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Receptor
PDB id Resolution Class Description Source Keywords
3H55 1.91 Å EC: 3.2.1.49 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, WITH GALACTOSE HOMO SAPIENS GLYCOPROTEIN CARBOHYDRATE-BINDING PROTEIN GLYCOSIDASE LYSENZYME (BETA/ALPHA)8 BARREL PROTEIN-LIGAND COMPLEX DISEAMUTATION DISULFIDE BOND HYDROLASE LYSOSOME
Ref.: THE 1.9 A STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE: THE MOLECULAR BASI SCHINDLER AND KANZAKI DISEASES J.MOL.BIOL. V. 393 435 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CIT A:1100;
B:2100;
Invalid;
Invalid;
none;
none;
submit data
192.124 C6 H8 O7 C(C(=...
GLA A:1000;
A:1500;
B:2000;
B:2500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
180.156 C6 H12 O6 C([C@...
NAG A:885;
B:885;
Invalid;
Invalid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
NAG NAG BMA MAN MAN A:677;
B:677;
Invalid;
Invalid;
none;
none;
submit data
910.826 n/a O=C(N...
NAG NAG FUC B:624;
Invalid;
none;
submit data n/a n/a n/a n/a
NAG NAG FUC BMA A:624;
Invalid;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3H55 1.91 Å EC: 3.2.1.49 CRYSTAL STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE, WITH GALACTOSE HOMO SAPIENS GLYCOPROTEIN CARBOHYDRATE-BINDING PROTEIN GLYCOSIDASE LYSENZYME (BETA/ALPHA)8 BARREL PROTEIN-LIGAND COMPLEX DISEAMUTATION DISULFIDE BOND HYDROLASE LYSOSOME
Ref.: THE 1.9 A STRUCTURE OF HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE: THE MOLECULAR BASI SCHINDLER AND KANZAKI DISEASES J.MOL.BIOL. V. 393 435 2009
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4DO4 - DJN C8 H16 N2 O4 CC(=O)N[C@....
2 4DO6 - BGC C6 H12 O6 C([C@@H]1[....
3 4DO5 - DGJ C6 H13 N O4 C1[C@@H]([....
4 3H55 - GLA C6 H12 O6 C([C@@H]1[....
5 3H54 - A2G C8 H15 N O6 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 3 families.
1 1KTC - NGA C8 H15 N O6 CC(=O)N[C@....
2 4DO4 - DJN C8 H16 N2 O4 CC(=O)N[C@....
3 4DO6 - BGC C6 H12 O6 C([C@@H]1[....
4 4DO5 - DGJ C6 H13 N O4 C1[C@@H]([....
5 3H55 - GLA C6 H12 O6 C([C@@H]1[....
6 3H54 - A2G C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1KTC - NGA C8 H15 N O6 CC(=O)N[C@....
2 4DO4 - DJN C8 H16 N2 O4 CC(=O)N[C@....
3 4DO6 - BGC C6 H12 O6 C([C@@H]1[....
4 4DO5 - DGJ C6 H13 N O4 C1[C@@H]([....
5 3H55 - GLA C6 H12 O6 C([C@@H]1[....
6 3H54 - A2G C8 H15 N O6 CC(=O)N[C@....
7 3GXP - GLA C6 H12 O6 C([C@@H]1[....
8 3HG5 - GAL C6 H12 O6 C([C@@H]1[....
9 3LX9 - A2G C8 H15 N O6 CC(=O)N[C@....
10 3HG3 - GLA GLC n/a n/a
11 3HG2 - GAL C6 H12 O6 C([C@@H]1[....
12 3S5Y Ki = 39 nM DGJ C6 H13 N O4 C1[C@@H]([....
13 3S5Z Ki = 16 mM GLA C6 H12 O6 C([C@@H]1[....
14 3HG4 - GAL C6 H12 O6 C([C@@H]1[....
15 1UAS - GLA C6 H12 O6 C([C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLA; Similar ligands found: 142
No: Ligand ECFP6 Tc MDL keys Tc
1 WOO 1 1
2 GLC 1 1
3 BGC 1 1
4 ALL 1 1
5 BMA 1 1
6 GXL 1 1
7 GIV 1 1
8 GAL 1 1
9 MAN 1 1
10 GLA 1 1
11 Z6J 0.653846 0.866667
12 32O 0.653846 0.866667
13 RIB 0.653846 0.866667
14 FUB 0.653846 0.866667
15 AHR 0.653846 0.866667
16 MLB 0.511628 0.848485
17 GLC GLC 0.511628 0.848485
18 BGC GLC 0.511628 0.848485
19 BGC GLA 0.511628 0.848485
20 GLA BMA 0.511628 0.848485
21 MAN BMA 0.511628 0.848485
22 BMA GLA 0.511628 0.848485
23 GLA BGC 0.511628 0.848485
24 MAN MAN 0.511628 0.848485
25 GLA GLC 0.511628 0.848485
26 BMA MAN 0.511628 0.848485
27 GAL GLC 0.511628 0.848485
28 GAL GAL 0.511628 0.848485
29 LAK 0.511628 0.848485
30 GLC BGC 0.511628 0.848485
31 YDR 0.5 0.8
32 GLC GLC GLC GLC BGC 0.488889 0.848485
33 GLC GLC GLC 0.488889 0.848485
34 MAN MAN MAN 0.488889 0.848485
35 BMA MAN MAN 0.488889 0.848485
36 GLC GLC GLC GLC GLC BGC 0.488889 0.848485
37 EMZ 0.472222 0.794118
38 BG6 0.461538 0.675
39 BGP 0.461538 0.675
40 G6P 0.461538 0.675
41 M6P 0.461538 0.675
42 M6D 0.461538 0.675
43 A6P 0.461538 0.675
44 GAF 0.457143 0.875
45 SHG 0.457143 0.875
46 2FG 0.457143 0.875
47 G2F 0.457143 0.875
48 2H5 0.457143 0.875
49 GCS 0.457143 0.777778
50 1GN 0.457143 0.777778
51 X6X 0.457143 0.777778
52 PA1 0.457143 0.777778
53 95Z 0.457143 0.777778
54 G3F 0.457143 0.875
55 NGR 0.454545 0.848485
56 MAL 0.454545 0.848485
57 MAN GLC 0.454545 0.848485
58 GAL BGC 0.454545 0.848485
59 GLA GLA 0.454545 0.848485
60 BGC BMA 0.454545 0.848485
61 M3M 0.454545 0.848485
62 GLA GAL 0.454545 0.848485
63 MAB 0.454545 0.848485
64 GLC GAL 0.454545 0.848485
65 B2G 0.454545 0.848485
66 LBT 0.454545 0.848485
67 BMA GAL 0.454545 0.848485
68 LAT 0.454545 0.848485
69 BGC GAL 0.454545 0.848485
70 CBI 0.454545 0.848485
71 CBK 0.454545 0.848485
72 N9S 0.454545 0.848485
73 LB2 0.454545 0.848485
74 3MG 0.444444 0.875
75 TCB 0.444444 0.8
76 GLC SGC 0.444444 0.8
77 YIO 0.441176 0.870968
78 2GS 0.432432 0.875
79 2M4 0.431818 0.848485
80 AHR AHR 0.428571 0.764706
81 GLF 0.428571 0.84375
82 FUB AHR 0.428571 0.764706
83 MAN BMA BMA 0.416667 0.848485
84 BMA MAN BMA 0.416667 0.848485
85 CTR 0.416667 0.848485
86 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.416667 0.848485
87 GLA GAL BGC 0.416667 0.848485
88 CE5 0.416667 0.848485
89 MLR 0.416667 0.848485
90 CE6 0.416667 0.848485
91 MT7 0.416667 0.848485
92 BMA BMA BMA 0.416667 0.848485
93 GLC BGC BGC BGC BGC 0.416667 0.848485
94 MAN MAN BMA BMA BMA BMA 0.416667 0.848485
95 BGC BGC BGC BGC BGC 0.416667 0.848485
96 BGC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
97 BGC GLC GLC 0.416667 0.848485
98 BMA BMA BMA BMA BMA 0.416667 0.848485
99 MAN BMA BMA BMA BMA 0.416667 0.848485
100 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.416667 0.848485
101 GLC BGC BGC BGC BGC BGC 0.416667 0.848485
102 MAN BMA BMA BMA BMA BMA 0.416667 0.848485
103 BGC BGC BGC BGC BGC BGC 0.416667 0.848485
104 BGC GLC GLC GLC 0.416667 0.848485
105 BGC BGC BGC GLC 0.416667 0.848485
106 CTT 0.416667 0.848485
107 GLA GAL GLC 0.416667 0.848485
108 MTT 0.416667 0.848485
109 GLC BGC BGC BGC 0.416667 0.848485
110 GLC GLC BGC 0.416667 0.848485
111 CEY 0.416667 0.848485
112 B4G 0.416667 0.848485
113 CE8 0.416667 0.848485
114 BMA BMA BMA BMA BMA BMA 0.416667 0.848485
115 GAL FUC 0.416667 0.848485
116 DXI 0.416667 0.848485
117 GLC BGC GLC 0.416667 0.848485
118 CT3 0.416667 0.848485
119 GAL GAL GAL 0.416667 0.848485
120 GLC GLC GLC GLC GLC 0.416667 0.848485
121 BGC BGC BGC BGC 0.416667 0.848485
122 BGC BGC BGC 0.416667 0.848485
123 BGC BGC GLC 0.416667 0.848485
124 CEX 0.416667 0.848485
125 GLC GAL GAL 0.416667 0.848485
126 BGC GLC GLC GLC GLC 0.416667 0.848485
127 GLC BGC BGC 0.416667 0.848485
128 GS1 GLC GS1 0.408163 0.8
129 SGC SGC BGC 0.408163 0.8
130 BGC BGC BGC GLC BGC BGC 0.408163 0.848485
131 GLC BGC BGC BGC BGC BGC BGC 0.408163 0.848485
132 1LL 0.405405 0.771429
133 TDG 0.405405 0.771429
134 TRE 0.405405 0.848485
135 NDG 0.404762 0.7
136 NGA 0.404762 0.7
137 NAG 0.404762 0.7
138 HSQ 0.404762 0.7
139 A2G 0.404762 0.7
140 BM3 0.404762 0.7
141 FUB AHR AHR 0.4 0.764706
142 AHR AHR AHR AHR AHR AHR 0.4 0.764706
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3H55; Ligand: GLA; Similar sites found with APoc: 50
This union binding pocket(no: 1) in the query (biounit: 3h55.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5FYR INS 1.67785
2 4KP7 1UQ 1.75
3 4KP7 NAP 1.75
4 3UPY FOM 2
5 2Y88 2ER 2.04918
6 3VKC FPQ 2.0979
7 4UWJ MYA 2.25
8 4UWJ 7L5 2.25
9 3NJ4 AFX 2.5
10 5DKY NOJ 2.5
11 4RJK TDL 2.5
12 4RJK TPP 2.5
13 4JOB TLA 2.52525
14 1O68 KIV 2.90909
15 6GVD FDK 3
16 2ZJ1 NAD 3
17 2ZJ1 ARJ 3
18 4AMW 5DI 3
19 4UDK BMA 3.17003
20 5XQW 8EU 3.22581
21 5NN6 MIG 3.25
22 5H9O GLC 3.40909
23 3WEO ACR GLC GLC GLC GLC 3.5
24 5HJO XD3 3.61446
25 3MKK GLC BGC 3.75
26 4Z1D PEP 3.98551
27 2F2H XTG 4
28 3LPP KTL 4
29 5NBW 8SK 4.05405
30 1M3U KPL 4.16667
31 2W92 NGT 4.25
32 4BFW ZVW 4.71698
33 3OND ADN 4.75
34 1H8S AIC 5.55556
35 4XPQ FUL 5.69444
36 5E1Q LAT GLA 5.75
37 5F7U GLC GLC GLC 5.75
38 4H6Q TFB 5.76923
39 4H6Q FAD 5.76923
40 2YFO GLA 6
41 2YFO GAL 6
42 3L4U DSK 6.25
43 4B9Z ACR 6.75
44 2G37 FAD 7.33945
45 2XN2 GLA 8.25
46 3V91 UPG 9.27835
47 5AWQ GLC GLC GLC 11.5
48 4OGQ 7PH 24.1379
49 4NZF ARB 37.75
50 3A23 GAL 47
Pocket No.: 2; Query (leader) PDB : 3H55; Ligand: GLA; Similar sites found with APoc: 8
This union binding pocket(no: 2) in the query (biounit: 3h55.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2Z49 AMG 1.75
2 3EBL GA4 3
3 3CQO FUC 3.07167
4 3A76 SPD 3.97727
5 2ZQ0 ACR 4.25
6 1EC9 XYH 4.5
7 1M13 HYF 6.96203
8 2X7J TPP 17
Pocket No.: 3; Query (leader) PDB : 3H55; Ligand: GLA; Similar sites found with APoc: 38
This union binding pocket(no: 3) in the query (biounit: 3h55.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 2HKA C3S 1.53846
2 4L9Z COA 1.76991
3 3UES DFU 1.88285
4 4W93 3L9 2
5 1W4R TTP 2.05128
6 3ZGJ RMN 2.15633
7 4OOE FOM 2.25
8 4WW8 VD9 2.28137
9 4UDG NDG 3.17003
10 5I0F GLC GLC 3.5
11 2C42 PYR 3.5
12 2C42 TPP 3.5
13 2WSA 646 3.75
14 2WSA MYA 3.75
15 1B1C FMN 3.8674
16 2V77 PAY 3.8835
17 1REQ DCA 4
18 1TIW FAD 4
19 1TIW TFB 4
20 1VEM GLC GLC 4
21 4I9A NCN 4.16667
22 1E2K TMC 4.22961
23 1MH5 HAL 4.34783
24 1MJJ HAL 4.40529
25 3OND NAD 4.75
26 4X17 SIA SIA 4.77941
27 2CJF RP4 5.09554
28 1Y57 MPZ 5.25
29 5KF6 TFB 6.25
30 5KF6 FAD 6.25
31 4NMC FAD 7
32 4JEJ 1GP 7.37705
33 5JZI LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 8
34 5M42 FMN 8.60215
35 2YFB SIN 10.0775
36 1P4A PCP 10.1754
37 2YNE NHW 13.2812
38 2YNE YNE 13.2812
Pocket No.: 4; Query (leader) PDB : 3H55; Ligand: GLA; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 3h55.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4I3V NAD 1.75
2 4UXH T5A 2.71739
3 4LOC OXM 4.25
4 3MTX PGT 8.60927
5 2ZSH GA3 17.2727
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