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Receptor
PDB id Resolution Class Description Source Keywords
4XRZ 2.4 Å NON-ENZYME: OTHER HUMAN CYTOCHROME P450 2D6 BACE1 INHIBITOR 6 COMPLEX HOMO SAPIENS CYP2D6 P450 2D6 CYTOCHROME P450 MONOOXYGENASE OXIDOREDUCOXIDOREDUCTASE INHIBITOR COMPLEX BACE1
Ref.: UTILIZING STRUCTURES OF CYP2D6 AND BACE1 COMPLEXES RISK OF DRUG-DRUG INTERACTIONS WITH A NOVEL SERIES CENTRALLY EFFICACIOUS BACE1 INHIBITORS. J.MED.CHEM. V. 58 3223 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN D:603;
D:605;
A:603;
B:604;
A:604;
A:605;
A:607;
D:604;
C:605;
C:604;
B:603;
C:603;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
GOL C:606;
D:606;
B:605;
A:606;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
SI6 C:602;
D:602;
A:602;
B:602;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 0.37 uM
350.386 C16 H16 F2 N4 O S c1cc(...
NA D:607;
B:606;
A:608;
C:607;
Part of Protein;
Part of Protein;
Invalid;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
HEM D:601;
C:601;
A:601;
B:601;
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
4XRZ 2.4 Å NON-ENZYME: OTHER HUMAN CYTOCHROME P450 2D6 BACE1 INHIBITOR 6 COMPLEX HOMO SAPIENS CYP2D6 P450 2D6 CYTOCHROME P450 MONOOXYGENASE OXIDOREDUCOXIDOREDUCTASE INHIBITOR COMPLEX BACE1
Ref.: UTILIZING STRUCTURES OF CYP2D6 AND BACE1 COMPLEXES RISK OF DRUG-DRUG INTERACTIONS WITH A NOVEL SERIES CENTRALLY EFFICACIOUS BACE1 INHIBITORS. J.MED.CHEM. V. 58 3223 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 4XRZ ic50 = 0.37 uM SI6 C16 H16 F2 N4 O S c1cc(c(cc1....
2 4WNU - QDN C20 H24 N2 O2 COc1ccc2c(....
3 4WNV - QI9 C20 H24 N2 O2 COc1ccc2c(....
4 4XRY ic50 = 13.9 uM SI5 C17 H18 F2 N4 O S Cn1cc(cn1)....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 4XRZ ic50 = 0.37 uM SI6 C16 H16 F2 N4 O S c1cc(c(cc1....
2 4WNU - QDN C20 H24 N2 O2 COc1ccc2c(....
3 4WNV - QI9 C20 H24 N2 O2 COc1ccc2c(....
4 4XRY ic50 = 13.9 uM SI5 C17 H18 F2 N4 O S Cn1cc(cn1)....
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: SI6; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 SI6 1 1
2 SI5 0.690476 0.892308
3 3VP 0.578313 0.790323
4 3VO 0.494118 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found with APoc: 122
This union binding pocket(no: 1) in the query (biounit: 4xrz.bio4) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 3F8C HT1 None
2 1RV1 IMZ None
3 3RS8 ALA TRP LEU PHE GLU ALA 1.46138
4 4I90 CHT 1.65016
5 2JGV ADP 1.81818
6 5WIU AQD 1.89573
7 3OJF IMJ 1.94553
8 1T27 PCW 2.21402
9 5WS9 ATP 2.31579
10 4GNC ASO 2.34114
11 5ZKC 3C0 2.3753
12 1P72 THM 2.39521
13 1M13 HYF 2.53165
14 5LX9 OLB 2.60586
15 4QEK GLC 2.65781
16 1XHL TNE 2.6936
17 1SR7 MOF 2.7027
18 4I6G FAD 2.71399
19 6C4A PYR 2.71493
20 1IGW PYR 2.76498
21 5ZM0 FAD 3.13152
22 3LN0 52B 3.34029
23 3NIP 16D 3.37423
24 3C8E GSH 3.47222
25 5B0I BOG 3.49854
26 5W7B MYR 3.5461
27 2ITM XUL 3.54906
28 3WFD AXO 3.55556
29 3LA3 2FT 3.7037
30 5OLK DTP 3.72093
31 4MRP GSH 3.75783
32 2AX9 BHM 3.75783
33 3TL1 JRO 3.77358
34 3B8I OXL 3.83275
35 2F7A BEZ 3.87931
36 3W5N RAM 3.9666
37 5MB4 NAG 3.99003
38 2UW1 GVM 4.14201
39 1ZPD CIT 4.38413
40 3HKW IX6 4.38413
41 1ZED PNP 4.5929
42 5IM3 DTP 4.5929
43 1MJT NAD 4.61095
44 4Q0A 4OA 4.63576
45 5Y02 MXN 4.6729
46 5Y02 HBX 4.6729
47 1R6N 434 4.73934
48 2W3L DRO 4.86111
49 6A5Y 9CR 5.04202
50 4B2Z P5S 5.13393
51 1DKF OLA 5.15021
52 1Y4Z PCI 5.33333
53 1MID LAP 5.49451
54 5VGS 9A7 5.73248
55 6BVJ EAS 5.98802
56 4M52 M52 6.00858
57 3ROE THM 6.03774
58 5M36 9SZ 6.11354
59 6H8S FSZ 6.31229
60 4EKQ NPO 6.41711
61 6BVM EBV 6.58683
62 6BVK EAV 6.58683
63 6BVI EC4 6.58683
64 6BVL EBY 6.58683
65 6FBA D48 6.59026
66 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 6.66667
67 5KOH HCA 6.88935
68 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 6.96721
69 5V3Y 5V8 6.99301
70 5CHR 4NC 7.29927
71 2YFB SIN 7.75194
72 5X3R 7Y3 7.80488
73 3P9T TCL 8.21918
74 5C1M CLR 8.44595
75 3KP6 SAL 9.27152
76 1T0S BML 9.30233
77 3RUG DB6 9.31373
78 2D09 FLV 9.58231
79 2WH8 II2 9.68523
80 4L77 CNL 10.0503
81 3G4Q MCH 10.274
82 4JX1 CAH 10.6195
83 4JX1 CAM 10.6195
84 6CB2 OLC 10.9215
85 3OGN 3OG 11.2903
86 5Y6Q MCN 11.7284
87 4UP4 GAL NAG 12.9676
88 5W97 CHD 13.6054
89 5Z84 CHD 13.6054
90 5ZCO PGV 13.6054
91 5ZCO CHD 13.6054
92 5M37 9SZ 14.7826
93 3RET SAL 14.8515
94 3R9C ECL 15.311
95 2WM4 VGJ 15.4023
96 5FOI MY8 16.1765
97 4UBS DIF 16.285
98 3A51 VDY 16.7883
99 1N8V BDD 16.9643
100 4B7S QLE 18.3486
101 2Y69 CHD 18.75
102 2Z3U CRR 18.8235
103 4J6C STR 19.5122
104 2X5W K2B 19.5455
105 6CR2 LFV 19.9161
106 3MDV CL6 20.1754
107 3WVS RRM 20.1995
108 6M7X JD7 20.2505
109 3N9Y CLR 20.3285
110 2XFH CL6 20.438
111 1ZOA 140 20.5074
112 2GBB CIT 20.5128
113 5IBE 69M 20.7071
114 6GK6 MYR 20.9246
115 1Z8O DEB 21.2871
116 2YOO K2B 21.8673
117 3NA0 2DC 26.4706
118 3ABA FLI 33.2506
119 3UA1 08Y 40.2923
120 1NU4 MLA 41.2371
121 2VE3 REA 41.7537
122 2HI4 BHF 48.2255
Pocket No.: 2; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 4xrz.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3SQP 3J8 0.83682
3 5CX6 CDP 2.2695
4 2ZCQ B65 2.38908
5 5A86 D7E 2.54777
6 1SBR VIB 3
7 3E5P PPI 3.50404
8 2OZ5 7XY 4.05405
9 1KHT AMP 4.16667
10 3DTU DXC 4.59364
11 1KNM LAT 4.61538
12 4URX FK1 5.40541
13 4OJ8 2TQ 5.46075
14 1VJ7 GPX 5.59796
15 1I0B PEL 5.72289
16 4DE3 DN8 6.08365
17 1Z6K OAA 6.14334
18 5KOD IAC 6.88935
19 4O4Z N2O 7.14286
20 4DXJ 0M9 7.18232
21 1XQP 8HG 8.14196
22 3ETG GWD 8.35073
23 5C1M OLC 8.44595
24 3RLF MAL 9.44882
25 5UGW GSH 9.71429
26 4ZGM 32M 9.83607
27 3N7S 3N7 10.4348
28 4OGQ 1O2 10.8108
29 2EG7 OTD 11.5274
30 5TV6 PML 12.9167
31 4WGF HX2 16.0976
32 4F4S EFO 25
Pocket No.: 3; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 4xrz.bio3) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 3V1S 0LH 2.48447
2 1RL4 BRR 3.19149
3 2HFK E4H 4.5929
4 4URG C2E 4.79042
5 5X2N ALA 7.11111
6 3NGU ADP 8.60927
Pocket No.: 4; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 4xrz.bio2) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 6D5L FW7 6.58683
2 1V7Z CRN 8.07692
3 3MAG 3MA 9.12052
4 3MZS HC9 20.4593
5 2CI0 1CM 40.8791
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