Receptor
PDB id Resolution Class Description Source Keywords
5FQH 2.1 Å EC: 7.-.-.- THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURA OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRI CLOSTRIDIUM PERFRINGENS BETA-N-ACETYLGALACTOSAMINIDASE GLYCOSIDE HYDROLASE GH123 GLYCOSPHINGOLIPID GANGLIOSIDE GLOBOSIDE SUBSTRATE- ASSISCATALYSIS HYDROLASE
Ref.: THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDRO CLOSTRIDIUM PERFRINGENS J.MOL.BIOL. V. 428 3253 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:1589;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
BGC GAL NGA B:1;
 Valid;
 none;
 submit data
545.491 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FR0 1.75 Å EC: 7.-.-.- THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURA OF A FAMILY 123 GLYCOSIDE HYDROLASE FROM CLOSTRIDIUM PERFRI CLOSTRIDIUM PERFRINGENS HYDROLASE GLYCOSIDE HYDROLASE GH123 GLYCOSPHINGOLIPID GANGLIOSIDE GLOBOSIDE SUBSTRATE-ASSISTED CATALYSIS.
Ref.: THE DETAILS OF GLYCOLIPID GLYCAN HYDROLYSIS BY THE STRUCTURAL ANALYSIS OF A FAMILY 123 GLYCOSIDE HYDRO CLOSTRIDIUM PERFRINGENS J.MOL.BIOL. V. 428 3253 2016
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 319 families.
1 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
2 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
3 5FQG - GAL NGA n/a n/a
4 5FQH - BGC GAL NGA n/a n/a
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 271 families.
1 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
2 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
3 5FQG - GAL NGA n/a n/a
4 5FQH - BGC GAL NGA n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 223 families.
1 5L7U - NGA C8 H15 N O6 CC(=O)N[C@....
2 5L7V Kd = 9.6 nM GNL C8 H13 N O4 S CC1=N[C@@H....
3 5FQF - NGA C8 H15 N O6 CC(=O)N[C@....
4 5FR0 - SIZ C8 H13 F2 N O6 C([C@@H]1[....
5 5FQG - GAL NGA n/a n/a
6 5FQH - BGC GAL NGA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BGC GAL NGA; Similar ligands found: 210
No: Ligand ECFP6 Tc MDL keys Tc
1 BGC GAL NGA 1 1
2 BGC GAL GLA NGA 0.842857 1
3 BMA MAN NAG 0.782609 1
4 BGC GAL NAG 0.771429 1
5 BGC GAL NGA GAL 0.746479 1
6 MBG A2G 0.701493 0.957447
7 BGC GAL GLA NGA GAL 0.666667 1
8 GDL NAG 0.661765 0.9375
9 BGC GAL FUC A2G 0.658537 0.978261
10 MAN BMA BMA BMA BMA BMA BMA 0.650794 0.733333
11 GLC GLC GLC GLC BGC GLC GLC 0.650794 0.733333
12 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.650794 0.733333
13 NAG NAG NAG NAG NAG 0.647887 0.918367
14 NAG NAG NAG NAG NAG NAG NAG NAG 0.647887 0.918367
15 NAG NAG NAG NAG NAG NAG 0.647887 0.918367
16 NDG NAG NAG NAG NAG 0.647887 0.918367
17 BGC GAL NAG GAL 0.615385 1
18 MAN NAG 0.608696 1
19 BMA BMA BMA BMA 0.591549 0.733333
20 NAG GAL NAG 0.589744 0.9375
21 GLC GAL NAG GAL FUC A2G 0.585106 0.918367
22 GAL NAG GAL 0.584416 1
23 BGC GAL NAG NAG GAL GAL 0.573034 0.9375
24 MAN NAG GAL 0.571429 1
25 BGC BGC BGC BGC BGC BGC BGC BGC 0.569444 0.733333
26 A2G NAG 0.569444 0.9375
27 GAL NGA A2G 0.565789 0.9375
28 NAG NAG BMA MAN NAG 0.556818 0.918367
29 NAG NAG NAG 0.55 0.849057
30 NAG NAG NAG NAG 0.55 0.849057
31 NAG NAG NAG NAG NAG NAG NAG 0.55 0.849057
32 NAG GAL 0.549296 1
33 GAL NAG GAL NAG GAL 0.548781 0.9375
34 BMA MAN MAN NAG GAL NAG 0.542553 0.9375
35 BGC FUC GAL NAG 0.54023 0.978261
36 BGC GLC GLC GLC 0.539474 0.733333
37 GLC GLC GLC GLC GLC 0.539474 0.733333
38 GAL FUC A2G 0.5375 0.978261
39 Z3Q NGA 0.536585 0.762712
40 BGC FUC GAL FUC A2G 0.534091 0.957447
41 GAL NGA 0.533333 0.93617
42 NDG NAG 0.533333 0.918367
43 GLC GLC GLC GLC GLC GLC GLC GLC GLC 0.532468 0.733333
44 BMA BMA BMA BMA GLA 0.532468 0.733333
45 NAG GAL NAG GAL NAG GAL 0.53012 0.918367
46 NAG GAL NAG GAL 0.53012 0.9375
47 BGC GAL NAG GAL FUC 0.527473 0.978261
48 MBG NAG 0.527027 0.957447
49 NAG GAL BGC GAL 0.52439 1
50 BGC GAL SIA NAG 0.52381 0.865385
51 BMA Z4Y NAG 0.523256 0.978261
52 GLC GLC AC1 0.520548 0.851064
53 SN5 SN5 0.52 0.803922
54 NAG NGO 0.518519 0.849057
55 NAG NAG BMA 0.518072 0.865385
56 AMU NAG 0.518072 0.9
57 BGC GAL GLA 0.513889 0.733333
58 NGT NAG 0.506024 0.775862
59 Z4S NAG NAG 0.505882 0.849057
60 NAG NOJ NAG NAG 0.505882 0.803571
61 NAG NOJ NAG 0.505882 0.818182
62 NAG NAG BMA MAN MAN NAG GAL NAG 0.504951 0.918367
63 MAN MAN MAN NAG NAG 0.5 0.9375
64 BGC GLA GAL 0.5 0.733333
65 NAG BDP NAG BDP NAG BDP NAG 0.5 0.9
66 G4D G4D G4D G4D G4D G4D G4D G4D G4D G4D G4D 0.5 0.717391
67 GAL NAG 0.5 1
68 GLC GAL NAG GAL FUC GLA 0.5 0.978261
69 NDG BMA MAN MAN NAG GAL NAG 0.49505 0.918367
70 MAN MAN NAG 0.493976 0.957447
71 GLC GAL BGC FUC 0.493506 0.755556
72 BGC GAL FUC 0.493506 0.755556
73 2F8 0.492537 0.893617
74 MAG 0.492537 0.893617
75 BGC GAL NAG GAL FUC FUC 0.489583 0.957447
76 BGC FUC GAL NAG GAL 0.489362 0.978261
77 AMV NAG AMU NAG 0.488889 0.882353
78 NAG NGT NAG 0.488636 0.762712
79 6Y2 0.488636 0.703125
80 NAG NAG NAG TMX 0.488095 0.775862
81 MMA MAN NAG 0.487805 0.957447
82 NAG GAL GAL 0.4875 1
83 BGC GLC GLC 0.486842 0.733333
84 TVD GAL 0.486486 0.918367
85 G2F SHG BGC BGC 0.486486 0.673469
86 ARE 0.484211 0.836735
87 AAO 0.484211 0.836735
88 3QL 0.481481 0.865385
89 GUM 0.478723 0.803571
90 BGC GLC AGL GLC GLC GLC 0.477273 0.93617
91 TXT 0.477273 0.87234
92 BGC BGC BGC XYS 0.47619 0.702128
93 NM9 NAG 0.47619 0.882353
94 NDG BMA MAN MAN NAG MAN MAN 0.475728 0.9375
95 NAG NAG MAN MAN MAN 0.473684 0.9375
96 AO3 0.473118 0.692308
97 NAA AMI NAA 0.473118 0.692308
98 BGC BGC BGC BGC BGC XYS 0.471264 0.702128
99 BGC BGC BGC XYS BGC XYS BGC XYS BGC 0.471264 0.702128
100 BGC BGC BGC BGC XYS BGC XYS BGC BGC 0.471264 0.702128
101 UMG 0.46875 0.803571
102 NAG FUC GAL FUC A2G 0.468085 0.918367
103 NAG GAL FUC FUC A2G 0.468085 0.918367
104 NAG NAG BMA MAN 0.467391 0.865385
105 A2G GAL 0.466667 1
106 A2G GAL NAG 0.465116 0.9375
107 AH0 NAG 0.465116 0.833333
108 NG1 0.464789 0.75
109 GN1 0.464789 0.75
110 BGC GAL SIA NGA SIA 0.462185 0.849057
111 GLC GAL EMB GAL MEC 0.458333 0.75
112 MGL GAL 0.457143 0.73913
113 BDP NPO NDG BDP NDG 0.456311 0.703125
114 C4W NAG FUC BMA MAN NAG 0.453704 0.865385
115 3YW 0.453333 0.913043
116 NAG G6S 0.452381 0.725806
117 NAG GAL FUC A2G 0.452381 0.978261
118 NAG GAL GLC NAG GLC RAM 0.450549 0.9375
119 MAN NAG PO4 NGA PO4 0.449438 0.789474
120 ACG 0.44898 0.8
121 NAG BMA 0.448718 0.897959
122 BGC BGC BGC XYS BGC XYS 0.448276 0.702128
123 MAN BMA BMA 0.447368 0.702128
124 BGC 5VQ GAL GLA 0.447368 0.708333
125 BGC GAL FUC GLA 0.447059 0.755556
126 NAG BMA MAN MAN NAG GAL NAG GAL 0.445545 0.918367
127 C4W NAG FUC BMA 0.443299 0.865385
128 NDG NAG GLA NAG GLC RAM 0.442308 0.918367
129 NDG GLA NAG GLC RAM 0.442308 0.918367
130 QV4 0.442105 0.836735
131 GLC GLC GLC G6D ACI GLC GLC 0.442105 0.836735
132 BGC XGP 0.44 0.611111
133 NAG AH0 0.43956 0.833333
134 NAG NAG BMA MAN MAN NAG NAG 0.439252 0.849057
135 GLC GLC AC1 GLC GLC GLC 0.438776 0.803922
136 GLC GLC AGL HMC GLC 0.438776 0.803922
137 GLC GLC G6D GLC ACI GLC 0.438776 0.803922
138 MA8 0.4375 0.843137
139 BGC GAL SIA 0.436893 0.882353
140 GAL SIA NGA 0.436893 0.865385
141 HSH A2G FUC 0.43617 0.818182
142 GYU 0.435897 0.767857
143 GLC GLC FRU 0.435294 0.66
144 BGC GAL GLA NGA GAL SIA 0.434783 0.865385
145 GAL GLC GLD ACI 0.433333 0.836735
146 G2F BGC BGC BGC BGC BGC 0.43038 0.66
147 GLC NBU GAL GLA 0.43038 0.68
148 GDL PHJ NAG 0.43 0.737705
149 7SA 0.43 0.803922
150 NDG GLA GLC NAG GLC RAM 0.429907 0.918367
151 GLA NAG GAL FUC 0.428571 0.978261
152 GAL NAG FUC GAL 0.428571 0.978261
153 MGC GAL 0.428571 0.957447
154 BGC GAL NAG GAL SIA 0.42735 0.849057
155 BGC BGC BGC XYS BGC XYS XYS 0.426966 0.702128
156 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.425926 0.9375
157 MMA MAN NAG MAN NAG NAG 0.425532 0.9
158 FUC GAL 0.424658 0.733333
159 LEC NGA 0.423913 0.703125
160 NAG NAG BMA BMA 0.423913 0.833333
161 NAG FUC GAL 0.423529 0.978261
162 JXD 0.423077 0.661765
163 BGC GAL SIA NGA GAL 0.422414 0.865385
164 GYP GZL NAG 0.421053 0.9
165 G2I 0.419753 0.76
166 G3I 0.419753 0.76
167 NAG GCU NAG GCD 0.419048 0.833333
168 BGC Z9D 0.418919 0.717391
169 C4W NAG FUC BMA MAN MAN NAG 0.418803 0.865385
170 YZ0 MAN MAN NAG MAN 0.418367 0.957447
171 A2G 0.41791 0.888889
172 BM3 0.41791 0.888889
173 NAG 0.41791 0.888889
174 NDG 0.41791 0.888889
175 NGA 0.41791 0.888889
176 HSQ 0.41791 0.888889
177 SER A2G 0.417722 0.843137
178 TNR 0.417722 0.86
179 MUB ALA NAG DGN 0.415094 0.818182
180 BGC BGC BGC XYS XYS GAL GAL 0.414894 0.702128
181 C4W NAG FUC BMA MAN NAG GAL 0.414414 0.775862
182 C4W NAG FUC BMA MAN MAN NAG NAG 0.413793 0.865385
183 GLC EDO GLC 0.413333 0.702128
184 BGC FUC GAL 0.4125 0.755556
185 GLC BGC FUC GAL 0.4125 0.755556
186 GAL NAG GAL FUC FUC 0.410526 0.957447
187 FHY 0.410526 0.849057
188 BGC GLC GLD GLC ACI GLD GLC ACI G6D 0.41 0.754717
189 XYS GLC GLC 0.409639 0.755556
190 AMU ALA NAG DGL 0.409524 0.833333
191 GAL NGA GAL SIA 0.409091 0.865385
192 NAG GAL FUC GLA 0.408602 0.978261
193 C4W NAG FUC BMA MAN MAN NAG GAL NAG 0.408333 0.775862
194 FRU BGC BGC BGC 0.407407 0.66
195 BGC BGC BGC XYS BGC XYS GAL 0.40625 0.702128
196 MUB ALA NAG ZGL 0.40566 0.818182
197 C4W NAG FUC BMA MAN 0.40566 0.865385
198 NDG GAL 0.405063 0.741379
199 NAG NAG 0.404762 0.918367
200 NDG FUC GAL FUC 0.404494 0.957447
201 NAG GAL FUC FUC 0.404494 0.957447
202 SN5 NGT 0.404494 0.694915
203 GLC GLC AGL HMC 0.40404 0.784314
204 BGC OXZ BGC 0.402439 0.690909
205 NAG GAL UNU 0.402174 0.918367
206 MUB ALA NAG GLN 0.401869 0.833333
207 GLC GLC GLC AC1 0.4 0.803922
208 GLC GLC G6D ADH GLC GLC 0.4 0.784314
209 GLC BGC G6D ACI 0.4 0.836735
210 GLC GLC GLC GLC GLC GLC AC1 0.4 0.803922
Similar Ligands (3D)
Ligand no: 1; Ligand: BGC GAL 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 : 5FR0; Ligand: SIZ; 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: 5fr0.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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