Receptor
PDB id Resolution Class Description Source Keywords
4I91 2 Å EC: 1.14.13.- CRYSTAL STRUCTURE OF CYTOCHROME P450 2B6 (Y226H/K262R) IN CO ALPHA-PINENE. HOMO SAPIENS OXIDOREDUCTASE MEMBRANE PROTEIN CYP2B6 P450 CYTOCHROME PMONOOXYGENASE ENDOPLASMIC RETICULUM HEME IRON MEMBRANEBINDING MICROSOME
Ref.: STRUCTURAL AND THERMODYNAMIC BASIS OF (+)-ALPHA-PIN BINDING TO HUMAN CYTOCHROME P450 2B6. J.AM.CHEM.SOC. V. 135 10433 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CM5 A:504;
A:503;
A:505;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
494.573 C23 H42 O11 C1CCC...
TMH A:506;
 Valid;
 none;
 Kd = 0.22 uM
136.234 C10 H16 CC1=C...
HEM A:501;
 Part of Protein;
 none;
 submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
FRU A:502;
 Invalid;
 none;
 submit data
180.156 C6 H12 O6 C([C@...
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: TMH; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 TMH 1 1
2 85D 0.486486 0.73913
Similar Ligands (3D)
Ligand no: 1; Ligand: TMH; Similar ligands found: 337
No: Ligand Similarity coefficient
1 3OC 0.9664
2 4CS 0.9642
3 FPK 0.9503
4 23B 0.9464
5 CNL 0.9436
6 WTZ 0.9403
7 TLA 0.9387
8 PCA 0.9372
9 UYA 0.9330
10 AC5 0.9330
11 UY7 0.9326
12 QFH 0.9314
13 VAH 0.9265
14 THE 0.9252
15 2XX 0.9235
16 2AS 0.9216
17 BDR 0.9199
18 GLU 0.9193
19 5HY 0.9184
20 CAM 0.9183
21 PRO 0.9182
22 RSF 0.9182
23 ISD 0.9182
24 TAR 0.9176
25 LMR 0.9176
26 AKG 0.9176
27 ASN 0.9172
28 ASP 0.9170
29 THR 0.9164
30 IT9 0.9164
31 NCM 0.9159
32 26D 0.9157
33 SKJ 0.9157
34 ILE 0.9153
35 34V 0.9148
36 MLT 0.9140
37 IQ0 0.9134
38 PRS 0.9130
39 XYL 0.9128
40 RB0 0.9128
41 RUU 0.9126
42 ASC 0.9123
43 IMR 0.9123
44 URA 0.9121
45 TEO 0.9113
46 FUB 0.9110
47 CMS 0.9108
48 2DR 0.9106
49 HZP 0.9103
50 VAL 0.9103
51 KMT 0.9101
52 R1X 0.9099
53 R2B 0.9099
54 TFB 0.9099
55 SF6 0.9097
56 192 0.9097
57 RBL 0.9092
58 DPR 0.9091
59 4RW 0.9091
60 QDK 0.9090
61 DUC 0.9086
62 32O 0.9080
63 XLS 0.9068
64 HY3 0.9061
65 CRN 0.9060
66 IOM 0.9056
67 RNS 0.9053
68 SRT 0.9052
69 CRS 0.9047
70 RIP 0.9047
71 ORN 0.9047
72 2TQ 0.9046
73 YHO 0.9046
74 RP7 0.9046
75 HPY 0.9045
76 MRZ 0.9043
77 308 0.9042
78 2AL 0.9038
79 LER 0.9035
80 ROR 0.9034
81 DAS 0.9029
82 UGC 0.9027
83 2BN 0.9027
84 SNE 0.9023
85 8EZ 0.9021
86 HDA 0.9019
87 PBE 0.9016
88 Z6J 0.9007
89 PAV 0.9006
90 3V4 0.9003
91 SF9 0.9003
92 RIB 0.9003
93 AKB 0.8996
94 HYP 0.8990
95 FAC 0.8987
96 XUL 0.8987
97 DTL 0.8983
98 4PW 0.8980
99 O7U 0.8979
100 0MK 0.8967
101 FRU 0.8967
102 HCS 0.8963
103 ABE 0.8963
104 LEU 0.8959
105 GIF 0.8956
106 H76 0.8955
107 DMV 0.8955
108 DIG 0.8954
109 CAE 0.8953
110 CP 0.8952
111 98J 0.8948
112 FX1 0.8948
113 HSE 0.8947
114 AUD 0.8944
115 PAF 0.8942
116 IFL 0.8941
117 AHR 0.8939
118 AGK 0.8939
119 DFU 0.8936
120 51F 0.8934
121 DPF 0.8933
122 ITN 0.8929
123 XYS 0.8925
124 PTO 0.8924
125 1AB 0.8923
126 HGQ 0.8923
127 MET 0.8922
128 N7P 0.8922
129 284 0.8921
130 IDH 0.8921
131 H3M 0.8913
132 OAA 0.8912
133 TCM 0.8909
134 NXA 0.8908
135 CAH 0.8907
136 6UA 0.8907
137 LRH 0.8906
138 MRY 0.8906
139 I2M 0.8905
140 EDG 0.8904
141 DMJ 0.8904
142 T2C 0.8902
143 FUF 0.8900
144 4XR 0.8899
145 8EW 0.8895
146 GG6 0.8895
147 BMA 0.8894
148 3SY 0.8893
149 4NG 0.8893
150 1LN 0.8892
151 NVA 0.8891
152 WBU 0.8891
153 YTB 0.8886
154 URF 0.8883
155 5DI 0.8883
156 LG5 0.8883
157 CYT 0.8882
158 3SL 0.8880
159 BDF 0.8879
160 KIV 0.8878
161 BVF 0.8876
162 8GF 0.8875
163 IPM 0.8874
164 OEM 0.8872
165 FUL 0.8872
166 LG3 0.8871
167 RCO 0.8870
168 KDF 0.8869
169 SVJ 0.8868
170 285 0.8865
171 PPR 0.8860
172 3DY 0.8859
173 URQ 0.8859
174 40O 0.8859
175 GLL 0.8856
176 ARA 0.8850
177 FLA 0.8849
178 KPL 0.8849
179 3ZQ 0.8847
180 XXR 0.8845
181 LDU 0.8845
182 3CH 0.8841
183 IF7 0.8838
184 1XX 0.8838
185 GCS 0.8837
186 TNE 0.8837
187 ADE 0.8835
188 CIG 0.8831
189 CIZ 0.8830
190 ADO 0.8828
191 ARB 0.8823
192 SIN 0.8823
193 7HP 0.8822
194 LNO 0.8820
195 APY 0.8820
196 M3T 0.8814
197 ALO 0.8813
198 FSG 0.8812
199 NMJ 0.8811
200 SER 0.8809
201 TZE 0.8808
202 03W 0.8807
203 C2A 0.8802
204 HEW 0.8802
205 B3R 0.8801
206 ICN 0.8800
207 4DX 0.8798
208 4H2 0.8797
209 DXX 0.8795
210 SEJ 0.8789
211 SYN 0.8787
212 MEV 0.8787
213 LFR 0.8780
214 CYS 0.8773
215 RNT 0.8772
216 RAM 0.8771
217 SPV 0.8771
218 MLI 0.8770
219 DGJ 0.8769
220 FA1 0.8766
221 FPI 0.8762
222 PAE 0.8760
223 23W 0.8760
224 BGC 0.8757
225 IHG 0.8753
226 DSN 0.8752
227 PRI 0.8751
228 MLA 0.8749
229 PYG 0.8743
230 HHQ 0.8741
231 AI2 0.8738
232 6JN 0.8737
233 13P 0.8732
234 3PG 0.8732
235 DZX 0.8731
236 FUC 0.8726
237 9X7 0.8725
238 9X6 0.8724
239 2PG 0.8722
240 IFM 0.8718
241 WDL 0.8718
242 1P3 0.8715
243 HPA 0.8712
244 0OC 0.8710
245 280 0.8708
246 DGL 0.8706
247 5AC 0.8705
248 GLA 0.8704
249 6PC 0.8704
250 A1U 0.8703
251 2PN 0.8702
252 SOE 0.8701
253 FCN 0.8697
254 PEP 0.8694
255 GAL 0.8692
256 NMG 0.8688
257 149 0.8682
258 ADM 0.8680
259 GLY PRO 0.8679
260 FUD 0.8679
261 ICC 0.8676
262 BAE 0.8676
263 MAN 0.8672
264 MFU 0.8670
265 BFM 0.8669
266 TZZ 0.8667
267 SSN 0.8667
268 S0H 0.8666
269 GLC 0.8665
270 MWM 0.8664
271 KOJ 0.8663
272 TM7 0.8662
273 XYP 0.8661
274 9HX 0.8658
275 AX2 0.8657
276 4ZE 0.8657
277 9DA 0.8655
278 3AY 0.8654
279 3XX 0.8654
280 FCB 0.8652
281 HY1 0.8652
282 MCT 0.8651
283 13X 0.8650
284 MFB 0.8649
285 TB6 0.8648
286 CGB 0.8645
287 HT4 0.8642
288 RM4 0.8641
289 7VD 0.8639
290 TDR 0.8639
291 6HQ 0.8639
292 DFB 0.8638
293 PM6 0.8637
294 1DQ 0.8634
295 ARW 0.8632
296 MAE 0.8630
297 L3Q 0.8630
298 4HO 0.8629
299 282 0.8627
300 5ZE 0.8626
301 URP 0.8623
302 HIU 0.8622
303 FPY 0.8622
304 QIC 0.8621
305 NBE 0.8619
306 XYD 0.8615
307 PRZ 0.8612
308 ICP 0.8612
309 XBZ 0.8608
310 PYJ 0.8605
311 911 0.8605
312 3Z7 0.8604
313 1MC 0.8604
314 286 0.8598
315 G4D 0.8592
316 ZZ3 0.8590
317 7EX 0.8589
318 MBD 0.8589
319 HYN 0.8588
320 ABN 0.8586
321 SAL 0.8582
322 5UC 0.8576
323 MMA 0.8561
324 3MC 0.8560
325 MED 0.8558
326 HIS 0.8557
327 BZX 0.8553
328 SS2 0.8551
329 5MH 0.8549
330 L60 0.8543
331 K6H 0.8530
332 BTE 0.8530
333 HV2 0.8529
334 2A7 0.8525
335 271 0.8524
336 ODV 0.8524
337 PGA 0.8512
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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