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Receptor
PDB id Resolution Class Description Source Keywords
2W1U 2 Å EC: 3.2.1.35 A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA- D -GLCNAC-BETA(1,3)GALNAC CLOSTRIDIUM PERFRINGENS FAMILY 32 CARBOHYDRATE BINDING MODULE FAMILY 84 GLYCOSIDE HYDROLASE GLYCOSIDASE HEXOSAMINIDASE CLOSTRIDIUM PERFRINGENS CBM TOXIN SECRETED VIRULENCE HYDROLASE
Ref.: N-ACETYLGLUCOSAMINE RECOGNITION BY A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM CLOSTRIDIUM PERFRINGENS NAGH. J.MOL.BIOL. V. 390 208 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT B:1953;
C:1951;
D:1951;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
59.044 C2 H3 O2 CC(=O...
CA A:1948;
B:1952;
C:1950;
D:1950;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
NAG A2G C:1948;
Invalid;
none;
submit data
424.403 n/a O=C(N...
NAG NGA A:1946;
B:1950;
D:1948;
Valid;
Valid;
Valid;
none;
none;
none;
Ka = 5910 M^-1
424.403 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2WDB 2.03 Å EC: 3.2.1.35 A FAMILY 32 CARBOHYDRATE-BINDING MODULE, FROM THE MU TOXIN PRODUCED BY CLOSTRIDIUM PERFRINGENS, IN COMPLEX WITH BETA- D -GLCNAC-BETA(1,2)MANNOSE CLOSTRIDIUM PERFRINGENS FAMILY 32 CARBOHYDRATE BINDING MODULE FAMILY 84 GLYCOSIDE HYDROLASE GLYCOSIDASE HEXOSAMINIDASE CLOSTRIDIUM PERFRINGENS CBM TOXIN SECRETED VIRULENCE HYDROLASE
Ref.: N-ACETYLGLUCOSAMINE RECOGNITION BY A FAMILY 32 CARBOHYDRATE-BINDING MODULE FROM CLOSTRIDIUM PERFRINGENS NAGH. J.MOL.BIOL. V. 390 208 2009
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2W1U Ka = 5910 M^-1 NAG NGA n/a n/a
2 2WDB Ka = 7860 M^-1 NAG MAN n/a n/a
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2W1U Ka = 5910 M^-1 NAG NGA n/a n/a
2 2WDB Ka = 7860 M^-1 NAG MAN n/a n/a
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2W1U Ka = 5910 M^-1 NAG NGA n/a n/a
2 2WDB Ka = 7860 M^-1 NAG MAN n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG NGA; Similar ligands found: 182
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG NGA 1 1
2 NAG A2G 1 1
3 GAL NGA 0.716667 0.9375
4 A2G GAL 0.716667 0.9375
5 GAL A2G 0.716667 0.9375
6 GAL NGA A2G 0.69697 1
7 GAL NAG 0.693548 0.9375
8 NAG GAL 0.693548 0.9375
9 NAG BDP NAG BDP NAG BDP NAG 0.684211 0.96
10 NAG GDL 0.65625 1
11 NDG NAG 0.65625 1
12 CBS 0.65625 1
13 CBS CBS 0.65625 1
14 NAG NAG NDG 0.617647 0.979592
15 NDG NAG NAG NAG 0.617647 0.979592
16 NDG NAG NAG 0.617647 0.979592
17 NAG NAG NAG NAG NDG 0.617647 0.979592
18 NAG NAG NAG NAG NAG NAG NAG NAG 0.617647 0.979592
19 NAG NAG NAG NAG NAG 0.617647 0.979592
20 NAG NAG NDG NAG 0.617647 0.979592
21 NAG NAG NAG NAG NAG NAG 0.617647 0.979592
22 NDG NAG NAG NDG 0.617647 0.979592
23 CTO 0.617647 0.979592
24 NAG NAG NAG NDG 0.617647 0.979592
25 NGA GAL 0.61194 0.88
26 NAG AMU 0.608108 0.96
27 NAG MUB 0.608108 0.96
28 NAG A2G GAL 0.608108 1
29 NAG MBG 0.606061 0.938776
30 NAG MAN BMA 0.605634 0.9375
31 A2G GAL FUC 0.589041 0.958333
32 NGA GAL FUC 0.589041 0.958333
33 DR3 0.589041 0.958333
34 A2G GLA FUC 0.589041 0.958333
35 FUC GLA A2G 0.589041 0.958333
36 FUC GAL A2G 0.589041 0.958333
37 NAG GAL NAG 0.581081 1
38 NAG BDP 0.57971 0.9
39 A2G MBG 0.573529 0.938776
40 MBG A2G 0.573529 0.938776
41 NAG NDG 0.571429 0.903846
42 NAG NAG 0.571429 0.903846
43 3QL 0.569444 0.923077
44 NGA GAL BGC 0.569444 0.9375
45 NAG GAL BGC 0.56 0.9375
46 FUC GAL NAG A2G FUC 0.559524 0.979592
47 NAG GAL FUC FUC A2G 0.559524 0.979592
48 NAG MAN MAN 0.552632 0.9375
49 MAG 0.55 0.877551
50 2F8 0.55 0.877551
51 GC4 NAG 0.547945 0.9
52 1GN ACY GAL ACY 1GN BGC GAL BGC 0.547619 1
53 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.547619 1
54 UCD 0.540541 0.882353
55 GN1 0.539683 0.741379
56 NG1 0.539683 0.741379
57 MAN MAN NAG 0.539474 0.9
58 NAG GAD 0.533333 0.865385
59 NGA GCD 0.533333 0.865385
60 GAD NDG 0.533333 0.865385
61 GCD NGA 0.533333 0.865385
62 NAG MAN MMA 0.533333 0.938776
63 LEC NGA 0.530864 0.75
64 AH0 NAG 0.525641 0.888889
65 NGA GLA GAL BGC 0.525 0.9375
66 NAG MAN 0.521127 0.938776
67 NAG NAG NAG NAG 0.519481 0.90566
68 NAG NM9 0.519481 0.941176
69 NAG NAG NAG 0.519481 0.90566
70 HSQ 0.517241 0.833333
71 BM3 0.517241 0.833333
72 A2G 0.517241 0.833333
73 NAG 0.517241 0.833333
74 NGA 0.517241 0.833333
75 NDG 0.517241 0.833333
76 Z4S NAG NAG 0.5125 0.90566
77 BMA Z4Y NAG 0.512195 0.918367
78 NAG MAN MAN MAN NAG 0.506024 1
79 FUC GAL NAG A2G 0.5 0.979592
80 A2G GAL NAG FUC 0.5 0.979592
81 FUC BGC GAL NAG 0.494118 0.958333
82 NGT NAG 0.493671 0.79661
83 AMU 0.492537 0.895833
84 BGC FUC GAL FUC A2G 0.488372 0.938776
85 GLC FUC GAL FUC A2G 0.488372 0.938776
86 SN5 SN5 0.486111 0.826923
87 A2G GAL BGC FUC 0.482759 0.958333
88 DLD 0.481481 0.827586
89 GAL NDG FUC 0.480519 0.958333
90 FUC NDG GAL 0.480519 0.958333
91 TNR 0.478873 0.882353
92 3YW 0.478261 0.857143
93 NAG AH0 0.47619 0.888889
94 NOJ NAG NAG NAG 0.47561 0.857143
95 NOJ NAG NAG 0.47561 0.872727
96 NLC 0.471429 0.9375
97 GAL NDG 0.471429 0.9375
98 NDG GAL 0.471429 0.9375
99 GAL MGC 0.471429 0.938776
100 NAG AMU ALA DGL 0.46875 0.888889
101 NAG MU2 0.463918 0.872727
102 NAG GAL GAL NAG 0.463415 1
103 NAG GAL GAL NAG GAL 0.463415 1
104 GAL NAG GAL NAG GAL NAG 0.463415 0.979592
105 NAG BDP NAG BDP 0.462366 0.90566
106 HD4 0.461538 0.733333
107 GAL NAG MAN 0.461538 0.9375
108 NAG AMU NAG AMV 0.45977 0.941176
109 MA8 0.459459 0.830189
110 NAG NAG NGT 0.458824 0.813559
111 6Y2 0.458824 0.75
112 GYU 0.458333 0.821429
113 GAL NAG FUC FUC 0.45679 0.938776
114 TCG 0.45679 0.827586
115 FUC NAG GAL FUC 0.45679 0.938776
116 GAL NDG FUC FUC 0.45679 0.938776
117 BDZ 0.45679 0.938776
118 FUC GAL NDG FUC 0.45679 0.938776
119 BCW 0.45679 0.938776
120 FUC GAL NAG FUC 0.45679 0.938776
121 FUC NDG GAL FUC 0.45679 0.938776
122 57S 0.455696 0.733333
123 3PV 0.454545 0.884615
124 GAL NAG GAL GLC 0.451219 0.9375
125 BGC GAL NAG GAL 0.451219 0.9375
126 WZ5 0.450549 0.938776
127 GLC GAL NAG GAL FUC A2G 0.44898 0.979592
128 A2G GAL NAG FUC GAL GLC 0.44898 0.979592
129 BGA 0.444444 0.807018
130 NAG BMA NAG MAN MAN NAG NAG 0.443299 0.979592
131 NAG BDP NAG BDP NAG BDP 0.443299 0.923077
132 FHY 0.443182 0.90566
133 MMA MAN NAG MAN NAG NAG 0.443182 0.96
134 GLC GAL NAG GAL 0.440476 0.9375
135 LAT NAG GAL 0.440476 0.9375
136 GAL NAG GAL 0.439024 0.9
137 NAG MAN BMA MAN NAG GAL 0.4375 1
138 MAN BMA NAG 0.435897 0.9375
139 GLA GAL NAG 0.435897 0.9375
140 GUM 0.434783 0.857143
141 SNG 0.430769 0.803922
142 GAL NGA GLA BGC GAL 0.430233 0.9375
143 AO3 0.428571 0.738462
144 NAA NAA AMI 0.428571 0.738462
145 NAG MAN BMA NDG MAN NAG GAL 0.425743 0.979592
146 UMG 0.425532 0.857143
147 6ZC 0.423077 0.703125
148 LEC 0.423077 0.703125
149 NAG NAG BMA MAN MAN NAG GAL NAG 0.421569 0.979592
150 M5G 0.421569 1
151 SIA GAL A2G 0.418367 0.923077
152 NGA GAL SIA 0.418367 0.923077
153 ALA NAG AH0 DAL 0.416667 0.872727
154 NAG NAG BMA 0.416667 0.923077
155 NAG NDG BMA 0.416667 0.923077
156 SIA 2FG NAG 0.415842 0.857143
157 NAG NAG BMA MAN NAG 0.414141 0.90566
158 GYT 0.4125 0.813559
159 4QY 0.411765 0.724138
160 16G 0.411765 0.724138
161 BMX 0.411765 0.724138
162 8VZ 0.410959 0.979592
163 JXD 0.41 0.705882
164 SIA GAL NGA 0.41 0.923077
165 GAL NAG GAL BGC 0.409091 0.9
166 NAG GAL 2NA 0.408163 0.833333
167 GAL A2G MBN 0.404762 0.9
168 NGA SER GAL 0.402439 0.903846
169 GAL TNR 0.402439 0.903846
170 G6S NAG 0.402439 0.71875
171 FUC GAL NAG 0.402439 0.958333
172 GAL NAG FUC 0.402439 0.958333
173 NDG GAL FUC 0.402439 0.958333
174 FUC GAL NDG 0.402439 0.958333
175 A2G SER GAL 0.402439 0.903846
176 GAL SER A2G 0.402439 0.903846
177 NAG GAL FUC 0.402439 0.958333
178 FUL GAL NAG 0.402439 0.958333
179 DR2 0.402439 0.958333
180 NAG GDL PHJ 0.402062 0.786885
181 NAG NAG BMA MAN MAN 0.4 1
182 NAG FUC 0.4 0.916667
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WDB; Ligand: NAG MAN; Similar sites found with APoc: 12
This union binding pocket(no: 1) in the query (biounit: 2wdb.bio4) has 7 residues
No: Leader PDB Ligand Sequence Similarity
1 6F4W FMC 1.5625
2 3CM2 X23 3.07692
3 1VFS DCS 3.125
4 3N3T C2E 3.64583
5 5MWJ EBU 5.20833
6 1PNF NDG NAG 5.41401
7 3GFZ C2E 5.72917
8 3U40 ADN 6.77083
9 5X1M THG 7.29167
10 5X1M DHB 7.29167
11 5CUO COA 9.89583
12 1C7S CBS 10.4167
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