Receptor
PDB id Resolution Class Description Source Keywords
3QOA 2.1 Å EC: 1.14.13.- CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/K262 COMPLEX WITH THE INHIBITOR 4-BENZYLPYRIDINE. HOMO SAPIENS P450 CYTOCHROME P450 2B6 MONOOXYGENASE MEMBRANE PROTEIN ENDOPLASMIC RETICULUM HEME IRON MEMBRANE METAL BINDINGMIRCOSOME PHOSPHOPROTEIN OXIDOREDUCTASE-OXIDOREDUCTASE INCOMPLEX
Ref.: STRUCTURES OF CYTOCHROME P450 2B6 BOUND TO 4-BENZYL AND 4-(4-NITROBENZYL)PYRIDINE: INSIGHT INTO INHIBIT BINDING AND REARRANGEMENT OF ACTIVE SITE SIDE CHAIN MOL.PHARMACOL. V. 80 1047 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
3QO A:501;
 Valid;
 none;
 Kd = 0.21 uM
169.222 C12 H11 N c1ccc...
CM5 A:604;
A:605;
 Invalid;
Invalid;
 none;
none;
 submit data
494.573 C23 H42 O11 C1CCC...
HEM A:500;
 Part of Protein;
 none;
 submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4RQL 2.1 Å EC: 1.14.13.- CRYSTAL STRUCTURE OF A HUMAN CYTOCHROME P450 2B6 (Y226H/K262 COMPLEX WITH A MONOTERPENE - SABINENE HOMO SAPIENS P450 CYTOCHROME P450 2B6 MONOOXYGENASE MEMBRANE PROTEIN ENDOPLASMIC RETICULUM HEME IRON METAL BINDING MICROSOMEOXIDOREDUCTASE
Ref.: STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF HUMA CYTOCHROMES P450 2B6 AND 2A6 BOUND TO VOLATILE HYDR ANALYSIS AND COMPARISON. MOL.PHARMACOL. V. 87 649 2015
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 4RRT Kd = 1.82 uM 3V4 C10 H16 CC1=CC[C@H....
2 4ZV8 - TMH C10 H16 CC1=CC[C@@....
3 5UEC - 85D C10 H15 Br CC1([C@@H]....
4 3IBD - CPZ C9 H7 Cl N2 c1cc(ccc1c....
5 5UAP - 82S C10 H17 Br C[C@@]12CC....
6 4RQL Kd = 0.08 uM SNE C10 H16 CC(C)[C@@]....
7 4I91 Kd = 0.22 uM TMH C10 H16 CC1=CC[C@@....
8 5UFG - 85D C10 H15 Br CC1([C@@H]....
9 3QOA Kd = 0.21 uM 3QO C12 H11 N c1ccc(cc1)....
10 5UDA - CAE C10 H18 CC1(C2CCC1....
70% Homology Family (42)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3T3R Ki = 101 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
2 2FDY - D4G C10 H8 N2 S2 c1cnccc1SS....
3 2FDV Ki = 800 nM D2G C11 H12 N2 O CNCc1ccc(o....
4 4EJH Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
5 3EBS Kd = 21 uM N4E C10 H13 N O2 CCOc1ccc(c....
6 1Z10 Kd = 0.27 uM COU C9 H6 O2 c1ccc2c(c1....
7 4EJI Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
8 2FDU Ki = 14200 nM D1G C12 H14 N2 O CN(C)Cc1cc....
9 2FDW Ki = 130 nM D3G C10 H10 N2 O c1cc(cnc1)....
10 2P85 - IND C8 H7 N c1ccc2c(c1....
11 1Z11 Kd = 1.9 uM 8MO C12 H8 O4 COc1c2c(cc....
12 4EJJ Kd = 470 uM NCT C10 H14 N2 C[N@@]1CCC....
13 4EJG - NCT C10 H14 N2 C[N@@]1CCC....
14 3T3Q Ki = 49 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
15 5E58 Kd = 2.3 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
16 1NR6 Kd ~ 50 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
17 1N6B Kd = 20 uM DMZ C17 H17 N3 O2 S Cc1ccc(cc1....
18 4RRT Kd = 1.82 uM 3V4 C10 H16 CC1=CC[C@H....
19 4ZV8 - TMH C10 H16 CC1=CC[C@@....
20 5UEC - 85D C10 H15 Br CC1([C@@H]....
21 3IBD - CPZ C9 H7 Cl N2 c1cc(ccc1c....
22 5UAP - 82S C10 H17 Br C[C@@]12CC....
23 4RQL Kd = 0.08 uM SNE C10 H16 CC(C)[C@@]....
24 4I91 Kd = 0.22 uM TMH C10 H16 CC1=CC[C@@....
25 5UFG - 85D C10 H15 Br CC1([C@@H]....
26 3QOA Kd = 0.21 uM 3QO C12 H11 N c1ccc(cc1)....
27 5UDA - CAE C10 H18 CC1(C2CCC1....
28 2NNJ Ki = 90 nM 225 C18 H19 Cl2 N O4 CCOC(=O)C1....
29 3G5N ic50 = 0.035 uM PB2 C16 H14 N2 c1ccc(cc1)....
30 3TMZ ic50 = 2 uM 06X C20 H25 Cl N2 O5 CCOC(=O)C1....
31 2BDM ic50 = 0.9 uM TMI C22 H18 N2 c1ccc(cc1)....
32 4JLT Kd = 0.7 uM 8PR C19 H20 F N O3 c1cc(ccc1[....
33 4MGJ - CPZ C9 H7 Cl N2 c1cc(ccc1c....
34 1SUO ic50 = 0.04 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
35 5W0C - 9W6 C15 H12 N4 O4 S2 CCOC(=O)NC....
36 4NZ2 Kd = 2 uM 2QJ C16 H12 Br Cl F3 N O4 S C[C@@](C(=....
37 5X24 - LSN C22 H23 Cl N6 O CCCCc1nc(c....
38 5X23 - LSN C22 H23 Cl N6 O CCCCc1nc(c....
39 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
40 5XXI - LSN C22 H23 Cl N6 O CCCCc1nc(c....
41 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
42 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
50% Homology Family (46)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3T3R Ki = 101 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
2 2FDY - D4G C10 H8 N2 S2 c1cnccc1SS....
3 2FDV Ki = 800 nM D2G C11 H12 N2 O CNCc1ccc(o....
4 4EJH Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
5 3EBS Kd = 21 uM N4E C10 H13 N O2 CCOc1ccc(c....
6 1Z10 Kd = 0.27 uM COU C9 H6 O2 c1ccc2c(c1....
7 4EJI Kd = 4.4 uM 0QA C10 H13 N3 O2 CN(CCCC(=O....
8 2FDU Ki = 14200 nM D1G C12 H14 N2 O CN(C)Cc1cc....
9 2FDW Ki = 130 nM D3G C10 H10 N2 O c1cc(cnc1)....
10 2P85 - IND C8 H7 N c1ccc2c(c1....
11 1Z11 Kd = 1.9 uM 8MO C12 H8 O4 COc1c2c(cc....
12 4EJJ Kd = 470 uM NCT C10 H14 N2 C[N@@]1CCC....
13 4EJG - NCT C10 H14 N2 C[N@@]1CCC....
14 3T3Q Ki = 49 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
15 5E58 Kd = 2.3 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
16 1NR6 Kd ~ 50 uM DIF C14 H11 Cl2 N O2 c1ccc(c(c1....
17 1N6B Kd = 20 uM DMZ C17 H17 N3 O2 S Cc1ccc(cc1....
18 4RRT Kd = 1.82 uM 3V4 C10 H16 CC1=CC[C@H....
19 4ZV8 - TMH C10 H16 CC1=CC[C@@....
20 5UEC - 85D C10 H15 Br CC1([C@@H]....
21 3IBD - CPZ C9 H7 Cl N2 c1cc(ccc1c....
22 5UAP - 82S C10 H17 Br C[C@@]12CC....
23 4RQL Kd = 0.08 uM SNE C10 H16 CC(C)[C@@]....
24 4I91 Kd = 0.22 uM TMH C10 H16 CC1=CC[C@@....
25 5UFG - 85D C10 H15 Br CC1([C@@H]....
26 3QOA Kd = 0.21 uM 3QO C12 H11 N c1ccc(cc1)....
27 5UDA - CAE C10 H18 CC1(C2CCC1....
28 2NNJ Ki = 90 nM 225 C18 H19 Cl2 N O4 CCOC(=O)C1....
29 4XRZ ic50 = 0.37 uM SI6 C16 H16 F2 N4 O S c1cc(c(cc1....
30 4WNU - QDN C20 H24 N2 O2 COc1ccc2c(....
31 4WNV - QI9 C20 H24 N2 O2 COc1ccc2c(....
32 4XRY ic50 = 13.9 uM SI5 C17 H18 F2 N4 O S Cn1cc(cn1)....
33 3G5N ic50 = 0.035 uM PB2 C16 H14 N2 c1ccc(cc1)....
34 3TMZ ic50 = 2 uM 06X C20 H25 Cl N2 O5 CCOC(=O)C1....
35 2BDM ic50 = 0.9 uM TMI C22 H18 N2 c1ccc(cc1)....
36 4JLT Kd = 0.7 uM 8PR C19 H20 F N O3 c1cc(ccc1[....
37 4MGJ - CPZ C9 H7 Cl N2 c1cc(ccc1c....
38 1SUO ic50 = 0.04 uM CPZ C9 H7 Cl N2 c1cc(ccc1c....
39 5W0C - 9W6 C15 H12 N4 O4 S2 CCOC(=O)NC....
40 4NZ2 Kd = 2 uM 2QJ C16 H12 Br Cl F3 N O4 S C[C@@](C(=....
41 5X24 - LSN C22 H23 Cl N6 O CCCCc1nc(c....
42 5X23 - LSN C22 H23 Cl N6 O CCCCc1nc(c....
43 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
44 5XXI - LSN C22 H23 Cl N6 O CCCCc1nc(c....
45 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
46 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 3QO; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 3QO 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 3QO; Similar ligands found: 394
No: Ligand Similarity coefficient
1 1BN 0.9771
2 54F 0.9750
3 BZQ 0.9685
4 HX8 0.9671
5 M6H 0.9664
6 LL2 0.9610
7 3VW 0.9583
8 11X 0.9573
9 M5E 0.9570
10 0OL 0.9569
11 N2Y 0.9568
12 9W5 0.9514
13 CH8 0.9504
14 4FP 0.9490
15 GNW 0.9485
16 TZM 0.9480
17 HXY 0.9472
18 C82 0.9468
19 FPL 0.9466
20 MJ5 0.9446
21 N9J 0.9435
22 PFF 0.9409
23 TYR 0.9398
24 DTY 0.9398
25 S0F 0.9393
26 SOJ 0.9391
27 PPY 0.9388
28 YIE 0.9386
29 YOF 0.9384
30 PHE 0.9368
31 3IP 0.9353
32 2J5 0.9334
33 4TB 0.9325
34 DAH 0.9320
35 848 0.9320
36 6J5 0.9315
37 MMS 0.9312
38 AHN 0.9311
39 ENO 0.9307
40 J4K 0.9300
41 YIP 0.9293
42 EQW 0.9289
43 XI7 0.9278
44 4PN 0.9273
45 4BF 0.9256
46 NFA 0.9252
47 A7Q 0.9249
48 C53 0.9248
49 B3U 0.9243
50 FK8 0.9239
51 C0H 0.9237
52 0QW 0.9235
53 22F 0.9232
54 DXG 0.9221
55 HIC 0.9220
56 8OE 0.9211
57 PHI 0.9208
58 4ZD 0.9207
59 0OY 0.9203
60 O45 0.9199
61 HCI 0.9195
62 2UB 0.9194
63 0OO 0.9191
64 1YO 0.9189
65 OJD 0.9186
66 SLY 0.9182
67 IYR 0.9181
68 56D 0.9181
69 GLR 0.9172
70 A6H 0.9170
71 GZ2 0.9169
72 P58 0.9168
73 A8K 0.9168
74 DHC 0.9163
75 TOH 0.9159
76 YIH 0.9156
77 5O5 0.9155
78 RLG 0.9154
79 BPY 0.9151
80 DPN 0.9146
81 OA1 0.9143
82 CUT 0.9142
83 8OB 0.9141
84 TIH 0.9138
85 CXP 0.9137
86 TCC 0.9135
87 7ZL 0.9134
88 BNL 0.9133
89 JZA 0.9133
90 S8V 0.9128
91 CLU 0.9128
92 1PS 0.9127
93 DCN 0.9126
94 OOG 0.9120
95 9VQ 0.9120
96 HFA 0.9115
97 PUE 0.9115
98 6HO 0.9110
99 H48 0.9106
100 SB7 0.9106
101 TRP 0.9105
102 AOT 0.9102
103 M2E 0.9095
104 XRX 0.9094
105 0A9 0.9094
106 D4G 0.9093
107 7QS 0.9093
108 HNL 0.9090
109 LVD 0.9083
110 EYV 0.9083
111 LJ4 0.9082
112 DIR 0.9082
113 E79 0.9079
114 GGB 0.9076
115 SHI 0.9070
116 TYE 0.9070
117 7VY 0.9068
118 NCT 0.9067
119 1L5 0.9062
120 KYN 0.9060
121 C6Z 0.9060
122 A3M 0.9047
123 HIS 0.9046
124 2LT 0.9043
125 R2P 0.9040
126 XRS 0.9040
127 S7A 0.9040
128 CMU 0.9037
129 EYJ 0.9036
130 AX4 0.9036
131 Q9Z 0.9035
132 EXG 0.9022
133 7R4 0.9021
134 E9P 0.9018
135 5TO 0.9017
136 5PV 0.9017
137 4LV 0.9013
138 61M 0.9012
139 HNK 0.9009
140 NNH 0.9005
141 SV4 0.9005
142 D8Y 0.9004
143 YZM 0.9003
144 CUH 0.9001
145 1VK 0.9000
146 3YP 0.9000
147 HL4 0.8998
148 MES 0.8993
149 HPP 0.8987
150 AHC 0.8983
151 TCL 0.8982
152 BDJ 0.8980
153 KPV 0.8979
154 Z70 0.8978
155 ARG 0.8978
156 7Q1 0.8971
157 TZP 0.8971
158 JRB 0.8970
159 9PL 0.8968
160 K80 0.8967
161 P2L 0.8965
162 PPT 0.8964
163 FHC 0.8964
164 R9J 0.8959
165 DTR 0.8958
166 B41 0.8956
167 ALE 0.8954
168 2NP 0.8951
169 I2E 0.8951
170 JFM 0.8951
171 F06 0.8948
172 R9V 0.8942
173 S46 0.8939
174 DBE 0.8938
175 PO6 0.8938
176 TYC 0.8935
177 PCS 0.8935
178 F63 0.8933
179 BRH 0.8931
180 J0Z 0.8931
181 11C 0.8929
182 QME 0.8924
183 Q04 0.8924
184 6ZX 0.8923
185 GVQ 0.8919
186 ERZ 0.8919
187 4EU 0.8918
188 1X4 0.8918
189 GAE 0.8917
190 XDK 0.8915
191 6J9 0.8915
192 HLP 0.8913
193 5LD 0.8905
194 GCO 0.8904
195 R9G 0.8904
196 S7V 0.8899
197 HHH 0.8899
198 FB4 0.8898
199 S2P 0.8898
200 DHI 0.8897
201 PQT 0.8895
202 RE4 0.8894
203 5DL 0.8891
204 7BC 0.8889
205 DUR 0.8887
206 API 0.8887
207 3IL 0.8887
208 S7G 0.8886
209 PBN 0.8884
210 AVA 0.8878
211 KDG 0.8877
212 50Q 0.8877
213 DCZ 0.8873
214 3H2 0.8869
215 78U 0.8867
216 3CR 0.8864
217 92G 0.8861
218 HHV 0.8858
219 CS2 0.8857
220 EXR 0.8857
221 7Y3 0.8852
222 CUQ 0.8852
223 23N 0.8850
224 4LW 0.8849
225 SAF 0.8849
226 PBA 0.8848
227 HJH 0.8846
228 CIR 0.8845
229 AKG 0.8842
230 V15 0.8841
231 ZON 0.8841
232 6C5 0.8841
233 HHI 0.8838
234 BNF 0.8838
235 0OP 0.8836
236 IOS 0.8835
237 LVP 0.8834
238 RP3 0.8832
239 G14 0.8831
240 1OH 0.8829
241 F90 0.8828
242 LSQ 0.8826
243 ILO 0.8826
244 X6P 0.8824
245 3W1 0.8820
246 4HP 0.8819
247 PRO GLY 0.8817
248 LNR 0.8816
249 Y4L 0.8815
250 JF5 0.8815
251 B40 0.8811
252 2GA 0.8811
253 GLU 0.8809
254 50C 0.8807
255 CLT 0.8807
256 OGA 0.8807
257 Q06 0.8806
258 CFA 0.8800
259 PW1 0.8797
260 M74 0.8797
261 HNH 0.8796
262 BP3 0.8795
263 0L1 0.8792
264 4MP 0.8791
265 MQB 0.8790
266 URO 0.8784
267 EQA 0.8780
268 DNB 0.8779
269 2JX 0.8778
270 2OH 0.8778
271 DHY 0.8777
272 4WF 0.8775
273 KPA 0.8773
274 EYY 0.8770
275 ICB 0.8767
276 A18 0.8766
277 XIF XYP 0.8765
278 173 0.8765
279 CWD 0.8765
280 2IT 0.8764
281 XQI 0.8762
282 D3G 0.8757
283 3C4 0.8754
284 6FZ 0.8751
285 36M 0.8751
286 9BF 0.8743
287 7UC 0.8742
288 PH3 0.8738
289 C1M 0.8736
290 7O4 0.8735
291 7VP 0.8733
292 FWD 0.8732
293 7OD 0.8729
294 41K 0.8727
295 XYH 0.8723
296 MP5 0.8723
297 GLO 0.8722
298 TCA 0.8720
299 DZA 0.8717
300 L13 0.8715
301 46P 0.8712
302 1A5 0.8712
303 536 0.8712
304 DGN 0.8711
305 F4E 0.8710
306 ISA 0.8709
307 JA3 0.8707
308 TQL 0.8706
309 HX4 0.8703
310 0NX 0.8699
311 2B4 0.8694
312 RP5 0.8693
313 TLM 0.8693
314 0QA 0.8690
315 AEG 0.8690
316 G8V 0.8689
317 8U3 0.8685
318 D2G 0.8685
319 69K 0.8683
320 5WZ 0.8680
321 ATX 0.8680
322 TAG 0.8680
323 3VR 0.8677
324 531 0.8676
325 NYL 0.8674
326 F98 0.8673
327 12R 0.8673
328 2JJ 0.8673
329 3LR 0.8670
330 IAC 0.8670
331 PLP 0.8669
332 PIR 0.8669
333 7C3 0.8668
334 YPN 0.8667
335 E4P 0.8665
336 AX5 0.8664
337 XYP XIF 0.8664
338 LUQ 0.8663
339 HSX 0.8659
340 EGV 0.8655
341 LTT 0.8652
342 1KN 0.8651
343 URS 0.8648
344 WCU 0.8647
345 ZZU 0.8647
346 SOR 0.8646
347 PRA 0.8642
348 F52 0.8641
349 DI6 0.8637
350 657 0.8637
351 27M 0.8637
352 DBS 0.8634
353 AMQ 0.8634
354 ABF 0.8627
355 X48 0.8623
356 4TP 0.8621
357 FNA 0.8617
358 96Z 0.8616
359 ENV 0.8616
360 363 0.8616
361 9X3 0.8614
362 B4O 0.8614
363 GO8 0.8605
364 GVG 0.8604
365 2HG 0.8604
366 3HP 0.8600
367 JOV 0.8598
368 DLT 0.8596
369 D1G 0.8594
370 3XH 0.8593
371 DAR 0.8593
372 9RW 0.8592
373 RES 0.8588
374 GWM 0.8587
375 IOP 0.8582
376 LPK 0.8576
377 JF6 0.8576
378 AAN 0.8572
379 TT4 0.8567
380 FT2 0.8562
381 HSO 0.8560
382 PLR 0.8558
383 Q03 0.8554
384 8XL 0.8552
385 E0O 0.8551
386 PV4 0.8551
387 AVI 0.8550
388 FOM 0.8546
389 DGL 0.8543
390 2DL 0.8539
391 BZS 0.8526
392 HO6 0.8523
393 QY9 0.8517
394 C5A 0.8509
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RQL; Ligand: SNE; 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: 4rql.bio2) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4RQL; Ligand: SNE; 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: 4rql.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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