Receptor
PDB id Resolution Class Description Source Keywords
5GGO 1.5 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MA BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH GAB ETA1,3-GLCNAC-BETA-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
LEC NGA D:1;
C:1;
 Valid;
Valid;
 none;
none;
 Kd = 0.8 mM
547.514 n/a O=C(N...
EDO B:303;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
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: LEC NGA; Similar ligands found: 77
No: Ligand ECFP6 Tc MDL keys Tc
1 LEC NGA 1 1
2 A2G NPO GAL 0.782051 0.984375
3 LEC 0.767123 0.953125
4 6ZC 0.767123 0.953125
5 6Y2 0.753086 1
6 BDP NPO NDG BDP NDG 0.578431 1
7 GAL NGA A2G 0.547619 0.75
8 A2G NAG 0.530864 0.75
9 MBG NAG 0.512195 0.707692
10 GAL NGA 0.5 0.666667
11 MMA MAN NAG 0.494382 0.707692
12 147 0.493671 0.796875
13 MBE 0.493671 0.796875
14 NBZ GLA 0.493671 0.796875
15 GLA NPO 0.493671 0.796875
16 PNA 0.493671 0.796875
17 PNG 0.493671 0.796875
18 PNW 0.493671 0.796875
19 KHP 0.493506 0.742424
20 MAN NAG 0.487805 0.703125
21 NPJ 0.47191 0.828125
22 MBG A2G 0.470588 0.707692
23 MAN MAN NAG 0.467391 0.681818
24 RCB 0.461538 0.828125
25 NAG BDP NAG BDP NAG BDP NAG 0.46 0.78125
26 GDL NAG 0.458824 0.75
27 PNJ 0.457831 0.846154
28 GUM 0.456311 0.73913
29 NM9 NAG 0.451613 0.742424
30 NDG NAG 0.448276 0.765625
31 UMG 0.447619 0.73913
32 2F8 0.441558 0.661538
33 MAG 0.441558 0.661538
34 GAL FUC A2G 0.44086 0.71875
35 MGC GAL 0.440476 0.707692
36 NGB 0.43956 0.828125
37 3QL 0.43956 0.705882
38 NAG NAG NAG NAG NAG NAG 0.438202 0.765625
39 NDG NAG NAG NAG NAG 0.438202 0.765625
40 NAG NAG NAG NAG NAG 0.438202 0.765625
41 NAG NAG NAG NAG NAG NAG NAG NAG 0.438202 0.765625
42 BGC GAL NAG 0.43617 0.703125
43 NAG GAL NAG 0.43617 0.75
44 AMU NAG 0.427083 0.78125
45 AH0 NAG 0.427083 0.710145
46 BMA MAN NAG 0.425532 0.703125
47 BDP NPO GNS BDP GNS BDP GNS 0.424779 0.769231
48 BGC GAL NGA 0.423913 0.703125
49 LAM 0.423077 0.791045
50 FHY 0.421569 0.720588
51 AMV NAG AMU NAG 0.421569 0.769231
52 NAG AH0 0.42 0.735294
53 GN1 0.419753 0.671429
54 NG1 0.419753 0.671429
55 NGT NAG 0.416667 0.671233
56 MAN MAN MAN NAG NAG 0.415842 0.75
57 YZ0 MAN MAN NAG MAN 0.415094 0.707692
58 BGC GAL GLA NGA 0.414141 0.703125
59 NAG NGO 0.410526 0.695652
60 NAG NAG BMA MAN NAG 0.409524 0.765625
61 MMA MAN NAG MAN NAG NAG 0.407767 0.753846
62 BGC FUC GAL NAG 0.407767 0.71875
63 A2G THR GAL 0.40625 0.769231
64 NAG NAG NAG NAG 0.40625 0.720588
65 NAG NAG NAG 0.40625 0.720588
66 NAG NAG NAG NAG NAG NAG NAG 0.40625 0.720588
67 BMA Z4Y NAG 0.405941 0.692308
68 NAG GAL FUC FUC A2G 0.40566 0.765625
69 NAG FUC GAL FUC A2G 0.40566 0.765625
70 Z4S NAG NAG 0.40404 0.720588
71 BGC FUC GAL FUC A2G 0.403846 0.734375
72 HSH A2G FUC 0.403846 0.652778
73 BDP NPO GNS BDP 0.403509 0.75641
74 A2G MBN GAL 0.402062 0.734375
75 GAL A2G MBN 0.402062 0.75
76 NAG GAL GLC NAG GLC RAM 0.401961 0.75
77 BGC GAL FUC A2G 0.4 0.71875
Similar Ligands (3D)
Ligand no: 1; Ligand: LEC NGA; Similar ligands found: 0
No: Ligand Similarity coefficient
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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