Receptor
PDB id Resolution Class Description Source Keywords
2YGM 2.35 Å NON-ENZYME: OTHER THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAES P3-BS71, IN COMPLEX WITH THE BLOOD GROUP B ANTIGEN STREPTOCOCCUS PNEUMONIAE HYDROLASE CARBOHYDRATE-BINDING MODULE BLOOD GROUP ANTIGEN
Ref.: THE OVERALL ARCHITECTURE AND RECEPTOR BINDING OF PNEUMOCOCCAL CARBOHYDRATE ANTIGEN HYDROLYZING ENZYM J.MOL.BIOL. V. 411 1017 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1417;
B:1418;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
GLA NAG GAL FUC A:1414;
B:1414;
Valid;
Valid;
none;
none;
Ka = 69000 M^-1
691.633 n/a O=C(N...
NA A:1418;
B:1417;
Part of Protein;
Part of Protein;
none;
none;
submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YGM 2.35 Å NON-ENZYME: OTHER THE X-RAY CRYSTAL STRUCTURE OF TANDEM CBM51 MODULES OF SP3GH FAMILY 98 GLYCOSIDE HYDROLASE FROM STREPTOCOCCUS PNEUMONIAES P3-BS71, IN COMPLEX WITH THE BLOOD GROUP B ANTIGEN STREPTOCOCCUS PNEUMONIAE HYDROLASE CARBOHYDRATE-BINDING MODULE BLOOD GROUP ANTIGEN
Ref.: THE OVERALL ARCHITECTURE AND RECEPTOR BINDING OF PNEUMOCOCCAL CARBOHYDRATE ANTIGEN HYDROLYZING ENZYM J.MOL.BIOL. V. 411 1017 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 2YGM Ka = 69000 M^-1 GLA NAG GAL FUC n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 2YGM Ka = 69000 M^-1 GLA NAG GAL FUC n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 2YGM Ka = 69000 M^-1 GLA NAG GAL FUC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLA NAG GAL FUC; Similar ligands found: 145
No: Ligand ECFP6 Tc MDL keys Tc
1 GLA NAG GAL FUC 1 1
2 GAL NAG GAL FUC 1 1
3 FUC GAL NAG GAL FUC 0.822785 0.978723
4 MAG FUC GAL 0.701299 0.958333
5 FUC NAG GLA GAL 0.694118 0.978723
6 GAL NAG FUC 0.679487 1
7 FUC NDG GAL 0.679487 1
8 GAL NDG FUC 0.679487 1
9 FUC NAG GAL 0.679487 1
10 BGC GAL NAG GAL FUC FUC 0.663043 0.978723
11 GLC GAL NAG GAL FUC FUC 0.663043 0.978723
12 FUC BGC GAL NAG GAL 0.648352 1
13 FUC BGC GAL 0.618421 0.73913
14 FUC BGC GAL NAG 0.617977 1
15 NAG GAL GAL NAG GAL 0.611765 0.958333
16 FUC GAL MAG FUC 0.569767 0.958333
17 NAG GAL 0.564103 0.978261
18 NGA GAL 0.564103 0.978261
19 GAL NAG 0.564103 0.978261
20 SGA MAG FUC 0.56044 0.725806
21 GLA GAL NAG FUC GAL GLC 0.555556 1
22 FUC GAL NAG GAL BGC 0.552083 1
23 FUC NDG GAL FUC 0.551724 0.978723
24 FUC GAL NDG FUC 0.551724 0.978723
25 BCW 0.551724 0.978723
26 GAL NAG FUC FUC 0.551724 0.978723
27 BDZ 0.551724 0.978723
28 GAL NDG FUC FUC 0.551724 0.978723
29 FUC GAL NAG FUC 0.551724 0.978723
30 FUC NAG GAL FUC 0.551724 0.978723
31 M3M 0.549296 0.717391
32 MAN GLC 0.549296 0.717391
33 LB2 0.549296 0.717391
34 G4S MAG FUC 0.532609 0.725806
35 FUC GAL A2G 0.528736 1
36 A2G GLA FUC 0.528736 1
37 FUC GLA A2G 0.528736 1
38 A2G GAL FUC 0.528736 1
39 NGA GAL FUC 0.528736 1
40 FUC GL0 A2G 0.528736 1
41 GAL NAG GAL BGC 0.52809 0.978261
42 BGC GAL NAG GAL 0.52809 0.978261
43 LAT NAG GAL 0.52809 0.978261
44 GLC FUC GAL FUC A2G 0.526316 0.978723
45 BGC FUC GAL FUC A2G 0.526316 0.978723
46 GAL GAL FUC 0.525 0.73913
47 FUC GLA GLA 0.525 0.73913
48 GLA GAL FUC 0.525 0.73913
49 FUC GAL GLA 0.525 0.73913
50 GLA GLA FUC 0.525 0.73913
51 FUC NAG 0.525 0.978261
52 GAL NGA GLA BGC GAL 0.521739 0.978261
53 BGC BGC BGC GLC BGC BGC 0.513158 0.717391
54 BGC BGC BGC 0.513158 0.717391
55 GLC BGC BGC BGC BGC BGC BGC 0.513158 0.717391
56 BGC BGC BGC BGC BGC 0.513158 0.717391
57 BGC BGC BGC ASO BGC BGC ASO 0.513158 0.717391
58 GLC BGC BGC BGC 0.513158 0.717391
59 BGC BGC GLC 0.512821 0.717391
60 DR3 0.511364 1
61 NAG GAL FUC 0.511364 1
62 FUC GAL NAG A2G FUC 0.510204 0.938776
63 NAG GAL FUC FUC A2G 0.510204 0.938776
64 BMA MAN MAN 0.506329 0.717391
65 NAG FUC 0.506173 0.956522
66 FUL GAL NAG 0.5 1
67 GAL NGA 0.5 0.978261
68 FUC GAL NDG 0.5 1
69 GLC GAL NAG GAL FUC A2G 0.5 0.938776
70 DR2 0.5 1
71 FUC GAL NAG 0.5 1
72 A2G GAL 0.5 0.978261
73 GLC GAL NAG GAL 0.5 0.978261
74 A2G GAL NAG FUC GAL GLC 0.5 0.938776
75 GAL A2G 0.5 0.978261
76 NDG GAL FUC 0.5 1
77 A2G GAL BGC FUC 0.489796 1
78 GAL NAG GAL NAG GAL NAG 0.48913 0.938776
79 NAG GAL GAL NAG 0.48913 0.958333
80 NAG MAN GAL MAN MAN NAG GAL 0.485149 0.958333
81 GLA GAL NAG 0.482759 0.978261
82 MAN BMA NAG 0.482759 0.978261
83 NAG GAL GAL 0.482759 0.978261
84 GAL MGC 0.481481 0.978723
85 NLC 0.481481 0.978261
86 NDG GAL 0.481481 0.978261
87 GAL NDG 0.481481 0.978261
88 BGC GLA GAL FUC 0.477778 0.73913
89 FUC GAL NAG NON FUC 0.475728 0.836364
90 SIA NAG GAL GAL 0.473214 0.867925
91 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.466019 0.92
92 NGA GLA GAL BGC 0.463158 0.978261
93 A2G GAL NAG FUC 0.46 0.938776
94 GAL NGA A2G 0.45977 0.938776
95 CGC 0.45679 0.717391
96 NAG GAL BGC 0.456522 0.978261
97 GAL NAG MAN 0.455556 0.978261
98 MAN NAG GAL 0.455556 0.978261
99 BGC GAL FUC 0.453488 0.73913
100 FUC LAT 0.453488 0.73913
101 LAT FUC 0.453488 0.73913
102 GLC GAL FUC 0.453488 0.73913
103 FUC GAL GLC 0.453488 0.73913
104 GAL NAG GAL 0.451613 0.9375
105 8VZ 0.445783 0.938776
106 SIA GAL MAG FUC 0.444444 0.849057
107 FUC GAL 0.443038 0.717391
108 FUC GAL NAG A2G 0.441176 0.851852
109 NAG NAG BMA MAN 0.435644 0.884615
110 SIA GAL NDG FUC 0.432203 0.884615
111 FUC NDG GAL SIA 0.432203 0.884615
112 SIA GLA NAG FUC 0.432203 0.884615
113 SIA GAL NAG FUC 0.432203 0.884615
114 NAG FUC SIA GAL 0.432203 0.884615
115 NDG FUC SIA GAL 0.432203 0.884615
116 NAG NDG BMA 0.431579 0.884615
117 NAG NAG BMA 0.431579 0.884615
118 NAG BMA 0.430233 0.88
119 NGA GAL BGC 0.428571 0.978261
120 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.427184 0.958333
121 1GN ACY GAL ACY 1GN BGC GAL BGC 0.427184 0.958333
122 BGA 0.427184 0.836364
123 NAG GAL NAG 0.425532 0.958333
124 GAL FUC 0.425 0.717391
125 NGA SER GAL 0.423913 0.9
126 GAL SER A2G 0.423913 0.9
127 A2G SER GAL 0.423913 0.9
128 GAL TNR 0.423913 0.9
129 GAL A2G MBN 0.421053 0.918367
130 GAL BGC NAG GAL 0.421053 0.978261
131 BGB 0.421053 0.648148
132 SIA GAL NAG GAL 0.420168 0.867925
133 GAL NAG SIA GAL 0.420168 0.867925
134 LOG GAL 0.41573 0.789474
135 GAL LOG 0.41573 0.789474
136 BGC RAM BGC GAD 0.413462 0.7
137 GAL A2G THR 0.410526 0.92
138 GAL SIA NGA GAL 0.410256 0.884615
139 NAG MAN MAN MAN NAG 0.405941 0.958333
140 NOK GAL 0.404494 0.8
141 GAL NOK 0.404494 0.8
142 MAN MAN NAG MAN NAG 0.401869 0.958333
143 NAG NAG BMA MAN MAN 0.401869 0.958333
144 GLA GAL BGC 0.4 0.717391
145 GLA GAL GAL 0.4 0.717391
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YGM; Ligand: GLA NAG GAL FUC; Similar sites found: 82
This union binding pocket(no: 1) in the query (biounit: 2ygm.bio2) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2ZIF SAM 0.02047 0.40249 1.6835
2 1X87 NAD 0.01917 0.40871 1.69492
3 2VHW NAI 0.04452 0.40387 1.69492
4 2ZRU FMN 0.03234 0.41133 1.9774
5 4WAS NAP 0.0356 0.40909 1.9774
6 4WAS COO 0.04009 0.40632 1.9774
7 2NVA PL2 0.02686 0.40407 1.9774
8 2ZW5 COA 0.01854 0.40792 1.99336
9 1SAY PYR 0.02075 0.41953 2.25989
10 4HA6 FAD 0.04984 0.40731 2.25989
11 1SO2 666 0.01416 0.40488 2.25989
12 3H8V ATP 0.01814 0.40337 2.39726
13 1F3L SAH 0.01496 0.41263 2.49221
14 1C1X NAD 0.01309 0.42151 2.54237
15 1LVL FAD 0.0334 0.41684 2.54237
16 1VJT NAD 0.01087 0.41625 2.54237
17 1BW9 NAD 0.01739 0.40933 2.54237
18 1BXG NAD 0.02762 0.40478 2.54237
19 4GKV NAD 0.04606 0.40111 2.67857
20 1VKO NAD 0.01484 0.42497 2.82486
21 4C2Z MYA 0.04131 0.40749 2.82486
22 4K5S FAD 0.03436 0.40687 2.82486
23 4W6Z 8ID 0.002416 0.47102 2.88184
24 4D9C PMP 0.03091 0.40092 2.92398
25 4XF6 ADP 0.04052 0.40607 2.9304
26 4XF6 LIP 0.04807 0.40011 2.9304
27 4XF6 INS 0.04807 0.40011 2.9304
28 1HSK FAD 0.04251 0.40397 3.06748
29 1OBB NAD 0.001046 0.47436 3.10734
30 1ZK7 FAD 0.04938 0.40909 3.10734
31 1PL6 NAD 0.01674 0.40855 3.10734
32 1D1T NAD 0.03963 0.4025 3.10734
33 2FLI DX5 0.01973 0.40496 3.18182
34 2O07 MTA 0.03228 0.40254 3.28947
35 2O07 SPD 0.03588 0.40254 3.28947
36 1U3U NAD 0.03839 0.41271 3.38983
37 1U3U BNF 0.03839 0.41271 3.38983
38 3CGB FAD 0.04641 0.40384 3.38983
39 1PHP ADP 0.02239 0.40377 3.38983
40 3KLJ FAD 0.03615 0.40569 3.63636
41 1RM0 D6P 0.009903 0.44968 3.67232
42 2RAB FAD 0.0138 0.43854 3.67232
43 2RAB NAD 0.02398 0.43854 3.67232
44 2YNC YNC 0.0258 0.41556 3.67232
45 4PVR ASP 0.001682 0.45246 3.87097
46 4EDF UPG 0.04 0.41566 3.9548
47 2HQM FAD 0.03491 0.41496 3.9548
48 1Y8Q ATP 0.02055 0.40865 3.9548
49 2B4B COA 0.0216 0.40131 4.09357
50 1GA8 UPF 0.03157 0.40045 4.18006
51 4RDI ATP 0.01198 0.41234 4.51389
52 4RDH AMP 0.0106 0.41107 4.51389
53 2CDU FAD 0.02311 0.41912 4.51977
54 4PFW MAN MAN BMA BMA BMA BMA 0.04247 0.403 4.51977
55 4II2 ATP 0.01646 0.40892 4.80226
56 4C2X NHW 0.04284 0.40754 4.80226
57 4CMF PXG 0.02661 0.40145 4.96894
58 1MUU NAD 0.02789 0.40456 5.08475
59 1MV8 NAD 0.02976 0.4031 5.08475
60 4CE5 PDG 0.02247 0.40806 5.1051
61 5DX1 SFG 0.01149 0.423 5.44413
62 5DX0 SFG 0.01388 0.4188 5.44413
63 5DX8 SFG 0.01664 0.41185 5.44413
64 5DWQ SFG 0.01676 0.41013 5.44413
65 5DXA SFG 0.02526 0.4026 5.44413
66 1I1D 16G 0.02878 0.40873 5.59006
67 2Q1W NAD 0.02797 0.41051 5.64972
68 1LSS NAD 0.01522 0.41063 5.71429
69 1GPE FAD 0.04427 0.41172 5.9322
70 3VPH OXM 0.02685 0.41464 6.12903
71 2D3S TNR 0.005615 0.42241 6.19835
72 1KOL NAD 0.04237 0.40503 6.77966
73 1LLU NAD 0.03736 0.40597 7.01754
74 1UP7 NAD 0.01429 0.41816 7.62712
75 1GY8 NAD 0.03004 0.40775 7.62712
76 4ZUL UN1 0.03591 0.40252 7.62712
77 1IYK MYA 0.03837 0.40215 8.47458
78 2GAG NAD 0.0324 0.41225 8.57143
79 2DM6 IMN 0.03683 0.41109 9.00901
80 5ITV NAI 0.03559 0.40387 9.80392
81 1Z45 NAD 0.03254 0.40478 10.452
82 1JQ3 AAT 0.03864 0.40415 10.473
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