Receptor
PDB id Resolution Class Description Source Keywords
4D0T 2.45 Å EC: 2.4.1.41 GALNAC-T2 CRYSTAL SOAKED WITH UDP-GALNAC, EA2 PEPTIDE AND MANGANESE SYNTHETIC CONSTRUCT TRANSFERASE RETAINING GALNAC-T2 SUBSTRATE-GUIDED SNI-TYPE REACTION QM/MM METADYNAMICS BI-BI KINETIC MECHANISM SUBSSPECIFICITY PROTEIN X-RAY CRYSTALLOGRAPHY ACETAMIDO GROUP
Ref.: SUBSTRATE-GUIDED FRONT-FACE REACTION REVEALED BY CO STRUCTURAL SNAPSHOTS AND METADYNAMICS FOR THE POLYP ACETYLGALACTOSAMINYLTRANSFERASE 2. ANGEW.CHEM.INT.ED.ENGL. V. 53 8206 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:1573;
B:1572;
E:1572;
B:1571;
C:1573;
A:1572;
C:1574;
D:1573;
D:1572;
E:1573;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN E:1570;
C:1570;
F:1566;
D:1570;
A:1571;
B:1570;
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...
ASP SER THR THR PRO ALA PRO THR NGA P:4;
Valid;
none;
submit data
874.899 n/a O=C(N...
UD2 B:1573;
F:1567;
D:1571;
E:1571;
A:1574;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
submit data
607.354 C17 H27 N3 O17 P2 CC(=O...
UDP C:1571;
Valid;
none;
submit data
404.161 C9 H14 N2 O12 P2 C1=CN...
ASP SER THR THR PRO ALA PRO THR Z:6;
Valid;
none;
submit data
571.652 n/a O=C(N...
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: ASP SER THR THR PRO ALA PRO THR NGA; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP SER THR THR PRO ALA PRO THR NGA 1 1
2 ALA PRO ASP THR ARG PRO A2G 0.566879 0.917808
3 ALA PRO ASP THR ARG PRO ALA PRO NGA 0.566265 0.917808
4 ALA PRO ASP THR ARG PRO ALA PRO 0.503448 0.808219
5 ALA PRO ASP SER ARG PRO A2G 0.484663 0.917808
6 SIA GLY PRO ALA THR PRO ALA PRO 8B9 0.471591 0.971014
7 SIA GLY PRO ALA THR PRO ALA PRO A2G 0.460227 0.971014
8 SIA GLY PRO ALA THR PRO ALA PRO NDG 0.460227 0.971014
9 GLY THR LYS PRO PRO LEU GLU GLU LEU A2G 0.434524 0.956522
10 ALA PRO ASP CYS ARG PRO A2G 0.429412 0.868421
11 SER TYR SER PRO THR SEP PRO SER 0.415493 0.780822
12 ALA PRO ASP THR ARG PRO 0.407895 0.808219
13 ACE SER THR VAL GLY A2G 0.402878 0.75
Ligand no: 2; Ligand: UD2; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 UD2 1 1
2 UD1 1 1
3 UDZ 0.8 0.893333
4 HP7 0.793814 0.985294
5 EPZ 0.75 0.985507
6 EPU 0.742857 0.971429
7 EEB 0.742857 0.971429
8 F5P 0.742574 0.957143
9 UD4 0.742574 0.957143
10 F5G 0.742574 0.971014
11 UFM 0.73913 0.985294
12 GUD 0.73913 0.985294
13 UPG 0.73913 0.985294
14 GDU 0.73913 0.985294
15 UD7 0.722772 0.971014
16 MJZ 0.715686 0.957143
17 U2F 0.697917 0.930556
18 UPF 0.697917 0.930556
19 UMA 0.690265 0.985507
20 UDM 0.683168 0.957143
21 UFG 0.663265 0.930556
22 12V 0.660377 0.943662
23 HWU 0.660377 0.943662
24 U22 0.655462 0.85
25 U20 0.655462 0.871795
26 U21 0.655462 0.871795
27 UGB 0.65 0.970588
28 UGA 0.65 0.970588
29 USQ 0.633663 0.835443
30 UDX 0.63 0.956522
31 UAD 0.63 0.956522
32 UDP 0.622222 0.927536
33 UTP 0.619565 0.927536
34 UAG 0.617188 0.931507
35 660 0.6 0.942857
36 URM 0.6 0.942857
37 G3N 0.596154 0.929577
38 UPU 0.587629 0.955882
39 4RA 0.584615 0.87013
40 UNP 0.583333 0.901408
41 3UC 0.575472 0.930556
42 UML 0.564286 0.871795
43 IUG 0.561404 0.825
44 U5P 0.555556 0.913043
45 U 0.555556 0.913043
46 UD0 0.552239 0.858974
47 UPP 0.543689 0.928571
48 UDH 0.543689 0.855263
49 2KH 0.530612 0.901408
50 44P 0.521277 0.888889
51 C5G 0.518519 0.930556
52 UDP UDP 0.505155 0.898551
53 Y6W 0.504673 0.90411
54 2QR 0.485075 0.860759
55 2GW 0.482759 0.943662
56 URI 0.477273 0.852941
57 UP5 0.47541 0.844156
58 PMP UD1 0.467626 0.848101
59 1GW 0.467213 0.905405
60 CJB 0.461538 0.838235
61 UAG API 0.457516 0.87013
62 4TC 0.456 0.822785
63 CSV 0.452991 0.866667
64 CSQ 0.452991 0.866667
65 U3P 0.447917 0.898551
66 UA3 0.447917 0.898551
67 U U 0.446429 0.914286
68 NG1 0.444444 0.753623
69 GN1 0.444444 0.753623
70 C30 0.433628 0.696203
71 PUP 0.429825 0.875
72 CXY 0.422414 0.90411
73 A U 0.418605 0.820513
74 U2P 0.418367 0.913043
75 UMA FGA LYS DAL DAL 0.414634 0.8375
76 U1S 0.409091 0.789474
77 FN5 0.40458 0.883117
78 DAU 0.403361 0.905405
79 G U 0.401515 0.780488
Ligand no: 3; 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: 4; Ligand: ASP SER THR THR PRO ALA PRO THR; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 ASP SER THR THR PRO ALA PRO THR 1 1
2 ALA VAL PRO ILE ALA GLN LYS SER GLU 0.482759 0.758621
3 ALA VAL PRO ILE ALA GLN LYS 0.482759 0.758621
4 ALA VAL PRO ALA 0.481928 0.803571
5 ACE ALA PRO ALA 0.468354 0.8
6 ALA THR PRO PHE GLN GLU 0.458333 0.844828
7 ARG THR PRO SEP LEU PRO THR 0.457627 0.722222
8 ALA PRO THR 0.45 0.890909
9 SER THR CYS PRO ALA ALA 0.447917 0.864407
10 SER ALA PRO ASP THR ARG PRO ALA 0.433333 0.818182
11 PRO THR PRO SER ALA PRO VAL PRO LEU 0.429907 0.885246
12 ALA PRO ASP THR ARG PRO ALA PRO 0.422414 0.830769
13 SIN ALA ALA PRO LYS 0.416667 0.807018
14 ACE PRO ALA PRO TYR 0.41 0.790323
15 CYS THR PRO SER ARG 0.405405 0.757576
16 SER GLU CYS THR THR PRO CYS 0.405405 0.836066
17 ACE PRO ALA PRO PHE 0.40404 0.783333
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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