Receptor
PDB id Resolution Class Description Source Keywords
4XRY 2.5 Å NON-ENZYME: OTHER HUMAN CYTOCHROME P450 2D6 BACE1 INHIBITOR 5 COMPLEX HOMO SAPIENS CYP2D6 P450 2D6 CYTOCHROME P450 MONOOXYGENASE BACE1 OXIDOREDUCTASE
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;
C:607;
C:606;
A:606;
A:605;
D:606;
C:604;
C:605;
D:604;
B:605;
B:603;
C:603;
D:607;
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;
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;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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...
SI5 D:602;
B:602;
A:602;
C:602;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 13.9 uM
364.413 C17 H18 F2 N4 O S Cn1cc...
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 1256 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 1068 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 (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: SI5; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 SI5 1 1
2 SI6 0.690476 0.892308
3 3VP 0.564706 0.753846
4 3VO 0.482759 0.727273
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found: 38
This union binding pocket(no: 1) in the query (biounit: 4xrz.bio4) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I90 CHT 0.01794 0.40747 1.65016
2 1M13 HYF 0.009898 0.40403 2.53165
3 1SR7 MOF 0.00983 0.40416 2.7027
4 4I6G FAD 0.005367 0.41021 2.71399
5 1IGW PYR 0.008521 0.42797 2.76498
6 3WFD AXO 0.03691 0.40525 3.55556
7 4MRP GSH 0.02693 0.40961 3.75783
8 4IEH 1E9 0.005919 0.4038 4.14201
9 2W3L DRO 0.0162 0.41432 4.86111
10 1DKF OLA 0.008544 0.41066 5.15021
11 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 0.01934 0.40139 6.66667
12 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.02341 0.4012 6.96721
13 3P9T TCL 0.004353 0.43309 8.21918
14 3KP6 SAL 0.02506 0.41282 9.27152
15 1T0S BML 0.02868 0.40663 9.30233
16 2WH8 II2 0.003955 0.43999 9.68523
17 4L77 CNL 0.01631 0.4135 10.0503
18 4UP4 GAL NAG 0.02233 0.41201 12.9676
19 2WM4 VGJ 0.0001159 0.48636 15.4023
20 5FOI MY8 0.0002534 0.45103 16.1765
21 4UBS DIF 0.01889 0.41288 16.285
22 3A51 VDY 0.0008501 0.41661 16.7883
23 1N8V BDD 0.0096 0.41218 16.9643
24 5AAV GW5 0.01347 0.41756 18.254
25 4B7S QLE 0.001117 0.43255 18.3486
26 4J6C STR 0.0004898 0.48533 19.5122
27 2X5W K2B 0.001195 0.43657 19.5455
28 3MDV CL6 0.001087 0.44729 20.1754
29 3WVS RRM 0.003102 0.41214 20.1995
30 2XFH CL6 0.0002378 0.46991 20.438
31 1ZOA 140 0.01523 0.40032 20.5074
32 2GBB CIT 0.02169 0.40288 20.5128
33 5IBE 69M 0.0128 0.40473 20.7071
34 1Z8O DEB 0.0003053 0.46356 21.2871
35 4DVQ 1CA 0.004774 0.4359 21.7391
36 2YOO K2B 0.004694 0.41136 21.8673
37 3ABA FLI 0.0001052 0.41761 33.2506
38 2HI4 BHF 0.0001329 0.45611 48.2255
Pocket No.: 2; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found: 10
This union binding pocket(no: 2) in the query (biounit: 4xrz.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZCQ B65 0.01729 0.4019 2.38908
2 1SBR VIB 0.03009 0.40126 3
3 3WYJ H78 0.03588 0.4002 3.16206
4 3E5P PPI 0.02803 0.42043 3.50404
5 3DTU DXC 0.01685 0.40673 4.59364
6 4O4Z N2O 0.0363 0.40645 7.14286
7 3ETG GWD 0.01134 0.40298 8.35073
8 3N7S 3N7 0.02109 0.41473 10.4348
9 3N9Y CLR 0.003305 0.40141 20.3285
10 3NA0 2DC 0.003432 0.40094 26.4706
Pocket No.: 3; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 4xrz.bio3) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 4XRZ; Ligand: SI6; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 4xrz.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback