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 A:301;
B:301;
Valid;
Valid;
none;
none;
Kd = 0.8 mM
547.514 n/a ON(O)...
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 25 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 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@....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 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
Ligand no: 1; Ligand: LEC NGA; Similar ligands found: 98
No: Ligand ECFP6 Tc MDL keys Tc
1 LEC NGA 1 1
2 NPO A2G GAL 0.782051 0.984375
3 GAL A2G NPO 0.782051 0.984375
4 LEC 0.767123 0.953125
5 6ZC 0.767123 0.953125
6 6Y2 0.753086 1
7 NDG BDP BDP NPO NDG 0.578431 1
8 NAG NGA 0.530864 0.75
9 NAG A2G 0.530864 0.75
10 NAG MBG 0.512195 0.707692
11 CG3 A2G GAL 0.510638 0.969231
12 NAG MAN MMA 0.494382 0.707692
13 GLA NPO 0.493671 0.796875
14 GAL NPO 0.493671 0.796875
15 NBZ GLA 0.493671 0.796875
16 PNG 0.493671 0.796875
17 PNW 0.493671 0.796875
18 147 0.493671 0.796875
19 MBE 0.493671 0.796875
20 PNA 0.493671 0.796875
21 KHP 0.493506 0.742424
22 MAN NAG 0.487805 0.703125
23 GAL NAG 0.481928 0.703125
24 NGA GAL 0.481928 0.703125
25 NAG GAL 0.481928 0.703125
26 NPJ 0.47191 0.828125
27 MBG A2G 0.470588 0.707692
28 A2G MBG 0.470588 0.707692
29 MAN MAN NAG 0.467391 0.681818
30 RCB 0.461538 0.828125
31 NAG GCU NAG GCU NAG GCU 5AX 0.46 0.78125
32 NAG BDP NAG BDP NAG BDP NAG 0.46 0.78125
33 NAG NDG 0.458824 0.75
34 CBS CBS 0.458824 0.75
35 NAG GDL 0.458824 0.75
36 CBS 0.458824 0.75
37 PNJ 0.457831 0.846154
38 GUM 0.456311 0.73913
39 NAG NM9 0.451613 0.742424
40 NDG NAG 0.448276 0.765625
41 UMG 0.447619 0.73913
42 MAG 0.441558 0.661538
43 2F8 0.441558 0.661538
44 A2G GLA FUC 0.44086 0.71875
45 A2G GAL FUC 0.44086 0.71875
46 FUC GLA A2G 0.44086 0.71875
47 NGA GAL FUC 0.44086 0.71875
48 FUC GL0 A2G 0.44086 0.71875
49 FUC GAL A2G 0.44086 0.71875
50 GAL MGC 0.440476 0.707692
51 NGB 0.43956 0.828125
52 3QL 0.43956 0.705882
53 NAG NAG NAG NAG 0.438202 0.765625
54 NAG NAG NAG NAG NDG NAG 0.438202 0.765625
55 NAG NAG NAG NAG NAG NAG 0.438202 0.765625
56 NAG NAG NAG 0.438202 0.765625
57 NDG NAG NAG NAG 0.438202 0.765625
58 NDG NAG NAG NDG NAG 0.438202 0.765625
59 NAG NAG NAG NAG NAG 0.438202 0.765625
60 NAG NAG NAG NAG NDG 0.438202 0.765625
61 CTO 0.438202 0.765625
62 NAG NAG NDG 0.438202 0.765625
63 NAG NAG 0.438202 0.691176
64 NDG NAG NAG 0.438202 0.765625
65 NDG NAG NAG NDG 0.438202 0.765625
66 NAG NAG NAG NDG 0.438202 0.765625
67 NAG NAG NAG NAG NAG NAG NAG NAG 0.438202 0.765625
68 NAG GAL NAG 0.43617 0.75
69 NAG GAL BGC 0.43617 0.703125
70 NAG NGO 0.434783 0.705882
71 GNS BDP GNS BDP GNS BDP NPO 0.432432 0.789474
72 NAG MAN MAN 0.431579 0.703125
73 NAG MAN BMA 0.431579 0.703125
74 NAG AMU 0.427083 0.78125
75 AH0 NAG 0.427083 0.710145
76 NAG MUB 0.427083 0.78125
77 NGA GAL BGC 0.423913 0.703125
78 LAM 0.423077 0.791045
79 NAG AMU NAG AMV 0.421569 0.769231
80 NAG AH0 0.42 0.735294
81 NG1 0.419753 0.671429
82 GN1 0.419753 0.671429
83 NGT NAG 0.416667 0.671233
84 NAG MAN MAN MAN NAG 0.415842 0.75
85 WZ5 0.415094 0.707692
86 NGA GLA GAL BGC 0.414141 0.703125
87 DLD 0.408163 0.768116
88 FUC BGC GAL NAG 0.407767 0.71875
89 MMA MAN NAG MAN NAG NAG 0.407767 0.753846
90 FUC GAL NAG A2G FUC 0.40566 0.765625
91 NAG GAL FUC FUC A2G 0.40566 0.765625
92 NOJ NAG NAG NAG 0.40404 0.724638
93 NOJ NAG NAG 0.40404 0.710145
94 GLC FUC GAL FUC A2G 0.403846 0.734375
95 BGC FUC GAL FUC A2G 0.403846 0.734375
96 GAL A2G MBN 0.402062 0.75
97 A2G GAL NAG FUC 0.4 0.765625
98 A2G GAL BGC FUC 0.4 0.71875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5GGN; Ligand: LEC; Similar sites found: 1
This union binding pocket(no: 1) in the query (biounit: 5ggn.bio2) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4BTI 7R9 0.03273 0.40155 13.4146
Pocket No.: 2; Query (leader) PDB : 5GGN; Ligand: LEC; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback