Receptor
PDB id Resolution Class Description Source Keywords
5FV9 2.07 Å EC: 2.4.1.41 CRYSTAL STRUCTURE OF GALNAC-T2 IN COMPLEX WITH COMPOUND 16D HOMO SAPIENS TRANSFERASE
Ref.: GLYCOMIMETICS TARGETING GLYCOSYLTRANSFERASES: SYNTH COMPUTATIONAL AND STRUCTURAL STUDIES OF LESS-POLAR CONJUGATES. CHEMISTRY V. 22 7215 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO E:1576;
F:1575;
E:1574;
F:1574;
B:1573;
E:1573;
F:1573;
A:1574;
C:1573;
A:1572;
C:1572;
B:1574;
A:1573;
E:1575;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN B:1571;
D:1556;
F:1571;
E:1571;
C:1571;
A:1571;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
GOL F:1577;
F:1576;
C:1574;
A:1576;
A:1575;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
UDP E:1570;
D:1555;
F:1570;
A:1570;
B:1572;
C:1570;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
Y6W B:1570;
E:1572;
F:1572;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 254 uM
512.402 C18 H29 N2 O13 P C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NDF 2.3 Å EC: 2.4.1.41 SMALL-MOLECULE INHIBITION OF PPGALNAC-TS SELECTIVELY REDUCES TYPE O-GLYCOSYLATION HOMO SAPIENS GALNAC-T2 INHIBITION FLAVONOIDS MUCIN-TYPE O-GLYCOSYLATION ADISEASE TRANSFERASE
Ref.: THE SMALL MOLECULE LUTEOLIN INHIBITS N-ACETYL-ALPHA-GALACTOSAMINYLTRANSFERASES AND REDUC MUCIN-TYPE O-GLYCOSYLATION OF AMYLOID PRECURSOR PRO J. BIOL. CHEM. V. 292 21304 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5FV9 Kd = 254 uM Y6W C18 H29 N2 O13 P C1=CN(C(=O....
2 5NDF ic50 = 15 uM LU2 C15 H10 O6 c1cc(c(cc1....
3 4D0T - ASP SER THR THR PRO ALA PRO THR NGA n/a n/a
4 4D0Z - SER THR CYS PRO ALA ALA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UDP; Similar ligands found: 117
No: Ligand ECFP6 Tc MDL keys Tc
1 UDP 1 1
2 UTP 0.892308 1
3 UNP 0.8 0.970149
4 U5P 0.78125 0.984615
5 U 0.78125 0.984615
6 UPU 0.72973 0.940298
7 2KH 0.722222 0.970149
8 44P 0.720588 0.955882
9 UFM 0.717949 0.941176
10 GDU 0.717949 0.941176
11 URM 0.717949 0.927536
12 660 0.717949 0.927536
13 UPG 0.717949 0.941176
14 GUD 0.717949 0.941176
15 UDP UDP 0.714286 0.939394
16 UPP 0.705128 0.941176
17 UDH 0.705128 0.864865
18 U2F 0.691358 0.888889
19 UFG 0.691358 0.888889
20 UPF 0.691358 0.888889
21 UAD 0.670732 0.941176
22 UDX 0.670732 0.941176
23 3UC 0.658824 0.888889
24 USQ 0.654762 0.820513
25 UGB 0.654762 0.955224
26 UGA 0.654762 0.955224
27 G3N 0.647059 0.914286
28 UDM 0.636364 0.914286
29 URI 0.625 0.863636
30 UD1 0.622222 0.927536
31 UD2 0.622222 0.927536
32 Y6W 0.607143 0.888889
33 CDP 0.605263 0.942029
34 HP7 0.591398 0.941176
35 UD7 0.591398 0.927536
36 MJZ 0.585106 0.914286
37 IUG 0.583333 0.810127
38 F5G 0.578947 0.927536
39 12V 0.578947 0.901408
40 HWU 0.578947 0.901408
41 F5P 0.578947 0.914286
42 UD4 0.578947 0.914286
43 CJB 0.573529 0.820895
44 UDZ 0.571429 0.853333
45 DUD 0.571429 0.913043
46 UP5 0.571429 0.853333
47 U U 0.563218 0.955224
48 EPZ 0.56 0.914286
49 5GW 0.559524 0.942029
50 EPU 0.554455 0.901408
51 EEB 0.554455 0.901408
52 U3P 0.547945 0.939394
53 UA3 0.547945 0.939394
54 4TC 0.544554 0.831169
55 HF4 0.54321 0.942029
56 CTP 0.54321 0.942029
57 CSQ 0.531915 0.851351
58 CSV 0.531915 0.851351
59 DUT 0.52439 0.913043
60 4GW 0.516484 0.915493
61 UMA 0.513761 0.914286
62 U4S 0.513158 0.753425
63 U2P 0.506667 0.954545
64 U2S 0.5 0.767123
65 U3S 0.5 0.753425
66 PUP 0.48913 0.913043
67 U21 0.486957 0.810127
68 U20 0.486957 0.810127
69 U22 0.486957 0.790123
70 DKX 0.486486 0.746479
71 U1S 0.482759 0.75
72 A U 0.481132 0.805195
73 2QR 0.478632 0.822785
74 5FU 0.474359 0.914286
75 G U 0.472222 0.7875
76 8OD 0.47191 0.851351
77 C5G 0.468085 0.888889
78 7XL 0.465909 0.888889
79 U U U U 0.461538 0.940298
80 UMF 0.461538 0.857143
81 G8D 0.460674 0.855263
82 UTP U U U 0.456522 0.895522
83 2TU 0.452055 0.774648
84 4RA 0.451613 0.855263
85 C2G 0.450549 0.901408
86 DU 0.45 0.898551
87 UMP 0.45 0.898551
88 C 0.45 0.927536
89 CAR 0.45 0.927536
90 C5P 0.45 0.927536
91 UAG 0.448 0.864865
92 CDC 0.446809 0.777778
93 5BU 0.444444 0.914286
94 UD0 0.444444 0.844156
95 N3E 0.440476 0.733333
96 UC5 0.440476 0.9
97 UUA 0.438356 0.772727
98 DUP 0.431818 0.887324
99 2GW 0.431373 0.901408
100 M7G 0.430108 0.780488
101 CNU 0.428571 0.927536
102 CDM 0.427083 0.842105
103 H6Y 0.425532 0.851351
104 16B 0.421687 0.888889
105 S5P 0.419753 0.915493
106 8GT 0.419355 0.855263
107 CXY 0.418367 0.888889
108 UPA 0.418182 0.842105
109 U2G 0.410714 0.822785
110 U A A U 0.409836 0.842105
111 UML 0.408759 0.810127
112 UP6 0.407407 0.871429
113 M7M 0.40625 0.771084
114 1GW 0.40367 0.864865
115 BMP 0.402439 0.970149
116 APU 0.401786 0.828947
117 PMP UD1 0.401575 0.7875
Ligand no: 2; Ligand: Y6W; Similar ligands found: 69
No: Ligand ECFP6 Tc MDL keys Tc
1 Y6W 1 1
2 URM 0.674157 0.957747
3 660 0.674157 0.957747
4 44P 0.65 0.90411
5 U 0.632911 0.875
6 U5P 0.632911 0.875
7 UDP 0.607143 0.888889
8 UPU 0.588889 0.915493
9 UTP 0.586207 0.888889
10 UFM 0.585106 0.916667
11 GUD 0.585106 0.916667
12 GDU 0.585106 0.916667
13 UPG 0.585106 0.916667
14 2KH 0.561798 0.864865
15 UDM 0.558824 0.944444
16 UDP UDP 0.551724 0.861111
17 U2F 0.55102 0.868421
18 UPF 0.55102 0.868421
19 UNP 0.549451 0.864865
20 URI 0.545455 0.816901
21 CJB 0.544304 0.802817
22 UDH 0.525773 0.945946
23 UFG 0.52 0.868421
24 UPP 0.510204 0.890411
25 UGA 0.509804 0.902778
26 UGB 0.509804 0.902778
27 USQ 0.509804 0.804878
28 UD2 0.504673 0.90411
29 UD1 0.504673 0.90411
30 3UC 0.5 0.868421
31 UAD 0.490196 0.916667
32 UDX 0.490196 0.916667
33 UA3 0.488372 0.861111
34 U3P 0.488372 0.861111
35 CSQ 0.485981 0.833333
36 CSV 0.485981 0.833333
37 U U 0.480392 0.876712
38 MJZ 0.477477 0.866667
39 G3N 0.47619 0.891892
40 HP7 0.468468 0.890411
41 IUG 0.464912 0.77381
42 EPZ 0.461538 0.891892
43 12V 0.460177 0.88
44 HWU 0.460177 0.88
45 UD4 0.460177 0.866667
46 F5P 0.460177 0.866667
47 EPU 0.457627 0.88
48 EEB 0.457627 0.88
49 UD7 0.455357 0.878378
50 U2P 0.454545 0.875
51 4TC 0.449153 0.814815
52 F5G 0.447368 0.878378
53 A U 0.445378 0.790123
54 UP5 0.444444 0.8125
55 UDZ 0.444444 0.8125
56 DKX 0.436782 0.733333
57 U2S 0.434783 0.824324
58 U4S 0.428571 0.786667
59 UMA 0.428571 0.891892
60 G U 0.42623 0.752941
61 PUP 0.420561 0.916667
62 U20 0.419847 0.910256
63 U21 0.419847 0.910256
64 U22 0.419847 0.8875
65 U3S 0.419355 0.810811
66 UMF 0.417582 0.789474
67 UC5 0.416667 0.878378
68 U U U U 0.409524 0.863014
69 UTP U U U 0.40566 0.847222
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NDF; Ligand: UDP; 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: 5ndf.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5ndf.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ndf.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ndf.bio5) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5ndf.bio5) has 36 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5ndf.bio5) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5ndf.bio3) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5ndf.bio3) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5ndf.bio3) has 37 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5NDF; Ligand: LU2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5ndf.bio3) has 39 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5ndf.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5ndf.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 13; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 13) in the query (biounit: 5ndf.bio4) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 14; Query (leader) PDB : 5NDF; Ligand: UDP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 14) in the query (biounit: 5ndf.bio4) has 27 residues
No: Leader PDB Ligand Sequence Similarity
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