Receptor
PDB id Resolution Class Description Source Keywords
6TOG 1.69 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
DMS A:202;
 Invalid;
 none;
 submit data
78.133 C2 H6 O S CS(=O...
CL A:203;
 Invalid;
 none;
 submit data
35.453 Cl [Cl-]
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...
NQH A:201;
 Valid;
 none;
 ic50 = 207 uM
207.659 C10 H10 Cl N3 c1cnc...
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: 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
Ligand no: 2; Ligand: NQH; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 NQH 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: ALA TRP VAL ILE PRO ALA; Similar ligands found: 0
No: Ligand Similarity coefficient
Ligand no: 2; Ligand: NQH; Similar ligands found: 311
No: Ligand Similarity coefficient
1 N7I 0.9347
2 5WU 0.9330
3 PLP 0.9306
4 G6P 0.9302
5 6HP 0.9250
6 CIY 0.9218
7 EOL 0.9190
8 SBK 0.9189
9 ARP 0.9169
10 PMP 0.9168
11 FER 0.9162
12 57O 0.9146
13 15A 0.9126
14 YO5 0.9122
15 EGR 0.9121
16 G1P 0.9121
17 GJK 0.9118
18 3RI 0.9106
19 NFM 0.9088
20 P7Y 0.9081
21 CR1 0.9078
22 5OO 0.9073
23 505 0.9072
24 A1Y 0.9072
25 NBG 0.9071
26 9F8 0.9067
27 YTX 0.9052
28 STT 0.9047
29 BG6 0.9039
30 JR2 0.9031
31 PRZ 0.9027
32 DHY 0.9023
33 F52 0.9016
34 4MX 0.9012
35 M6P 0.9008
36 QBM 0.9006
37 H7Y 0.9003
38 IOP 0.9002
39 UFO 0.8999
40 AC2 0.8997
41 DHC 0.8995
42 APS 0.8992
43 4R1 0.8992
44 ABF 0.8991
45 KTW 0.8989
46 GRX 0.8989
47 SYR 0.8970
48 4XS 0.8970
49 F69 0.8969
50 MPK 0.8969
51 C9E 0.8968
52 3C4 0.8966
53 EXL 0.8966
54 54X 0.8960
55 2HC 0.8959
56 NPA 0.8954
57 TB8 0.8949
58 4KL 0.8949
59 QMS 0.8946
60 61M 0.8943
61 PYU 0.8942
62 FF2 0.8941
63 BGP 0.8940
64 PXP 0.8940
65 HPT 0.8938
66 CKU 0.8937
67 GI4 0.8935
68 KLK 0.8933
69 TRP 0.8932
70 KYA 0.8932
71 AEH 0.8932
72 TOH 0.8928
73 CFA 0.8928
74 ESI 0.8920
75 1QP 0.8915
76 FUZ 0.8914
77 XFE 0.8914
78 AX3 0.8911
79 F5C 0.8910
80 L21 0.8910
81 AMR 0.8909
82 4XV 0.8909
83 3LJ 0.8908
84 9KH 0.8907
85 O2Y 0.8907
86 8GK 0.8906
87 42J 0.8904
88 BPY 0.8902
89 LDP 0.8900
90 IAC 0.8899
91 MNP 0.8896
92 DI6 0.8894
93 VXX 0.8891
94 NPL 0.8891
95 ZIP 0.8890
96 MXD 0.8889
97 2LY 0.8888
98 T6Z 0.8887
99 OSB 0.8884
100 2K8 0.8880
101 IBM 0.8879
102 K3Q 0.8877
103 9BF 0.8874
104 KED 0.8870
105 B21 0.8870
106 MP5 0.8869
107 JND 0.8869
108 IPD 0.8862
109 D6G 0.8860
110 9GP 0.8859
111 MFZ 0.8856
112 MQB 0.8852
113 TSS 0.8850
114 LNR 0.8846
115 EV0 0.8845
116 GLP 0.8845
117 4ME 0.8844
118 28S 0.8843
119 M3Q 0.8843
120 S3C 0.8842
121 IPT 0.8840
122 KG1 0.8840
123 PLR 0.8838
124 535 0.8837
125 GO8 0.8835
126 F06 0.8835
127 2KU 0.8835
128 ALN 0.8831
129 C4L 0.8830
130 M5H 0.8825
131 22L 0.8825
132 TLM 0.8822
133 H35 0.8822
134 EMZ 0.8821
135 HJB 0.8819
136 FTV 0.8817
137 8U3 0.8817
138 BDI 0.8816
139 AS3 0.8815
140 C9M 0.8815
141 MD6 0.8814
142 AAN 0.8812
143 SLY 0.8810
144 DTR 0.8809
145 6Q3 0.8807
146 CLU 0.8806
147 ALE 0.8806
148 B61 0.8804
149 SRO 0.8804
150 X04 0.8802
151 2LT 0.8802
152 NLA 0.8801
153 W8G 0.8797
154 49O 0.8797
155 692 0.8795
156 ZON 0.8794
157 XQI 0.8793
158 96R 0.8792
159 BIO 0.8788
160 1QV 0.8786
161 3B4 0.8785
162 H4B 0.8779
163 M4E 0.8779
164 N3W 0.8778
165 ZSP 0.8777
166 ASC 0.8776
167 HBI 0.8775
168 SQ4 0.8775
169 JYT 0.8775
170 EXR 0.8774
171 3Y7 0.8773
172 7AP 0.8770
173 RP5 0.8767
174 N91 0.8765
175 8HC 0.8765
176 YOF 0.8763
177 Q5M 0.8763
178 6DP 0.8762
179 MPP 0.8762
180 7WR 0.8762
181 FCD 0.8761
182 EYV 0.8760
183 5OF 0.8760
184 I59 0.8758
185 0LH 0.8758
186 6XI 0.8757
187 HBO 0.8757
188 B2J 0.8756
189 GT0 0.8756
190 HHR 0.8756
191 L46 0.8755
192 TSR 0.8755
193 PH2 0.8750
194 5V7 0.8749
195 LIP 0.8746
196 7I2 0.8746
197 TRF 0.8743
198 OX2 0.8743
199 BGC 0.8740
200 BCK 0.8739
201 IOS 0.8738
202 512 0.8737
203 H4E 0.8736
204 GDE 0.8732
205 UQ1 0.8731
206 N8Y 0.8731
207 7MX 0.8730
208 4GP 0.8729
209 BRH 0.8727
210 5JT 0.8725
211 67Y 0.8723
212 A9O 0.8721
213 CCV 0.8721
214 AMQ 0.8720
215 ITW 0.8719
216 AY4 0.8716
217 4AB 0.8715
218 6VD 0.8713
219 K37 0.8713
220 P0P 0.8711
221 JXK 0.8709
222 CH9 0.8708
223 I2E 0.8706
224 ONZ 0.8703
225 SG2 0.8701
226 OMD 0.8700
227 CP6 0.8698
228 SNY 0.8697
229 H2B 0.8697
230 6J9 0.8697
231 68A 0.8694
232 MOK 0.8694
233 BHS 0.8690
234 SJK 0.8689
235 CXH 0.8687
236 56N 0.8687
237 5WN 0.8683
238 DTE 0.8681
239 MFR 0.8679
240 NYL 0.8677
241 0J5 0.8676
242 50C 0.8676
243 B23 0.8672
244 2LX 0.8671
245 8W9 0.8671
246 R2P 0.8670
247 1A7 0.8669
248 NVU 0.8666
249 AKD 0.8666
250 I4D 0.8661
251 RGG 0.8659
252 KF5 0.8659
253 MMS 0.8659
254 2FX 0.8658
255 BB4 0.8656
256 AIN 0.8654
257 DAH 0.8653
258 TQU 0.8650
259 JYK 0.8650
260 JF2 0.8647
261 NAG 0.8642
262 9UL 0.8641
263 A7K 0.8640
264 3VX 0.8639
265 M02 0.8638
266 QUB 0.8637
267 QIF 0.8636
268 5E4 0.8633
269 TLE 0.8633
270 4Z9 0.8631
271 HJ8 0.8628
272 3GC 0.8627
273 CX4 0.8626
274 0FK 0.8625
275 BK9 0.8622
276 HL4 0.8622
277 AJD 0.8621
278 BZE 0.8619
279 9R5 0.8617
280 KYN 0.8617
281 4Z1 0.8612
282 PQZ 0.8607
283 FP1 0.8605
284 0W1 0.8603
285 GI2 0.8603
286 F6P 0.8599
287 8NX 0.8595
288 EYY 0.8593
289 FNA 0.8591
290 BQ5 0.8588
291 B4O 0.8583
292 UFV 0.8582
293 I3E 0.8579
294 JRB 0.8575
295 8Y7 0.8573
296 BPW 0.8566
297 KP6 0.8566
298 V1T 0.8563
299 AM1 0.8563
300 R9Y 0.8559
301 TLG 0.8554
302 YPN 0.8545
303 89J 0.8543
304 MIG 0.8539
305 UAN 0.8536
306 BP7 0.8535
307 PO6 0.8534
308 8WT 0.8531
309 TYE 0.8524
310 IYR 0.8510
311 KMY 0.8503
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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