Receptor
PDB id Resolution Class Description Source Keywords
5ggl 1.27 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MA BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH GLA LPHA-PNP HOMO SAPIENS GLYCOSYLTRANSFEREASE O-MANNOSYLATION ALPHA-DYSTROGLYCAN SBINDING PROTEIN
Ref.: CARBOHYDRATE-BINDING DOMAIN OF THE POMGNT1 STEM REG MODULATES O-MANNOSYLATION SITES OF ALPHA-DYSTROGLYC PROC.NATL.ACAD.SCI.USA V. 113 9280 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
6ZC A:301;
B:301;
 Valid;
Valid;
 none;
none;
 Kd = 16.52 mM
342.301 C14 H18 N2 O8 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5GGN 1.21 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MA BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH GLP NP HOMO SAPIENS GLYCOSYLTRANSFEREASE O-MANNOSYLATION ALPHA-DYSTROGLYCAN SBINDING PROTEIN
Ref.: CARBOHYDRATE-BINDING DOMAIN OF THE POMGNT1 STEM REG MODULATES O-MANNOSYLATION SITES OF ALPHA-DYSTROGLYC PROC.NATL.ACAD.SCI.USA V. 113 9280 2016
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 5GGP Kd = 0.5 mM THR PRO THR MAN NAG PRO VAL n/a n/a
2 5GGJ Kd = 17.78 mM PNA C12 H15 N O8 c1cc(ccc1[....
3 5GGN Kd = 0.22 mM LEC C14 H18 N2 O8 CC(=O)N[C@....
4 5GGK Kd = 0.29 mM MBE C12 H15 N O8 c1cc(ccc1[....
5 5GGO Kd = 0.8 mM LEC NGA n/a n/a
6 5GGL Kd = 16.52 mM 6ZC C14 H18 N2 O8 CC(=O)N[C@....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 32 families.
1 5GGP Kd = 0.5 mM THR PRO THR MAN NAG PRO VAL n/a n/a
2 5GGJ Kd = 17.78 mM PNA C12 H15 N O8 c1cc(ccc1[....
3 5GGN Kd = 0.22 mM LEC C14 H18 N2 O8 CC(=O)N[C@....
4 5GGK Kd = 0.29 mM MBE C12 H15 N O8 c1cc(ccc1[....
5 5GGO Kd = 0.8 mM LEC NGA n/a n/a
6 5GGL Kd = 16.52 mM 6ZC C14 H18 N2 O8 CC(=O)N[C@....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 5GGP Kd = 0.5 mM THR PRO THR MAN NAG PRO VAL n/a n/a
2 5GGJ Kd = 17.78 mM PNA C12 H15 N O8 c1cc(ccc1[....
3 5GGN Kd = 0.22 mM LEC C14 H18 N2 O8 CC(=O)N[C@....
4 5GGK Kd = 0.29 mM MBE C12 H15 N O8 c1cc(ccc1[....
5 5GGO Kd = 0.8 mM LEC NGA n/a n/a
6 5GGL Kd = 16.52 mM 6ZC C14 H18 N2 O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 6ZC; Similar ligands found: 58
No: Ligand ECFP6 Tc MDL keys Tc
1 6ZC 1 1
2 LEC 1 1
3 6Y2 0.767123 0.953125
4 LEC NGA 0.767123 0.953125
5 A2G NPO GAL 0.68 0.968254
6 KHP 0.59375 0.777778
7 NBZ GLA 0.590909 0.836066
8 147 0.590909 0.836066
9 PNW 0.590909 0.836066
10 MBE 0.590909 0.836066
11 GLA NPO 0.590909 0.836066
12 PNA 0.590909 0.836066
13 PNG 0.590909 0.836066
14 BDP NPO NDG BDP NDG 0.557895 0.953125
15 PNJ 0.542857 0.887097
16 MAG 0.53125 0.640625
17 2F8 0.53125 0.640625
18 NPJ 0.512821 0.809524
19 RCB 0.5 0.809524
20 NGB 0.493671 0.809524
21 NG1 0.478261 0.701493
22 GN1 0.478261 0.701493
23 NSQ 0.466667 0.657895
24 MAN NAG 0.453333 0.68254
25 JFZ 0.450704 0.737705
26 GAL NGA 0.448718 0.646154
27 SER A2G 0.447368 0.692308
28 GYU 0.447368 0.619718
29 C3G 0.445946 0.754098
30 3YW 0.445946 0.650794
31 MBG NAG 0.441558 0.661538
32 14T 0.439024 0.666667
33 MBG A2G 0.435897 0.661538
34 GAA 0.434211 0.852459
35 TNR 0.428571 0.676923
36 MMA MAN NAG 0.428571 0.661538
37 GUM 0.427083 0.695652
38 A2G NAG 0.423077 0.703125
39 BDP NPO GNS BDP GNS BDP GNS 0.423077 0.753247
40 GDL NAG 0.423077 0.703125
41 LAM 0.421053 0.772727
42 MAN MAN NAG 0.418605 0.661538
43 BMX BMX BMX BM3 0.418605 0.735294
44 UMG 0.418367 0.695652
45 GAL NAG 0.417722 0.68254
46 BDP NPO GNS BDP 0.413462 0.74026
47 NDG NAG 0.4125 0.71875
48 NAG 0.409091 0.655738
49 NDG 0.409091 0.655738
50 NGA 0.409091 0.655738
51 HSQ 0.409091 0.655738
52 A2G 0.409091 0.655738
53 BM3 0.409091 0.655738
54 NAG NAG NAG NAG NAG NAG NAG NAG 0.402439 0.71875
55 NAG NAG NAG NAG NAG NAG 0.402439 0.71875
56 NDG NAG NAG NAG NAG 0.402439 0.71875
57 NAG NAG NAG NAG NAG 0.402439 0.71875
58 NM9 NAG 0.402299 0.69697
Similar Ligands (3D)
Ligand no: 1; Ligand: 6ZC; Similar ligands found: 1
No: Ligand Similarity coefficient
1 FD7 0.8713
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GGN; Ligand: LEC; 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: 5ggn.bio2) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5GGN; Ligand: LEC; 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: 5ggn.bio1) has 8 residues
No: Leader PDB Ligand Sequence Similarity
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