL 0.428571 0.721311
17 ALA SER LEU ASN LEU PRO ALA VAL SER TRP 0.427632 0.808824
18 ALA LEU TRP GLY PHE PHE PRO VAL LEU 0.424837 0.887097
19 GLU PRO GLN ALA PRO TRP MET GLU GLN 0.422819 0.846154
20 GLY SER ASP PRO TRP LYS 0.42029 0.761194
21 ASN ARG PRO VAL TYR ILE PRO PRO PRO PRO 0.41791 0.828125
22 MET VAL TRP GLY PRO ASP PRO LEU TYR VAL 0.416667 0.763889
23 MET ASN TRP ASN ILE 0.415254 0.65625
24 ACE PRO TRP ALA THR CYS ASP SER NH2 0.414966 0.771429
25 ALA ASN SER ARG TRP PRO ALY SER ILE ILE 0.410714 0.746667
26 ALA ASN SER ARG TRP PRO THR SER ALY ILE 0.410714 0.736842
27 MET TRP ARG PRO TRP 0.408163 0.768116
28 SER SER VAL ILE GLY VAL TRP TYR LEU 0.408163 0.633803
29 LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.407186 0.716216
30 LYS VAL PRO ARG ASN GLN ASP TRP LEU 0.407186 0.774648
31 MDL 0.40625 0.731343
32 ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 0.405714 0.811594
33 LEU LEU TRP ALA GLY PRO MET ALA VAL 0.405229 0.861538
34 ALA ASN SER ARG TRP PRO THR THR ARG LEU 0.403846 0.733333
35 ACE GLU TRP TRP TRP 0.403509 0.672131
36 THR SER THR THR SER VAL ALA SER SER TRP 0.4 0.626866
Similar Ligands (3D)
Ligand no: 1; Ligand: NQE; Similar ligands found: 82
No: Ligand Similarity coefficient
1 7ZO 0.9364
2 TCT 0.9170
3 LI4 0.9158
4 DMB 0.9142
5 MYC 0.9128
6 KTM 0.9115
7 9FN 0.9080
8 2QU 0.9072
9 WCU 0.9057
10 2L2 0.9043
11 VXM 0.9005
12 FL9 0.9000
13 NPZ 0.8994
14 38E 0.8954
15 LU2 0.8949
16 3Q0 0.8937
17 NAB 0.8935
18 MXA 0.8902
19 OUA 0.8888
20 A0R 0.8887
21 D59 0.8887
22 EUN 0.8886
23 Q11 0.8870
24 MRE 0.8869
25 KS5 0.8868
26 D4O 0.8844
27 B5A 0.8838
28 NAL 0.8833
29 CDX 0.8830
30 ZW2 0.8814
31 5F7 0.8806
32 T5J 0.8786
33 D5F 0.8786
34 1V8 0.8783
35 FE5 0.8769
36 D4X 0.8754
37 KTV 0.8751
38 BUX 0.8750
39 GLC GLA 0.8746
40 NOJ BGC 0.8737
41 A5W 0.8734
42 RE2 0.8733
43 338 0.8726
44 NKH 0.8725
45 STL 0.8724
46 BC3 0.8713
47 IXG 0.8708
48 TH1 0.8707
49 4KN 0.8707
50 P2C 0.8706
51 5R9 0.8706
52 UAY 0.8694
53 PNW 0.8689
54 GAL NPO 0.8688
55 147 0.8687
56 CX5 0.8685
57 IW4 0.8684
58 KVN 0.8684
59 KUP 0.8682
60 94M 0.8678
61 GLC GLC 0.8678
62 ZZ1 GLA 0.8641
63 4YF 0.8638
64 NQN 0.8635
65 BNY 0.8629
66 5YA 0.8628
67 CMG 0.8626
68 5XK 0.8625
69 DX6 0.8607
70 HH2 0.8607
71 LFK 0.8602
72 6FX 0.8600
73 NIY 0.8584
74 C4E 0.8575
75 5RU 0.8574
76 35G 0.8555
77 80R 0.8554
78 0X2 0.8550
79 HA6 0.8546
80 O9Q 0.8539
81 CMP 0.8539
82 907 0.8538
Ligand no: 2; Ligand: ALA TRP VAL ILE PRO ALA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5MW2; Ligand: U52; 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: 5mw2.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5MW2; Ligand: U52; 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: 5mw2.bio1) has 44 residues
No: Leader PDB Ligand Sequence Similarity
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