Receptor
PDB id Resolution Class Description Source Keywords
6R8Q 1.5 Å EC: 3.1.1.98 STRUCTURE OF THE WNT DEACYLASE NOTUM IN COMPLEX WITH A BENZO FRAGMENT HOMO SAPIENS WNT SIGNALLING NOTUM INHIBITOR CRYSTALLOGRAPHIC FRAGMENT SHYDROLASE
Ref.: DISCOVERY OF 2-PHENOXYACETAMIDES AS INHIBITORS OF T WNT-DEPALMITOLEATING ENZYME NOTUM FROM AN X-RAY FRA SCREEN. MEDCHEMCOMM V. 10 1361 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:504;
A:506;
A:508;
A:505;
A:509;
A:503;
A:502;
A:507;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
EDO A:513;
A:511;
A:514;
A:512;
A:510;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
JV5 A:515;
 Valid;
 none;
 ic50 = 0.12 uM
282.297 C15 H14 N4 O2 Cc1cc...
NAG A:501;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6ZVL 1.3 Å EC: 3.1.1.98 ARUK3000263 COMPLEX WITH NOTUM HOMO SAPIENS NOTUM INHIBITOR WNT SIGNALING PROTEIN
Ref.: 5-PHENYL-1,3,4-OXADIAZOL-2(3 H )-ONES ARE POTENT IN OF NOTUM CARBOXYLESTERASE ACTIVITY IDENTIFIED BY TH OPTIMIZATION OF A CRYSTALLOGRAPHIC FRAGMENT SCREENI J.MED.CHEM. V. 63 12942 2020
Members (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6TR7 ic50 = 37 uM HWH C12 H13 F N2 O CC(=O)NCCc....
2 6YUY ic50 = 6.7 uM PQH C7 H6 F3 N O2 Cc1c(cc([n....
3 6YXI ic50 = 14 uM PZ8 C13 H12 Cl N O2 Cc1cc(c(n1....
4 6YV0 ic50 = 18.6 uM PQT C11 H12 Cl N O2 c1ccc(c(c1....
5 6R8P ic50 = 33 uM JVB C14 H14 N2 O2 Cc1ccccc1O....
6 6TR6 ic50 = 94 uM ASE C12 H14 N2 O2 CC(=O)NCCc....
7 6YSK ic50 = 0.11 uM PJK C12 H11 Cl F3 N O2 c1cc(c(cc1....
8 6R8R ic50 = 0.085 uM JV8 C18 H16 N2 O2 Cc1ccccc1O....
9 6TR5 ic50 = 75 uM ML1 C13 H16 N2 O2 CC(=O)NCCc....
10 6TV4 Kd = 85 uM CFF C8 H10 N4 O2 Cn1cnc2c1C....
11 4UZL - MYZ C14 H26 O2 CCCC/C=CCC....
12 4UZ9 - GU4 YYJ n/a n/a
13 4UZ6 - GU4 YYJ n/a n/a
14 4UZQ - CYS HIS GLY VAL SER GLY SER CYS PAM n/a n/a
15 6YV2 ic50 = 48 uM PUE C11 H13 N O2 c1ccc(cc1)....
16 6R8Q ic50 = 0.12 uM JV5 C15 H14 N4 O2 Cc1ccccc1O....
17 6T2K - M9K C11 H9 Cl N2 O2 S2 c1nc2c(c(s....
18 6T2H - M9N C9 H11 Cl N2 O2 S2 Cc1c(c2c(s....
19 6ZVL ic50 = 18 nM QR2 C9 H4 Cl F3 N2 O2 c1cc(c(cc1....
20 6YUW ic50 = 12.7 uM PQZ C11 H15 N O2 Cc1cc(c(n1....
21 6ZUV ic50 = 11.5 uM B1J C9 H8 Cl N3 O c1cc(ccc1n....
22 4UYW Kd = 6.4 uM SGN UAP n/a n/a
23 6YV4 ic50 = 6.3 uM PQK C10 H13 N O2 Cc1cc(c(n1....
24 6TUZ Kd = 6.8 mM TEP C7 H8 N4 O2 CN1c2c([nH....
70% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6TR7 ic50 = 37 uM HWH C12 H13 F N2 O CC(=O)NCCc....
2 6YUY ic50 = 6.7 uM PQH C7 H6 F3 N O2 Cc1c(cc([n....
3 6YXI ic50 = 14 uM PZ8 C13 H12 Cl N O2 Cc1cc(c(n1....
4 6YV0 ic50 = 18.6 uM PQT C11 H12 Cl N O2 c1ccc(c(c1....
5 6R8P ic50 = 33 uM JVB C14 H14 N2 O2 Cc1ccccc1O....
6 6TR6 ic50 = 94 uM ASE C12 H14 N2 O2 CC(=O)NCCc....
7 6YSK ic50 = 0.11 uM PJK C12 H11 Cl F3 N O2 c1cc(c(cc1....
8 6R8R ic50 = 0.085 uM JV8 C18 H16 N2 O2 Cc1ccccc1O....
9 6TR5 ic50 = 75 uM ML1 C13 H16 N2 O2 CC(=O)NCCc....
10 6TV4 Kd = 85 uM CFF C8 H10 N4 O2 Cn1cnc2c1C....
11 4UZL - MYZ C14 H26 O2 CCCC/C=CCC....
12 4UZ9 - GU4 YYJ n/a n/a
13 4UZ6 - GU4 YYJ n/a n/a
14 4UZQ - CYS HIS GLY VAL SER GLY SER CYS PAM n/a n/a
15 6YV2 ic50 = 48 uM PUE C11 H13 N O2 c1ccc(cc1)....
16 6R8Q ic50 = 0.12 uM JV5 C15 H14 N4 O2 Cc1ccccc1O....
17 6T2K - M9K C11 H9 Cl N2 O2 S2 c1nc2c(c(s....
18 6T2H - M9N C9 H11 Cl N2 O2 S2 Cc1c(c2c(s....
19 6ZVL ic50 = 18 nM QR2 C9 H4 Cl F3 N2 O2 c1cc(c(cc1....
20 6YUW ic50 = 12.7 uM PQZ C11 H15 N O2 Cc1cc(c(n1....
21 6ZUV ic50 = 11.5 uM B1J C9 H8 Cl N3 O c1cc(ccc1n....
22 4UYW Kd = 6.4 uM SGN UAP n/a n/a
23 6YV4 ic50 = 6.3 uM PQK C10 H13 N O2 Cc1cc(c(n1....
24 6TUZ Kd = 6.8 mM TEP C7 H8 N4 O2 CN1c2c([nH....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6TR7 ic50 = 37 uM HWH C12 H13 F N2 O CC(=O)NCCc....
2 6YUY ic50 = 6.7 uM PQH C7 H6 F3 N O2 Cc1c(cc([n....
3 6YXI ic50 = 14 uM PZ8 C13 H12 Cl N O2 Cc1cc(c(n1....
4 6YV0 ic50 = 18.6 uM PQT C11 H12 Cl N O2 c1ccc(c(c1....
5 6R8P ic50 = 33 uM JVB C14 H14 N2 O2 Cc1ccccc1O....
6 6TR6 ic50 = 94 uM ASE C12 H14 N2 O2 CC(=O)NCCc....
7 6YSK ic50 = 0.11 uM PJK C12 H11 Cl F3 N O2 c1cc(c(cc1....
8 6R8R ic50 = 0.085 uM JV8 C18 H16 N2 O2 Cc1ccccc1O....
9 6TR5 ic50 = 75 uM ML1 C13 H16 N2 O2 CC(=O)NCCc....
10 6TV4 Kd = 85 uM CFF C8 H10 N4 O2 Cn1cnc2c1C....
11 4UZL - MYZ C14 H26 O2 CCCC/C=CCC....
12 4UZ9 - GU4 YYJ n/a n/a
13 4UZ6 - GU4 YYJ n/a n/a
14 4UZQ - CYS HIS GLY VAL SER GLY SER CYS PAM n/a n/a
15 6YV2 ic50 = 48 uM PUE C11 H13 N O2 c1ccc(cc1)....
16 6R8Q ic50 = 0.12 uM JV5 C15 H14 N4 O2 Cc1ccccc1O....
17 6T2K - M9K C11 H9 Cl N2 O2 S2 c1nc2c(c(s....
18 6T2H - M9N C9 H11 Cl N2 O2 S2 Cc1c(c2c(s....
19 6ZVL ic50 = 18 nM QR2 C9 H4 Cl F3 N2 O2 c1cc(c(cc1....
20 6YUW ic50 = 12.7 uM PQZ C11 H15 N O2 Cc1cc(c(n1....
21 6ZUV ic50 = 11.5 uM B1J C9 H8 Cl N3 O c1cc(ccc1n....
22 4UYW Kd = 6.4 uM SGN UAP n/a n/a
23 6YV4 ic50 = 6.3 uM PQK C10 H13 N O2 Cc1cc(c(n1....
24 6TUZ Kd = 6.8 mM TEP C7 H8 N4 O2 CN1c2c([nH....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: JV5; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 JV5 1 1
2 JVB 0.5 0.719298
3 JV8 0.5 0.719298
Similar Ligands (3D)
Ligand no: 1; Ligand: JV5; Similar ligands found: 102
No: Ligand Similarity coefficient
1 00G 0.9216
2 BAI 0.9182
3 4B8 0.9139
4 N4N 0.9131
5 JQN 0.9129
6 4AJ 0.9118
7 F6B 0.9085
8 5RU 0.9077
9 RF2 0.9059
10 DN8 0.9030
11 6XR 0.9019
12 43G 0.9016
13 ZUF 0.9003
14 C9J 0.9003
15 ZX7 0.8993
16 9YD 0.8982
17 2WF 0.8971
18 55H 0.8967
19 HCC 0.8967
20 F5N 0.8951
21 0UC 0.8939
22 N0E 0.8938
23 BXB 0.8934
24 BUN 0.8920
25 17W 0.8919
26 JZJ 0.8911
27 E8Z 0.8909
28 0UA 0.8903
29 M62 0.8901
30 JPW 0.8900
31 40N 0.8890
32 F41 0.8888
33 D9T 0.8885
34 BSB 0.8878
35 F33 0.8872
36 39R 0.8864
37 135 0.8864
38 1GV 0.8859
39 JP3 0.8849
40 0U7 0.8845
41 3DL 0.8839
42 LIT 0.8834
43 5ET 0.8833
44 4KN 0.8829
45 JXA 0.8826
46 0RA 0.8820
47 E98 0.8820
48 ZX8 0.8804
49 YH1 0.8800
50 YH4 0.8800
51 6NF 0.8783
52 20P 0.8782
53 3Q2 0.8781
54 IPJ 0.8779
55 87F 0.8776
56 4P9 0.8776
57 INV 0.8772
58 246 0.8771
59 E92 0.8766
60 Y0R 0.8765
61 F13 0.8765
62 797 0.8763
63 9PC 0.8762
64 675 0.8758
65 L02 0.8754
66 0HD 0.8751
67 BZH 0.8734
68 6NL 0.8724
69 K3T 0.8717
70 GYZ 0.8711
71 A9E 0.8711
72 745 0.8708
73 K5D 0.8705
74 XZ1 0.8704
75 BER 0.8701
76 3Q1 0.8692
77 0RB 0.8687
78 J2W 0.8674
79 A46 0.8655
80 JP8 0.8651
81 88S 0.8645
82 4VC 0.8639
83 4UJ 0.8639
84 78H 0.8633
85 1SX 0.8632
86 WMM 0.8627
87 F91 0.8625
88 82E 0.8613
89 ZQC 0.8609
90 FZ8 0.8608
91 ENY 0.8600
92 E1E 0.8600
93 MT6 0.8578
94 MNI 0.8576
95 C0V 0.8574
96 GJW 0.8568
97 DEH 0.8565
98 M05 0.8563
99 T5J 0.8556
100 7FC 0.8554
101 IOE 0.8553
102 80R 0.8528
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6ZVL; Ligand: QR2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6zvl.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
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