Receptor
PDB id Resolution Class Description Source Keywords
2FDW 2.05 Å EC: 1.14.14.1 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 WITH THE INHIBITOR (5-(PYRIDIN-3-YL)FURAN-2-YL)METHANAMINE BOUND HOMO SAPIENS CYP2A6 P450 2A6 P450 MONOOXYGENASE DRUG METABOLIZING ENZYME COUMARIN 7-HYDROXYLASE NICOTINE OXIDASE OXIDOREDUCTASE
Ref.: SYNTHETIC INHIBITORS OF CYTOCHROME P-450 2A6: INHIBITORY ACTIVITY, DIFFERENCE SPECTRA, MECHANISM OF INHIBITION, AND PROTEIN COCRYSTALLIZATION. J.MED.CHEM. V. 49 6987 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
D3G A:501;
B:501;
C:501;
D:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 130 nM
174.199 C10 H10 N2 O c1cc(...
HEM A:500;
B:500;
C:500;
D:500;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
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
2FDW 2.05 Å EC: 1.14.14.1 CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 2A6 WITH THE INHIBITOR (5-(PYRIDIN-3-YL)FURAN-2-YL)METHANAMINE BOUND HOMO SAPIENS CYP2A6 P450 2A6 P450 MONOOXYGENASE DRUG METABOLIZING ENZYME COUMARIN 7-HYDROXYLASE NICOTINE OXIDASE OXIDOREDUCTASE
Ref.: SYNTHETIC INHIBITORS OF CYTOCHROME P-450 2A6: INHIBITORY ACTIVITY, DIFFERENCE SPECTRA, MECHANISM OF INHIBITION, AND PROTEIN COCRYSTALLIZATION. J.MED.CHEM. V. 49 6987 2006
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 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....
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: D3G; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 D3G 1 1
2 D1G 0.625 0.657895
3 D2G 0.612245 0.818182
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found: 82
This union binding pocket(no: 1) in the query (biounit: 2fdw.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4A2A ATP 0.01901 0.4041 1.90931
2 3GYT DL4 0.01129 0.4204 2.45902
3 5EW9 5VC 0.03227 0.44359 2.95203
4 3L9R L9R 0.03488 0.40652 3.06122
5 1BGQ RDC 0.02489 0.40712 3.11111
6 4JD3 PLM 0.01234 0.4403 3.11615
7 2E3N 6CM 0.01895 0.41941 3.13725
8 4QWT ACD 0.02521 0.40549 3.15126
9 2Q2Y MKR 0.01435 0.45509 3.54223
10 2Q2Y ADP 0.01435 0.45509 3.54223
11 3KDU NKS 0.01433 0.43931 3.61011
12 5CHR 4NC 0.003715 0.40847 3.64964
13 3T03 3T0 0.01316 0.40646 3.87324
14 1RDT 570 0.02503 0.40426 3.87324
15 2VWA PTY 0.0123 0.40376 3.9604
16 5AAV GW5 0.0216 0.43408 3.96825
17 2P4Y C03 0.01067 0.44791 3.97112
18 2OBD PCW 0.02439 0.41133 3.9916
19 3OZ2 OZ2 0.02299 0.4161 4.03023
20 2QE4 JJ3 0.04625 0.41361 4.03226
21 3FUR Z12 0.01691 0.43376 4.04412
22 1FM9 570 0.01419 0.4236 4.04412
23 3H0A D30 0.01742 0.41511 4.04412
24 3G9E RO7 0.04492 0.40067 4.05904
25 1H9G COA MYR 0.01005 0.4274 4.11523
26 1JQ9 PHE LEU SER TYR LYS 0.03112 0.40806 4.13223
27 1D6H COA 0.03051 0.41899 4.13437
28 3LN0 52B 0.01895 0.42664 4.41176
29 5B4B LP5 0.02133 0.41316 4.43548
30 4ORM FMN 0.01123 0.45522 4.48878
31 4ORM 2V6 0.01123 0.45522 4.48878
32 4ORM ORO 0.01123 0.45522 4.48878
33 5L2J 70E 0.03042 0.43211 5
34 5L2J 6UL 0.029 0.43211 5
35 4HBM 0Y7 0.01303 0.41052 5
36 5ICK FEZ 0.00408 0.45672 5.67686
37 4WT2 3UD 0.0227 0.41049 5.71429
38 4OAS 2SW 0.009159 0.41205 6.25
39 5UR1 YY9 0.01777 0.41852 6.43087
40 1BZL FAD 0.03126 0.44359 6.72269
41 1ATL 0QI 0.01358 0.41477 6.93069
42 4MNS 2AX 0.003718 0.47112 7.54717
43 2Z7I 742 0.03831 0.427 7.64706
44 3UP3 XCA 0.01074 0.42151 7.81893
45 4X6F 3XU 0.01345 0.43363 7.82918
46 3TMK T5A 0.02718 0.40887 7.87037
47 2Z77 HE7 0.02387 0.40386 7.91367
48 5G3N X28 0.009841 0.42015 8.66142
49 2F99 AKV 0.02044 0.40078 9.80392
50 4JGX PLM 0.01265 0.40521 10.0775
51 5HCV 60R 0.01789 0.4071 10.8949
52 3S0E EOL 0.01129 0.40762 10.9244
53 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.002007 0.42737 12.381
54 5IBE 69M 0.0071 0.44631 13.1313
55 2WM4 VGJ 0.0005771 0.4753 13.5632
56 3A51 VDY 0.004114 0.43122 13.8686
57 1RE9 DSO 0.01178 0.42244 14.4928
58 2WH8 II2 0.008034 0.40758 14.5278
59 4JX1 CAH 0.0005321 0.40764 14.6988
60 3LXI CAM 0.009218 0.41005 17.5772
61 5XJN 88L 0.001071 0.45482 18.2418
62 3KXC PLM 0.01672 0.41322 18.5567
63 4B7S QLE 0.0001498 0.51314 18.8073
64 3NA0 2DC 0.02243 0.40049 18.896
65 4OQR 2UO 0.01308 0.40231 19.256
66 3ZSN MIV 0.007491 0.43801 19.4245
67 3WVS RRM 0.001724 0.45802 19.7007
68 4ZE0 VOR 0.005318 0.44572 20.4082
69 5GWE GWM 0.005999 0.41363 20.4938
70 1Z8O DEB 0.003208 0.45281 22.0297
71 5TZ1 VT1 0.01221 0.41373 22.0588
72 4LWU 20U 0.01102 0.40814 22.3529
73 4J6C STR 0.0004557 0.46684 23.1707
74 2Y69 CHD 0.006946 0.42193 25.6757
75 5L92 C0R 0.006692 0.43924 25.8537
76 5L92 MLA 0.004792 0.43924 25.8537
77 3ABA FLI 0.003711 0.45514 28.0397
78 4UHL VFV 0.006306 0.42985 39.4619
79 4DVQ 1CA 0.0007304 0.44929 42.8571
80 3UA1 08Y 0.0277 0.41956 44.3277
81 3MDV CL6 0.0002687 0.51578 45.3947
82 4NKW PLO 0.00004896 0.53052 48.7395
Pocket No.: 2; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found: 25
This union binding pocket(no: 2) in the query (biounit: 2fdw.bio4) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DLY 5D7 0.03372 0.41317 1.8797
2 1YUC EPH 0.02211 0.40978 2.7451
3 3V66 D3A 0.03083 0.41527 2.94118
4 5DM1 SAH 0.048 0.40396 2.99625
5 4JD3 COA 0.04502 0.40893 3.11615
6 5JE0 SAH 0.04087 0.40179 3.23887
7 5JE0 AZ8 0.04087 0.40179 3.23887
8 3PE6 ZYH 0.01673 0.41173 3.30033
9 3OVR 5SP 0.0126 0.4164 3.94737
10 3BGD SAH 0.01773 0.40562 4.23077
11 1XJD STU 0.02031 0.40092 4.34783
12 3H7J PPY 0.01601 0.40021 4.52675
13 4BQH 9VU 0.01887 0.40067 4.62185
14 2X68 CTE 0.009872 0.41047 5.26316
15 5VQ4 ICS 0.03093 0.40091 6.30252
16 1SO2 666 0.01701 0.40097 7.38095
17 4L77 CNL 0.002171 0.43463 8.79397
18 5U7D 19F 0.01634 0.41917 9.85507
19 4BNU 9KQ 0.02537 0.40101 10.7807
20 5A0U CHT 0.007631 0.40414 11.1345
21 3E8T UQ8 0.02747 0.42829 12.2727
22 2GKL PD2 0.01191 0.40428 14.978
23 3TIK JKF 0.008184 0.41444 37.8855
24 2CI0 1CM 0.004862 0.40407 38.4615
25 4C0C WVH 0.01782 0.41721 43.2548
Pocket No.: 3; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found: 10
This union binding pocket(no: 3) in the query (biounit: 2fdw.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1Z45 GAL 0.03347 0.40173 3.15126
2 4R29 SAM 0.01057 0.41905 5.35714
3 5U9J GER 0.00372 0.44643 5.91716
4 2XFH CL6 0.0002453 0.43438 10.7056
5 5D3U TRP 0.01056 0.42803 19.3277
6 1Q5D EPB 0.001517 0.40671 21.0024
7 2YOO K2B 0.003877 0.42007 21.1302
8 3N9Y CLR 0.0007611 0.41864 21.1499
9 3MZS HC9 0.000947 0.41483 22.0588
10 3TL1 JRO 0.03376 0.40153 24.5283
Pocket No.: 4; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 2fdw.bio3) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4WCX SAM 0.01568 0.40998 2.31092
2 2WPX ACO 0.02071 0.40049 3.24484
3 3TKY SAH 0.01376 0.41114 4.8913
4 5IXH OTP 0.03842 0.41185 7.45342
5 1B7H LYS NLE LYS 0.0406 0.40301 7.98319
6 3RET PYR 0.01538 0.40106 12.8713
7 3RET SAL 0.01538 0.40106 12.8713
8 1QY1 PRZ 0.01678 0.4085 13.2184
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