Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CM5 B:505;
A:504;
A:502;
A:503;
B:503;
B:504;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
494.573 C23 H42 O11 C1CCC...
HEM B:501;
A:501;
Part of Protein;
Part of Protein;
none;
none;
submit data
616.487 C34 H32 Fe N4 O4 Cc1c2...
SNE B:502;
A:505;
Valid;
Valid;
none;
none;
Kd = 0.08 uM
136.234 C10 H16 CC(C)...
EDO A:506;
B:506;
Invalid;
Invalid;
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
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 11 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 (39)
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 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 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
38 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
39 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
50% Homology Family (43)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 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 1R9O - FLP C15 H13 F O2 C[C@@H](c1....
42 5K7K ic50 = 36 nM 6RJ C19 H12 Cl N5 O3 S2 c1cc(c(cc1....
43 3T3Z Ki = 765 uM 9PL C11 H16 N2 O2 CC[C@H]1[C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SNE; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 SNE 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4RQL; Ligand: SNE; Similar sites found: 31
This union binding pocket(no: 1) in the query (biounit: 4rql.bio2) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4YZC STU 0.04595 0.40697 2.22222
2 4V24 GYR 0.02524 0.4087 2.42588
3 4P6X HCY 0.0185 0.40981 2.7451
4 1LSH PLD 0.0197 0.42089 2.94118
5 1QM5 GLC GLC GLC PO4 SGC GLC 0.03763 0.40902 2.94118
6 5JNN 6LM 0.0226 0.41097 3.15789
7 3LXI CAM 0.006767 0.41271 3.56295
8 1MEX RAC 0.01165 0.40982 3.72093
9 1MJJ HAL 0.01639 0.41813 4.56621
10 4GJY OGA 0.01072 0.40232 4.68085
11 4MO2 FDA 0.04412 0.4098 5.43478
12 4P6C RES 0.01015 0.41657 5.46218
13 2YAJ 4HP 0.00961 0.41534 5.88235
14 5IXH OTP 0.03366 0.417 6.21118
15 1JW0 GUA 0.01188 0.40355 6.96203
16 4ZW9 GLC 0.02325 0.40189 7.35294
17 4ZW9 BGC 0.02325 0.40189 7.35294
18 1CZI PRO PHI SMC NOR 0.01478 0.41833 8.97833
19 3OJI PYV 0.01111 0.42133 11.6402
20 1WKR IVA VAL VAL STA ALA STA 0.02813 0.40245 14.4118
21 2Z3U CRR 0.03236 0.40893 16.7059
22 2X5W K2B 0.003198 0.45706 18.6364
23 4B7S QLE 0.01987 0.41146 20.4128
24 2XFH CL6 0.02417 0.41573 20.9246
25 4J6C STR 0.00138 0.42731 31.2195
26 1ZOA 140 0.01317 0.43744 35.2941
27 2A06 SMA 0.02591 0.4197 35.4839
28 2VE3 REA 0.01303 0.41268 37.6126
29 3MDV CL6 0.02613 0.41675 42.1053
30 4NKW PLO 0.004857 0.43832 48.7395
31 2HI4 BHF 0.001281 0.46593 49.3697
Pocket No.: 2; Query (leader) PDB : 4RQL; Ligand: SNE; Similar sites found: 79
This union binding pocket(no: 2) in the query (biounit: 4rql.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3QXV MTX 0.01067 0.41293 None
2 1BWO LPC 0.01992 0.40134 None
3 3F3E LEU 0.04685 0.40361 1.47059
4 2CHN NGT 0.005533 0.42272 1.89076
5 1YOK P6L 0.01377 0.43003 1.95312
6 1YUC EPH 0.01905 0.41311 1.96078
7 4ZBR DIF 0.03126 0.40796 2.10084
8 4ZBR NPS 0.02977 0.40796 2.10084
9 3B12 FAH 0.00687 0.41862 2.30263
10 2Z6D FMN 0.01894 0.40243 2.30769
11 4QJR PIZ 0.01583 0.41588 2.44898
12 1ZDT PEF 0.01427 0.41674 2.48963
13 3BQD DAY 0.00751 0.42604 2.7451
14 4M26 SIN 0.02037 0.41025 2.74725
15 4M26 ZZU 0.02037 0.41025 2.74725
16 4JD3 COA 0.01188 0.44031 2.83286
17 1CX4 CMP 0.01132 0.41166 2.95082
18 2ZCQ B65 0.03635 0.41401 3.07167
19 4LSJ LSJ 0.01692 0.40831 3.10078
20 1YNH SUO 0.01242 0.41982 3.27511
21 5K52 OCD 0.01191 0.41598 3.39623
22 5KBE IPH 0.009894 0.40794 3.49345
23 3KFC 61X 0.02499 0.41078 3.55731
24 4RC8 STE 0.01935 0.40698 3.6036
25 1GCK ASP PLP 0.01209 0.41394 3.63636
26 2XCG XCG 0.03361 0.40403 3.78151
27 3T03 3T0 0.01766 0.40017 3.87324
28 4OAR 2S0 0.004748 0.43419 3.87597
29 5HYR EST 0.01537 0.40107 3.87597
30 2XUM OGA 0.00257 0.40784 4.29799
31 4CYI ATP 0.01972 0.4033 4.3379
32 3OVR 5SP 0.006034 0.43252 4.38596
33 3GN8 DEX 0.002627 0.44698 4.81928
34 2Q2Y MKR 0.04358 0.42749 4.83193
35 2Q2Y ADP 0.04358 0.42749 4.83193
36 3E8T UQ8 0.01148 0.44924 5
37 1ADO 13P 0.0303 0.40137 5.50964
38 2WKQ FMN 0.01441 0.40835 6.3253
39 2WCJ M21 0.02487 0.40145 6.38298
40 3AJH BL3 0.02001 0.40124 6.45161
41 5APK 76E 0.02808 0.40569 6.79245
42 5NTW 98N 0.02418 0.41032 7.00389
43 2GJ3 FAD 0.01995 0.40131 7.5
44 4JGX PLM 0.01195 0.40641 7.75194
45 1YYE 196 0.01095 0.40827 7.83582
46 4MNS 2AX 0.005546 0.46171 8.1761
47 1BC5 SAH 0.02089 0.40682 8.17844
48 1XVB BHL 0.03209 0.41341 8.23529
49 2LBD REA 0.01841 0.41109 8.2397
50 3H0A D30 0.02709 0.40522 8.33333
51 1MDC PLM 0.02628 0.40023 8.33333
52 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.002593 0.42242 8.57143
53 5LGA 6VH 0.04063 0.40403 9
54 5HCN DAO 0.004693 0.42381 9.1954
55 4DOL PLM 0.01469 0.40606 9.21659
56 4R38 RBF 0.01085 0.4163 9.28571
57 1JJE BYS 0.01745 0.40597 9.45946
58 4GGZ BTN 0.007353 0.41442 9.56522
59 3OLL EST 0.01022 0.41185 9.58333
60 4O4Z N2O 0.0105 0.40335 9.74026
61 4YZN 4K5 0.01535 0.41206 10.453
62 1UPR 4IP 0.007343 0.41565 11.3821
63 3QDJ ALA ALA GLY ILE GLY ILE LEU THR VAL 0.04139 0.40557 12
64 1PZL MYR 0.01172 0.41091 13.0802
65 5XJN 88L 0.003498 0.40928 13.4066
66 3FS1 MYR 0.01218 0.4081 13.4783
67 5T2Z 017 0.0113 0.42748 14.1414
68 4NJS G08 0.01818 0.41919 14.1414
69 4JX1 CAH 0.004696 0.41025 14.1593
70 5GWE GWM 0.01141 0.40032 15.3086
71 5IBE 69M 0.04335 0.40449 16.9192
72 4OQR 2UO 0.002532 0.41524 19.4748
73 1Z8O DEB 0.005283 0.44172 20.0495
74 5L92 MLA 0.009336 0.42458 23.4146
75 5L92 C0R 0.01285 0.42458 23.4146
76 3ZSN MIV 0.03056 0.4062 28.5372
77 4UBS DIF 0.002013 0.45016 28.7532
78 3A51 VDY 0.004096 0.43131 32.1168
79 4UHL VFV 0.01724 0.40623 38.8655
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