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: 183
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG A2G 1 1
2 NAG NGA 1 1
3 GAL NGA 0.716667 0.9375
4 GAL A2G 0.716667 0.9375
5 A2G GAL 0.716667 0.9375
6 NGA GAL 0.693548 0.9375
7 GAL NAG 0.693548 0.9375
8 NAG GAL 0.693548 0.9375
9 GAL NGA A2G 0.692308 0.979592
10 NAG GCU NAG GCU NAG GCU 5AX 0.684211 0.96
11 NAG BDP NAG BDP NAG BDP NAG 0.684211 0.96
12 NAG GDL 0.65625 1
13 CBS 0.65625 1
14 CBS CBS 0.65625 1
15 NAG NDG 0.65625 1
16 MAN NAG 0.650794 0.9375
17 NAG NAG NAG 0.617647 0.979592
18 NAG NAG NAG NDG 0.617647 0.979592
19 NAG NAG NAG NAG NDG NAG 0.617647 0.979592
20 CTO 0.617647 0.979592
21 NAG NAG NAG NAG NAG NAG 0.617647 0.979592
22 NAG NAG NAG NAG NDG 0.617647 0.979592
23 NDG NAG NAG 0.617647 0.979592
24 NDG NAG NAG NDG 0.617647 0.979592
25 NAG NAG NAG NAG NAG 0.617647 0.979592
26 NDG NAG NAG NAG 0.617647 0.979592
27 NAG NAG NAG NAG 0.617647 0.979592
28 NAG NAG NDG 0.617647 0.979592
29 NDG NAG NAG NDG NAG 0.617647 0.979592
30 NAG NAG NAG NAG NAG NAG NAG NAG 0.617647 0.979592
31 FUC NAG 0.615385 0.9375
32 NDG NAG 0.61194 0.979592
33 NAG MUB 0.608108 0.96
34 NAG AMU 0.608108 0.96
35 NAG MBG 0.606061 0.938776
36 A2G GLA FUC 0.589041 0.958333
37 FUC GL0 A2G 0.589041 0.958333
38 FUC GAL A2G 0.589041 0.958333
39 NAG GAL FUC 0.589041 0.958333
40 DR3 0.589041 0.958333
41 A2G GAL FUC 0.589041 0.958333
42 NGA GAL FUC 0.589041 0.958333
43 FUC GLA A2G 0.589041 0.958333
44 NAG GAL NAG 0.581081 1
45 NAG BDP 0.57971 0.9
46 MBG A2G 0.573529 0.938776
47 A2G MBG 0.573529 0.938776
48 NAG NAG 0.571429 0.903846
49 NGA GAL BGC 0.569444 0.9375
50 3QL 0.569444 0.923077
51 NAG GAL BGC 0.56 0.9375
52 FUC GAL NAG A2G FUC 0.559524 0.979592
53 NAG GAL FUC FUC A2G 0.559524 0.979592
54 NAG MAN MAN 0.552632 0.9375
55 NAG MAN BMA 0.552632 0.9375
56 2F8 0.55 0.877551
57 MAG 0.55 0.877551
58 GC4 NAG 0.547945 0.9
59 1GN ACY GAL ACY 1GN BGC GAL BGC 0.547619 1
60 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.547619 1
61 UCD 0.540541 0.882353
62 NG1 0.539683 0.741379
63 GN1 0.539683 0.741379
64 MAN MAN NAG 0.539474 0.9
65 GCD NGA 0.533333 0.865385
66 NAG MAN MMA 0.533333 0.938776
67 NAG GAD 0.533333 0.865385
68 NGA GCD 0.533333 0.865385
69 GAD NDG 0.533333 0.865385
70 LEC NGA 0.530864 0.75
71 AH0 NAG 0.525641 0.888889
72 NGA GLA GAL BGC 0.525 0.9375
73 NAG NGO 0.52 0.886792
74 NAG NM9 0.519481 0.941176
75 NDG 0.517241 0.833333
76 HSQ 0.517241 0.833333
77 BM3 0.517241 0.833333
78 NAG 0.517241 0.833333
79 A2G 0.517241 0.833333
80 NGA 0.517241 0.833333
81 NAG NAG NAG NAG NAG NAG NAG 0.506024 0.888889
82 NAG MAN MAN MAN NAG 0.506024 1
83 A2G GAL NAG FUC 0.5 0.979592
84 FUC BGC GAL NAG 0.494118 0.958333
85 NGT NAG 0.493671 0.79661
86 AMU 0.492537 0.895833
87 BGC FUC GAL FUC A2G 0.488372 0.938776
88 GLC FUC GAL FUC A2G 0.488372 0.938776
89 SN5 SN5 0.486111 0.826923
90 RAM GLC GAL NAG NAG GLC 0.485981 0.923077
91 A2G GAL BGC FUC 0.482759 0.958333
92 DLD 0.481481 0.827586
93 GAL NAG FUC 0.480519 0.958333
94 FUC NDG GAL 0.480519 0.958333
95 FUC NAG GAL 0.480519 0.958333
96 GAL NDG FUC 0.480519 0.958333
97 TNR 0.478873 0.882353
98 3YW 0.478261 0.857143
99 NAG AH0 0.47619 0.888889
100 NOJ NAG NAG NAG 0.47561 0.872727
101 NOJ NAG NAG 0.47561 0.888889
102 GAL MGC 0.471429 0.938776
103 NDG GAL 0.471429 0.9375
104 GAL NDG 0.471429 0.9375
105 NLC 0.471429 0.9375
106 NAG MU2 0.463918 0.872727
107 GAL NAG GAL NAG GAL NAG 0.463415 0.979592
108 NAG GAL GAL NAG GAL 0.463415 1
109 NAG GAL GAL NAG 0.463415 1
110 NAG BDP NAG BDP 0.462366 0.90566
111 GAL NAG MAN 0.461538 0.9375
112 MAN NAG GAL 0.461538 0.9375
113 NAG AMU NAG AMV 0.45977 0.941176
114 MA8 0.459459 0.830189
115 NAG NAG NGT 0.458824 0.813559
116 6Y2 0.458824 0.75
117 GYU 0.458333 0.821429
118 CTO TMX 0.45679 0.827586
119 GAL NAG FUC FUC 0.45679 0.938776
120 FUC GAL NDG FUC 0.45679 0.938776
121 FUC NAG GAL FUC 0.45679 0.938776
122 FUC NDG GAL FUC 0.45679 0.938776
123 BDZ 0.45679 0.938776
124 TCG 0.45679 0.827586
125 BCW 0.45679 0.938776
126 GAL NDG FUC FUC 0.45679 0.938776
127 FUC GAL NAG FUC 0.45679 0.938776
128 57S 0.455696 0.733333
129 NAG AMU ALA DGL 0.454545 0.888889
130 3PV 0.454545 0.884615
131 LAT NAG GAL 0.451219 0.9375
132 BGC GAL NAG GAL 0.451219 0.9375
133 GAL NAG GAL BGC 0.451219 0.9375
134 WZ5 0.450549 0.938776
135 A2G GAL NAG FUC GAL GLC 0.44898 0.979592
136 GLC GAL NAG GAL FUC A2G 0.44898 0.979592
137 BGA 0.444444 0.807018
138 NAG BDP NAG BDP NAG BDP 0.443299 0.923077
139 NAG BMA NAG MAN MAN NAG NAG 0.443299 0.979592
140 MMA MAN NAG MAN NAG NAG 0.443182 0.96
141 GLC GAL NAG GAL 0.440476 0.9375
142 GAL NAG GAL 0.439024 0.9
143 GLA GAL NAG 0.435897 0.9375
144 MAN BMA NAG 0.435897 0.9375
145 NAG GAL GAL 0.435897 0.9375
146 GUM 0.434783 0.857143
147 SNG 0.430769 0.803922
148 GAL NGA GLA BGC GAL 0.430233 0.9375
149 AO3 0.428571 0.738462
150 NAG MAN BMA NDG MAN NAG GAL 0.425743 0.979592
151 UMG 0.425532 0.857143
152 LEC 0.423077 0.703125
153 6ZC 0.423077 0.703125
154 M5G 0.421569 1
155 SIA GAL A2G 0.418367 0.923077
156 NGA GAL SIA 0.418367 0.923077
157 NAG NAG BMA 0.416667 0.923077
158 NAG NDG BMA 0.416667 0.923077
159 SIA 2FG NAG 0.415842 0.857143
160 NAA NAA AMI 0.414894 0.705882
161 NAG NAG BMA MAN NAG 0.414141 0.90566
162 GYT 0.4125 0.813559
163 16G 0.411765 0.724138
164 BMX 0.411765 0.724138
165 4QY 0.411765 0.724138
166 8VZ 0.410959 0.979592
167 SIA GAL NGA 0.41 0.923077
168 NAG GAL 2NA 0.408163 0.833333
169 A2G SER GAL 0.407407 0.94
170 GAL SER A2G 0.407407 0.94
171 NGA SER GAL 0.407407 0.94
172 GAL TNR 0.407407 0.94
173 ALA NAG AH0 DAL 0.40404 0.872727
174 DR2 0.402439 0.958333
175 FUC GAL NDG 0.402439 0.958333
176 G6S NAG 0.402439 0.725806
177 FUL GAL NAG 0.402439 0.958333
178 FUC GAL NAG 0.402439 0.958333
179 NDG GAL FUC 0.402439 0.958333
180 NAG GDL PHJ 0.402062 0.786885
181 MAN MAN NAG MAN NAG 0.4 1
182 NAG FUC 0.4 0.916667
183 NAG NAG BMA MAN MAN 0.4 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2WDB; Ligand: NAG MAN; Similar sites found: 6
This union binding pocket(no: 1) in the query (biounit: 2wdb.bio4) has 7 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CM2 X23 0.007864 0.42693 3.07692
2 5MWJ EBU 0.001302 0.46117 5.20833
3 1PNF NDG NAG 0.002207 0.42201 5.41401
4 3GFZ C2E 0.01651 0.42624 5.72917
5 3U40 ADN 0.02272 0.41104 6.77083
6 1C7S CBS 0.004586 0.41719 10.4167
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