Receptor
PDB id Resolution Class Description Source Keywords
2OSX 1.1 Å EC: 3.2.1.123 ENDO-GLYCOCERAMIDASE II FROM RHODOCOCCUS SP.: GANGLIOSIDE GM RHODOCOCCUS SP. (ALPHA/BETA)8 (TIM) BARREL HYDROLASE
Ref.: STRUCTURAL AND MECHANISTIC ANALYSES OF ENDO-GLYCOCE II, A MEMBRANE-ASSOCIATED FAMILY 5 GLYCOSIDASE IN T AND GM3 GANGLIOSIDE-BOUND FORMS. J.BIOL.CHEM. V. 282 14300 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:608;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NA A:604;
A:605;
A:606;
A:607;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
22.99 Na [Na+]
SIA GAL BGC 16C A:600;
Valid;
none;
submit data
913.985 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2OYL 1.8 Å EC: 3.2.1.123 ENDO-GLYCOCERAMIDASE II FROM RHODOCOCCUS SP.: CELLOBIOSE-LIK IMIDAZOLE COMPLEX RHODOCOCCUS SP. (ALPHA/BETA)8 (TIM) BARREL HYDROLASE
Ref.: THE STRUCTURAL BASIS OF GLYCOSIDASE INHIBITION BY FIVE-MEMBERED IMINOCYCLITOLS: THE CLAN A GLYCOSIDE ENDOGLYCOCERAMIDASE AS A MODEL SYSTEM. ANGEW.CHEM.INT.ED.ENGL. V. 46 4474 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - SIA GAL BGC 16C n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - SIA GAL BGC 16C n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2OYL Ki = 0.5 uM IDC C14 H22 N2 O9 c1cn2c(n1)....
2 2OSX - SIA GAL BGC 16C n/a n/a
3 2OYM Ki = 10 uM MNI C15 H23 N3 O4 CN(C)c1ccc....
4 2OYK Ki = 5 uM 9MR C12 H23 N O8 C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA GAL BGC 16C; Similar ligands found: 80
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL BGC 16C 1 1
2 BGC 18C GAL SIA 0.937984 1
3 BGC 18C GAL NGA SIA GAL 0.78 1
4 BGC GAL SIA 0.598485 0.806452
5 SIA GAL BGC 0.598485 0.806452
6 BGC SIA GAL 0.598485 0.806452
7 SIA BGC GAL 0.598485 0.806452
8 GAL BGC SIA 0.598485 0.806452
9 SIA GAL GLC 0.598485 0.806452
10 GLA GLC SIA 0.598485 0.806452
11 SIA GAL NAG 0.586466 0.83871
12 NAG SIA GAL 0.586466 0.83871
13 LGN 0.583942 0.903226
14 IGC 0.583942 0.903226
15 BGC 18C GAL 0.571429 0.903226
16 BGC SIA SIA GAL 0.5625 0.854839
17 SIA SIA GLA BGC 0.5625 0.854839
18 NAG GAL NGC 0.557143 0.83871
19 SIA GAL NGA GAL 0.553191 0.83871
20 GAL NGA GAL SIA 0.553191 0.83871
21 SIA GAL MAG FUC 0.537931 0.809524
22 SIA GAL A2G 0.532847 0.83871
23 NGA GAL SIA 0.532847 0.83871
24 MN0 GAL GLC 0.532374 0.806452
25 GAL BGC GAL SIA NGA SIA 0.530201 0.83871
26 BGC GAL SIA SIA GAL NGA 0.530201 0.83871
27 FUC NDG GAL SIA 0.527397 0.83871
28 SIA GAL NAG FUC 0.527397 0.83871
29 SIA GAL NDG FUC 0.527397 0.83871
30 NAG FUC SIA GAL 0.527397 0.83871
31 NDG FUC SIA GAL 0.527397 0.83871
32 SIA GLA NAG FUC 0.527397 0.83871
33 SIA GAL NGS 0.524138 0.702703
34 SIA SIA GAL NGA GAL 0.522876 0.854839
35 GAL SIA NGA GAL SIA 0.520833 0.83871
36 SIA GAL NDG SIA 0.506849 0.887097
37 NGC GAL NGA POL AZI 0.506579 0.75
38 GAL NGA SIA GAL BGC 0.506579 0.83871
39 BGC GAL SIA NGA GAL 0.506579 0.83871
40 GAL NGA GAL BGC SIA 0.506579 0.83871
41 SIA GAL BGC NGA GAL 0.506579 0.83871
42 SLT 0.503597 0.790323
43 BGC GAL CEQ SLB NGA GAL SIA SIA 0.5 0.794118
44 SIA SIA GAL NGA GAL SIA 0.496774 0.854839
45 SIA GAL NAG SIA 0.496599 0.854839
46 4U2 0.492857 0.822581
47 SIA GAL 0.48855 0.806452
48 SIA GLA NGS FUC 0.484076 0.702703
49 BGC GAL SIA NGA 0.483444 0.83871
50 GAL BGC SIA NGA 0.483444 0.83871
51 SIA GAL BGC NGA 0.483444 0.83871
52 GAL SIA NGA GAL 0.47973 0.83871
53 BGC GAL SIA NGA GAL SIA 0.478788 0.732394
54 SIA GAL SIA BGC NGA CEQ 0.476471 0.867647
55 NGC MBG 0.470588 0.793651
56 Z3Q GAL 5N6 0.464516 0.797101
57 SIA GAL NAG GAL GLC 0.462025 0.854839
58 BGC GAL NAG SIA GAL 0.462025 0.854839
59 SIA GAL NAG GAL BGC 0.462025 0.854839
60 SIA SIA GAL 0.461538 0.854839
61 SIA GAL SIA BGC NGA 0.460123 0.854839
62 SIA GAL SIA GLC NGA 0.460123 0.854839
63 03F 0.459854 0.870968
64 SLF 0.457143 0.74026
65 EIS 0.457143 0.74026
66 SIA 2FG 0.455882 0.757576
67 SIA GAL NGA 0.452055 0.83871
68 CIS 0.447552 0.74026
69 SIA 2FG NAG 0.445946 0.787879
70 5N6 GAL 0.442857 0.83871
71 NAG GAL SIA 0.439189 0.854839
72 4U0 0.432432 0.806452
73 GAL TNR SIA 0.431373 0.870968
74 GAL NAG SIA GAL 0.429487 0.854839
75 SIA GAL NAG GAL 0.429487 0.854839
76 SIA NAG GAL 0.426667 0.887097
77 4U1 0.42 0.83871
78 0SG 0.414966 0.727273
79 SIA NAG GAL GAL 0.412903 0.854839
80 LAT SPH OCA 0.402685 0.84375
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2OYL; Ligand: IDC; Similar sites found: 10
This union binding pocket(no: 1) in the query (biounit: 2oyl.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E9L BGC 0.003507 0.42154 1.49254
2 2E9L OLA 0.00657 0.41001 1.49254
3 2CER PGI 0.00128 0.43101 1.6632
4 1W9D SEH 0.00159 0.42608 2.4948
5 3PTQ NFG 0.0004338 0.4096 2.4948
6 2VWA PTY 0.01988 0.4103 2.9703
7 4EK7 BGC 0.004978 0.41527 3.9501
8 2E40 LGC 0.004376 0.44837 5.80645
9 2CET PGI 0.002768 0.40978 12.8898
10 3AXX CBI 0.004046 0.40625 17.0306
Pocket No.: 2; Query (leader) PDB : 2OYL; Ligand: IDC; Similar sites found: 17
This union binding pocket(no: 2) in the query (biounit: 2oyl.bio2) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2E9L PLM 0.01242 0.4113 1.49254
2 4BQ4 AAL GAL AAL GAL 0.008233 0.40559 1.6632
3 1V08 NTZ 0.001872 0.42086 2.4948
4 3F5K CE5 0.003806 0.42497 3.3264
5 1ECE BGC BGC BGC BGC 0.0047 0.41134 4.18994
6 3GNP SOG 0.003777 0.40033 4.71311
7 3ZMR GLO BGC BGC XYS BGC XYS XYS 0.0005142 0.42546 5.05263
8 3AI0 PNW 0.003726 0.40026 6.23701
9 4W8B GLC BGC BGC XYS BGC XYS XYS GAL 0.0004825 0.43202 6.73575
10 4M82 NGB 0.001039 0.43785 8.02005
11 4YHG CT3 0.0006363 0.42916 8.74036
12 5I79 CTT 0.002142 0.41146 9.21053
13 5D9O BGC BGC BGC BGC 0.006663 0.42385 9.91501
14 5H4R CTT 0.001053 0.41125 11.1111
15 4YZT BGC BGC BGC BGC 0.0004764 0.41969 12.0582
16 3AYS CT3 0.001317 0.4024 22.3404
17 2JEQ GAL BGC BGC BGC XYS BGC XYS 0.0006884 0.43302 26.1954
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