Receptor
PDB id Resolution Class Description Source Keywords
4D0Z 2.2 Å EC: 2.4.1.41 GALNAC-T2 CRYSTAL SOAKED WITH UDP-5SGALNAC, MEA2 AND MANGANESE (HIGHER RESOLUTION DATASET) HOMO SAPIENS TRANSFERASE-PEPTIDE COMPLEX RETAINING GALNAC-T2 SUBSTRATE-SNI-TYPE REACTION QM/MM METADYNAMICS BI-BI KINETIC MECHANSUBSTRATE SPECIFICITY ACETAMIDO GROUP
Ref.: SUBSTRATE-GUIDED FRONT-FACE REACTION REVEALED BY CO STRUCTURAL SNAPSHOTS AND METADYNAMICS FOR THE POLYP N- 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:1580;
B:1576;
B:1573;
D:1575;
A:1577;
A:1574;
A:1575;
E:1572;
E:1579;
E:1582;
E:1570;
E:1581;
A:1572;
A:1579;
E:1577;
A:1571;
D:1573;
B:1578;
E:1573;
E:1576;
E:1578;
D:1576;
A:1573;
E:1583;
B:1572;
A:1576;
E:1574;
B:1577;
D:1577;
B:1574;
E:1580;
E:1571;
E:1575;
B:1575;
A:1578;
D:1574;
B:1579;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
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;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
MN E:1586;
D:1570;
A:1570;
C:1570;
F:1570;
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...
SER THR CYS PRO ALA ALA X:5;
Y:5;
Valid;
Valid;
none;
none;
submit data
478.571 n/a SCC(N...
HWU E:1585;
B:1571;
A:1582;
D:1571;
F:1571;
C:1569;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
623.419 C17 H27 N3 O16 P2 S CC(=O...
BBK D:1572;
A:1581;
E:1584;
B:1580;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
237.273 C8 H15 N O5 S CC(=O...
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: SER THR CYS PRO ALA ALA; Similar ligands found: 19
No: Ligand ECFP6 Tc MDL keys Tc
1 SER THR CYS PRO ALA ALA 1 1
2 SER GLU CYS THR THR PRO CYS 0.514286 0.965517
3 SER ALA PRO ASP THR ARG PRO ALA 0.470588 0.820895
4 SER VAL PRO ILE 0.467391 0.883333
5 SER SER CYS PRO LEU SER LYS 0.454545 0.932203
6 SER TYR SER PRO THR SEP PRO SER 0.451923 0.830769
7 ARG VAL SER PRO SER THR SER TYR THR PRO 0.451327 0.887097
8 ALA PRO ASP THR ARG PRO ALA PRO 0.448276 0.80597
9 ASP SER THR THR PRO ALA PRO THR 0.447917 0.864407
10 CYS THR PRO SER ARG 0.445455 0.873016
11 TYR SEP PRO THR SEP PRO SER 0.434783 0.771429
12 ALA PRO THR 0.433735 0.827586
13 ALA THR PRO PHE GLN GLU 0.43 0.87931
14 ALA VAL PRO ALA 0.41573 0.775862
15 LYS LEU THR PRO LEU CYS VAL THR LEU 0.413223 0.916667
16 ARG VAL ALA SER PRO THR SER GLY VAL 0.41129 0.846154
17 TYR LEU GLU PRO ALA PRO VAL THR ALA 0.40625 0.791045
18 GLY THR SER SER PRO SER ALA ASP 0.405405 0.931035
19 MET CYS PRO ARG MET THR ALA VAL MET 0.402985 0.797101
Ligand no: 2; Ligand: HWU; Similar ligands found: 64
No: Ligand ECFP6 Tc MDL keys Tc
1 12V 1 1
2 HWU 1 1
3 UD1 0.660377 0.943662
4 UD2 0.660377 0.943662
5 HP7 0.633027 0.929577
6 UD7 0.618182 0.916667
7 MJZ 0.612613 0.90411
8 UDM 0.611111 0.930556
9 F5P 0.607143 0.90411
10 UD4 0.607143 0.90411
11 F5G 0.607143 0.916667
12 UDZ 0.6 0.846154
13 GUD 0.592233 0.929577
14 UPG 0.592233 0.929577
15 GDU 0.592233 0.929577
16 UFM 0.592233 0.929577
17 EPZ 0.589744 0.930556
18 EEB 0.584746 0.917808
19 EPU 0.584746 0.917808
20 UGA 0.579439 0.915493
21 UGB 0.579439 0.915493
22 UDP 0.578947 0.901408
23 UTP 0.57732 0.901408
24 UAD 0.560748 0.902778
25 UPF 0.560748 0.88
26 UDX 0.560748 0.902778
27 UFG 0.560748 0.88
28 U2F 0.560748 0.88
29 UNP 0.56 0.876712
30 USQ 0.550459 0.814815
31 UMA 0.547619 0.930556
32 URM 0.54717 0.916667
33 660 0.54717 0.916667
34 3UC 0.540541 0.88
35 U22 0.534351 0.807229
36 UPU 0.533981 0.928571
37 G3N 0.531532 0.878378
38 UPP 0.523364 0.902778
39 UDH 0.523364 0.833333
40 U21 0.522727 0.82716
41 U20 0.522727 0.82716
42 U5P 0.515789 0.887324
43 U 0.515789 0.887324
44 UDP UDP 0.515152 0.873239
45 44P 0.5 0.864865
46 UAG 0.496454 0.881579
47 2KH 0.495146 0.876712
48 IUG 0.491803 0.783133
49 4RA 0.478873 0.825
50 UD0 0.472222 0.814815
51 UP5 0.472 0.822785
52 UML 0.467105 0.82716
53 Y6W 0.460177 0.88
54 4TC 0.453125 0.802469
55 U U 0.431034 0.888889
56 2QR 0.429577 0.817073
57 URI 0.425532 0.828571
58 U3P 0.415842 0.873239
59 UA3 0.415842 0.873239
60 PMP UD1 0.414966 0.804878
61 CSV 0.414634 0.893333
62 CSQ 0.414634 0.893333
63 CJB 0.412371 0.814286
64 C5G 0.411765 0.88
Ligand no: 3; Ligand: BBK; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 0YT 1 1
2 BBK 1 1
3 GLT 0.439024 0.7
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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