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Receptor
PDB id Resolution Class Description Source Keywords
3ebs 2.15 Å EC: 1.14.14.1 HUMAN CYTOCHROME P450 2A6 I208S/I300F/G301A/S369G IN COMPLEX WITH PHENACETIN HOMO SAPIENS CYP2A6 P450 2A6 CYP2A13 P450 2A13 MONOOXYGENASE OXIDOREDUCATASE HEME ENDOPLASMIC RETICULUM IRON MEMBRANE METAL-BINDING MICROSOME PHENACETIN OXIDOREDUCTASE POLYMORPHISM
Ref.: KEY RESIDUES CONTROLLING PHENACETIN METABOLISM BY HUMAN CYTOCHROME P4502A ENZYMES. DRUG METAB.DISPOS. V. 36 2582 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
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...
N4E A:1;
B:1;
D:1;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 21 uM
179.216 C10 H13 N O2 CCOc1...
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 (42)
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 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 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 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
Ligand no: 1; Ligand: N4E; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 N4E 1 1
2 TYL 0.461538 0.733333
3 EE8 0.428571 0.823529
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found with APoc: 120
This union binding pocket(no: 1) in the query (biounit: 2fdw.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5J6A P46 1.25
2 5EEH P9P 1.32979
3 4Z87 GDP 1.47059
4 2I56 RNS 1.59817
5 5WIU AQD 1.65877
6 2ZKJ ADP 1.77665
7 4ZBA GDS 1.79372
8 4A2A ATP 1.90931
9 3GYT DL4 2.45902
10 3B6C SDN 2.5641
11 5Y02 HBX 2.80374
12 2EA1 GPG 2.85714
13 5EW9 5VC 2.95203
14 2R40 EPH 3.04183
15 3L9R L9R 3.06122
16 1BGQ RDC 3.11111
17 4JD3 PLM 3.11615
18 2E3N 6CM 3.13725
19 4QWT ACD 3.15126
20 4D7M TDC 3.22581
21 2Q2Y MKR 3.54223
22 2Q2Y ADP 3.54223
23 5W8Q BU4 3.58974
24 3KDU NKS 3.61011
25 5CHR 4NC 3.64964
26 4XU6 TDA 3.80952
27 3T03 3T0 3.87324
28 1RDT 570 3.87324
29 2VWA PTY 3.9604
30 5AAV GW5 3.96825
31 2P4Y C03 3.97112
32 2OBD PCW 3.9916
33 6HH6 A3R 3.9916
34 1CX9 NHP 4.03023
35 3OZ2 OZ2 4.03023
36 2QE4 JJ3 4.03226
37 3FUR Z12 4.04412
38 1FM9 570 4.04412
39 3H0A D30 4.04412
40 1H9G COA MYR 4.11523
41 1JQ9 PHE LEU SER TYR LYS 4.13223
42 1D6H COA 4.13437
43 3LN0 52B 4.41176
44 5B4B LP5 4.43548
45 4ORM ORO 4.48878
46 4ORM FMN 4.48878
47 4ORM 2V6 4.48878
48 3QLM PLM 4.83871
49 5WL1 CUY 5
50 4HBM 0Y7 5
51 3WHB DCC 5.15464
52 5NCB JZ3 5.62347
53 3SCM LGN 5.71429
54 4WT2 3UD 5.71429
55 5C9J DAO 6.04982
56 4OAS 2SW 6.25
57 3ZLR X0B 6.32911
58 3X01 AMP 6.36132
59 5UR1 YY9 6.43087
60 1YRX FMN 6.61157
61 1ATL 0QI 6.93069
62 1Y52 BTN 7.14286
63 5GUE GGS 7.25076
64 6BR8 6OU 7.53968
65 4MNS 2AX 7.54717
66 3G5D 1N1 7.69231
67 3UP3 XCA 7.81893
68 4X6F 3XU 7.82918
69 1UHK CZN 7.8534
70 3TMK T5A 7.87037
71 2Z77 HE7 7.91367
72 3QWB NDP 8.38323
73 5G3N X28 8.66142
74 4WGF HX2 8.78049
75 2F99 AKV 9.80392
76 4JGX PLM 10.0775
77 2XFH CL6 10.7056
78 5HCV 60R 10.8949
79 3S0E EOL 10.9244
80 5A0U CHT 11.1345
81 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 12.381
82 6BLD DXJ 12.6492
83 5IBE 69M 13.1313
84 2WM4 VGJ 13.5632
85 1GNI OLA 13.6555
86 3A51 VDY 13.8686
87 1RE9 DSO 14.4928
88 2WH8 II2 14.5278
89 4JX1 CAM 14.6988
90 4JX1 CAH 14.6988
91 3LXI CAM 17.5772
92 5XJN 88L 18.2418
93 6CR2 LFV 18.2773
94 3KXC PLM 18.5567
95 4B7S QLE 18.8073
96 5FOI MY8 18.8725
97 3NA0 2DC 18.896
98 4OQR 2UO 19.256
99 3ZSN MIV 19.4245
100 2X5W K2B 19.5455
101 3WVS RRM 19.7007
102 4ZE0 VOR 20.4082
103 5GWE GWM 20.4938
104 2YOO K2B 21.1302
105 1Z8O DEB 22.0297
106 5TZ1 VT1 22.0588
107 4LWU 20U 22.3529
108 3R9C ECL 22.7273
109 4J6C STR 23.1707
110 6GK6 MYR 25.3041
111 2Y69 CHD 25.6757
112 5L92 MLA 25.8537
113 5L92 C0R 25.8537
114 3ABA FLI 28.0397
115 5ZCO TGL 29.7872
116 5Z84 CHD 29.7872
117 5ZCO CHD 29.7872
118 4UHL VFV 39.4619
119 3MDV CL6 45.3947
120 4NKW PLO 48.7395
Pocket No.: 2; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found with APoc: 53
This union binding pocket(no: 2) in the query (biounit: 2fdw.bio4) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5DLY 5D7 1.8797
2 4OJP MAL 1.89076
3 2XXP DSL 2.01005
4 2CXS F6P 2.10084
5 4V1T ADP 2.52101
6 5NXX 3Q7 2.61194
7 4M0R 644 2.63852
8 1YUC EPH 2.7451
9 4OHU 2TK 2.76817
10 4OHU NAD 2.76817
11 3V66 D3A 2.94118
12 2UW1 GVM 2.95858
13 5DM1 SAH 2.99625
14 3WCA FPS 3.0137
15 4JD3 COA 3.11615
16 5JE0 SAH 3.23887
17 5JE0 AZ8 3.23887
18 5W7D MYR 3.57143
19 5W7D PX8 3.57143
20 3RUV ANP 3.57143
21 3OKI OKI 3.86266
22 3OVR 5SP 3.94737
23 5T9F NAP 3.9916
24 5T9F TYR 3.9916
25 3BGD SAH 4.23077
26 1XJD STU 4.34783
27 3H7J PPY 4.52675
28 1H41 GCV 4.62185
29 4BQH 9VU 4.62185
30 2X68 CTE 5.26316
31 1GA8 DEL 5.46624
32 5F1R 42O 5.48523
33 3VHH VHH 5.69106
34 6BYM HC3 5.91133
35 1SO2 666 7.38095
36 4JWF SAH 8.75576
37 4L77 CNL 8.79397
38 5ZUN 9JX 9.18033
39 2GQS C2R 9.70464
40 6C7D EOJ 9.94152
41 4BNU 9KQ 10.7807
42 3QUZ QUV 11.6183
43 3E8T UQ8 12.2727
44 1NU4 MLA 14.433
45 2Z3U CRR 17.8824
46 2W9S TOP 21.7391
47 5Z84 TGL 29.7872
48 5W97 CHD 29.7872
49 3TIK JKF 37.8855
50 2CI0 1CM 38.4615
51 4C0C WVH 43.2548
52 6AYB KKK 43.7768
53 3UA1 08Y 44.3277
Pocket No.: 3; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found with APoc: 43
This union binding pocket(no: 3) in the query (biounit: 2fdw.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5M37 9SZ 1.73913
2 2FVK DUC 1.89076
3 5A86 D7E 1.91083
4 4NWJ 3PG 2.31092
5 1V8B ADN 2.52101
6 6CIB ADP 2.65252
7 1YKD CMP 2.73109
8 1YOK P6L 2.73438
9 5NLM IOS 2.94118
10 2H7C COA 2.94118
11 4RHP PEF 2.97872
12 3KPX CZH 3.0303
13 3M3E GAL A2G NPO 3.72671
14 1SO0 GAL 3.77907
15 1OS7 TAU 3.88693
16 5NGL NOJ BGC 3.9916
17 3P9T TCL 4.10959
18 5HCN DAO 4.21456
19 4R29 SAM 5.35714
20 5U9J GER 5.91716
21 3HYW DCQ 6.27907
22 4MGB XDH 6.66667
23 4MG7 27H 6.66667
24 1RV1 IMZ 7.05882
25 2AGC MYR 7.40741
26 1ZEI CRS 7.54717
27 6BJO DUY 8
28 4J25 OGA 9.17031
29 5OLK DTP 9.53488
30 1J6X MET 10
31 2O5L MNR 11.1111
32 1X0P FAD 13.986
33 3P3Z P3Z 15.625
34 6F8A HIS 19.25
35 5D3U TRP 19.3277
36 4UBS DIF 19.3384
37 5EW0 3C7 20.0855
38 1Q5D EPB 21.0024
39 3N9Y CLR 21.1499
40 3MZS HC9 22.0588
41 3TL1 JRO 24.5283
42 5M36 9SZ 39.4737
43 6M7X JD7 43.1818
Pocket No.: 4; Query (leader) PDB : 2FDW; Ligand: D3G; Similar sites found with APoc: 13
This union binding pocket(no: 4) in the query (biounit: 2fdw.bio3) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4WCX SAM 2.31092
2 2WPX ACO 3.24484
3 5W7B MYR 3.5461
4 3TKY SAH 4.8913
5 2CJF RP4 5.09554
6 1U8V FAD 5.46218
7 5YX4 HCC 6.46552
8 5IXH OTP 7.45342
9 1B7H LYS NLE LYS 7.98319
10 3QRC SCR 12.1019
11 3RET SAL 12.8713
12 3RET PYR 12.8713
13 1QY1 PRZ 13.2184
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