Receptor
PDB id Resolution Class Description Source Keywords
5ggk 1.3 Å EC: 2.4.1.- CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MA BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH MA 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
EDO A:304;
A:305;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
MBE B:301;
A:301;
 Valid;
Valid;
 none;
none;
 Kd = 0.29 mM
301.249 C12 H15 N O8 c1cc(...
PEG B:303;
 Invalid;
 none;
 submit data
106.12 C4 H10 O3 C(COC...
GOL B:302;
A:303;
A:302;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
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: MBE; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 GLA NPO 1 1
2 NBZ GLA 1 1
3 PNA 1 1
4 PNW 1 1
5 MBE 1 1
6 147 1 1
7 PNG 1 1
8 KHP 0.895833 0.924528
9 NGB 0.754098 0.962264
10 NPJ 0.725806 0.962264
11 NSQ 0.706897 0.731343
12 RCB 0.703125 0.962264
13 GAA 0.661017 0.980769
14 PNJ 0.644068 0.910714
15 GAT 0.62963 0.716981
16 JFZ 0.614035 0.846154
17 GAL PHB 0.614035 0.634615
18 56N 0.611111 0.647059
19 LEC 0.590909 0.836066
20 6ZC 0.590909 0.836066
21 3XN 0.589041 0.809524
22 XTG 0.577465 0.862069
23 A2G NPO GAL 0.575342 0.809524
24 C3G 0.57377 0.830189
25 3X8 0.566667 0.622642
26 HNW 0.548387 0.611111
27 145 0.53125 0.962264
28 LAM 0.530864 0.910714
29 GLA BEZ 0.507692 0.653846
30 6Y2 0.493671 0.796875
31 LEC NGA 0.493671 0.796875
32 BDP NPO NDG BDP NDG 0.442105 0.796875
33 DCB 0.432099 0.822581
34 BDP NPO GNS BDP 0.431579 0.675676
35 SA0 0.430769 0.622642
36 BDP NPO GNS BDP GNS BDP GNS 0.427083 0.689189
37 6GR 0.426471 0.641509
38 A24 0.425287 0.689189
39 1DM 0.425287 0.68
40 NFG 0.424658 0.836066
41 M2F 0.424658 0.836066
42 7KP 0.410959 0.622642
43 04G GAL 0.407895 0.637931
44 MBF NIN BMA BMA 0.406977 0.822581
45 A32 0.406593 0.689189
46 XYS NPO XYS 0.405405 0.907407
47 AI1 0.4 0.610169
Similar Ligands (3D)
Ligand no: 1; Ligand: MBE; Similar ligands found: 93
No: Ligand Similarity coefficient
1 BO1 0.9343
2 F0C 0.9132
3 GAL NPO 0.9123
4 CT7 0.9021
5 BWG 0.9021
6 KUQ 0.9004
7 88X 0.8984
8 40W 0.8963
9 QTJ 0.8949
10 MRE 0.8940
11 U55 0.8940
12 KVW 0.8926
13 TYP 0.8924
14 122 0.8921
15 CR4 0.8921
16 KVQ 0.8916
17 22M 0.8909
18 205 0.8904
19 J90 0.8901
20 73E 0.8901
21 802 0.8897
22 121 0.8883
23 120 0.8873
24 KVN 0.8871
25 HI6 0.8867
26 124 0.8848
27 97K 0.8846
28 LZ4 0.8844
29 0QX 0.8839
30 GJG 0.8836
31 QC1 0.8825
32 135 0.8818
33 5R9 0.8818
34 801 0.8813
35 CWP 0.8801
36 H8B 0.8796
37 F1T 0.8782
38 J3B 0.8782
39 5YA 0.8781
40 4K9 0.8768
41 8E3 0.8751
42 7D1 MAN 0.8749
43 J2N 0.8748
44 ATU 0.8741
45 KOT 0.8740
46 9ME 0.8734
47 6MY 0.8729
48 MHB 0.8728
49 0NJ 0.8727
50 BGK 0.8726
51 7ZO 0.8712
52 DGO MAN 0.8698
53 JVB 0.8693
54 YX0 0.8687
55 T5J 0.8686
56 QRP 0.8682
57 J71 0.8678
58 08C 0.8676
59 XYP XIM 0.8671
60 VHD 0.8669
61 XYS XYS 0.8669
62 1R5 0.8668
63 907 0.8658
64 OUG 0.8653
65 697 0.8646
66 TVC 0.8643
67 IXE 0.8638
68 S13 0.8634
69 1FL 0.8634
70 EMU 0.8627
71 ZZ1 GAL 0.8626
72 M08 0.8622
73 CMZ 0.8612
74 3WK 0.8611
75 C0V 0.8607
76 P86 0.8602
77 MQR 0.8593
78 5ZM 0.8592
79 50Q 0.8592
80 1UR 0.8586
81 0MB 0.8585
82 BDE 0.8581
83 6BK 0.8580
84 KU3 0.8574
85 1Q2 0.8573
86 B7H 0.8572
87 XYP XYP 0.8571
88 Q92 0.8563
89 FLF 0.8561
90 SJR 0.8549
91 WDW 0.8524
92 5TU 0.8523
93 STL 0.8515
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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