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Receptor
PDB id Resolution Class Description Source Keywords
1W0O 1.9 Å EC: 3.2.1.18 VIBRIO CHOLERAE SIALIDASE VIBRIO CHOLERAE VIBRIO CHOLERAE SIALIDASE GLYCOSIDASE HYDROLASE
Ref.: SIALIC ACID RECOGNITION BY VIBRIO CHOLERAE NEURAMINIDASE J.BIOL.CHEM. V. 279 40819 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:1779;
A:1780;
A:1781;
A:1782;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
DAN A:1778;
Valid;
none;
Kd ~ 37 uM
291.255 C11 H17 N O8 CC(=O...
SIA A:1783;
Valid;
none;
Kd ~ 30 uM
309.27 C11 H19 N O9 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1W0O 1.9 Å EC: 3.2.1.18 VIBRIO CHOLERAE SIALIDASE VIBRIO CHOLERAE VIBRIO CHOLERAE SIALIDASE GLYCOSIDASE HYDROLASE
Ref.: SIALIC ACID RECOGNITION BY VIBRIO CHOLERAE NEURAMINIDASE J.BIOL.CHEM. V. 279 40819 2004
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 6EKU ic50 = 52 uM ZMR C12 H20 N4 O7 CC(=O)N[C@....
2 1W0P Kd ~ 30 uM SIA C11 H19 N O9 CC(=O)N[C@....
3 6EKS ic50 = 144 uM G39 C14 H24 N2 O4 CCC(CC)O[C....
4 1W0O Kd ~ 37 uM DAN C11 H17 N O8 CC(=O)N[C@....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 20 families.
1 6EKU ic50 = 52 uM ZMR C12 H20 N4 O7 CC(=O)N[C@....
2 1W0P Kd ~ 30 uM SIA C11 H19 N O9 CC(=O)N[C@....
3 6EKS ic50 = 144 uM G39 C14 H24 N2 O4 CCC(CC)O[C....
4 1W0O Kd ~ 37 uM DAN C11 H17 N O8 CC(=O)N[C@....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 15 families.
1 6EKU ic50 = 52 uM ZMR C12 H20 N4 O7 CC(=O)N[C@....
2 1W0P Kd ~ 30 uM SIA C11 H19 N O9 CC(=O)N[C@....
3 6EKS ic50 = 144 uM G39 C14 H24 N2 O4 CCC(CC)O[C....
4 1W0O Kd ~ 37 uM DAN C11 H17 N O8 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DAN; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 DAN 1 1
2 9AM 0.767857 0.913043
3 4AM 0.661017 0.913043
4 ZMR 0.590909 0.792453
5 KFN 0.542373 0.704545
6 49A 0.507692 0.87234
7 0HX 0.454545 0.75
8 RP6 0.452055 0.934783
9 LNV 0.434211 0.701754
10 FSI 0.408451 0.82
11 SIA 0.4 0.911111
12 SLB 0.4 0.911111
Ligand no: 2; Ligand: SIA; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA 1 1
2 SLB 1 1
3 18D 0.758621 0.955556
4 42D 0.758621 0.875
5 NGC 0.754386 0.933333
6 NGE 0.754386 0.933333
7 MNA 0.629032 0.895833
8 79J 0.615385 0.934783
9 CNP 0.58209 0.875
10 KDN 0.568965 0.72093
11 KDM 0.568965 0.72093
12 SIA SIA 0.565789 0.826923
13 SLB SIA 0.565789 0.826923
14 SIA SIA SIA SIA SIA SIA SIA 0.558442 0.826923
15 SLB SIA SIA 0.558442 0.826923
16 FSI 0.515152 0.895833
17 6KL 0.5 0.807692
18 SFJ 0.5 0.875
19 MN0 0.485714 0.895833
20 EQP 0.470588 0.788462
21 AXP 0.470588 0.788462
22 GAL SIA 0.463415 0.86
23 SID 0.459459 0.82
24 SIA SIA SIA 0.453488 0.826923
25 MUS 0.449438 0.796296
26 NXD 0.447368 0.792453
27 SIA WIA 0.447059 0.767857
28 SIA 2FG 0.447059 0.796296
29 SLT 0.44086 0.877551
30 KDO 0.435484 0.704545
31 SIA GAL 0.435294 0.86
32 SIA NAG 0.430233 0.781818
33 4U0 0.427083 0.86
34 4U2 0.425532 0.843137
35 BND 0.416667 0.807692
36 SKD 0.414286 0.875
37 SIA SIA GAL 0.410526 0.811321
38 4U1 0.408163 0.826923
39 E3M 0.402778 0.606061
40 SIA GAL GLC 0.402062 0.86
41 BGC SIA GAL 0.402062 0.86
42 GAL BGC SIA 0.402062 0.86
43 BGC GAL SIA 0.402062 0.86
44 SIA GAL BGC 0.402062 0.86
45 GLA GLC SIA 0.402062 0.86
46 4AM 0.4 0.833333
47 DAN 0.4 0.911111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1W0O; Ligand: DAN; Similar sites found with APoc: 37
This union binding pocket(no: 1) in the query (biounit: 1w0o.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 4WG0 CHD None
2 3HYW DCQ 1.39535
3 4WA4 G39 1.80412
4 6I6X H6B 2.39234
5 6I6R H62 2.39234
6 5BRP PNG 2.46479
7 3VSV XYP 2.50784
8 4B7J G39 2.55864
9 2WZF BGC 2.66667
10 4QN7 G39 2.82051
11 1KYA XYD 3.00601
12 4ISS TAR 3.57143
13 2FN8 RIP 3.63036
14 6F1J EDG 3.69231
15 4QN6 LNV 3.83632
16 4HZX G39 4.12371
17 5A69 OGN 4.6225
18 2QB8 ATP 4.78589
19 3A72 AHR AHR 4.78873
20 1YRO UDP 4.8951
21 6F6D AKG 5.68627
22 5M1Z 6LW AHR 5.72207
23 6ARJ SAH 5.73066
24 6ARJ BW4 5.73066
25 2EPN NGT 5.74163
26 5B2D SLT 5.93047
27 5FWE OGA 7.34908
28 2OS2 OGA 7.34908
29 2YBP 2HG 7.34908
30 3HAV ATP 7.35786
31 4GZP G39 8.6514
32 1SQ5 PAU 8.76623
33 2J0B UDP 8.92857
34 3N29 GOL 9.09091
35 3KO0 TFP 9.90099
36 3TIC ZMR 10.2345
37 5LY2 OGA 42.8571
Pocket No.: 2; Query (leader) PDB : 1W0O; Ligand: SIA; Similar sites found with APoc: 105
This union binding pocket(no: 2) in the query (biounit: 1w0o.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 1RE8 BD2 1.42857
2 2PTR 2SA 1.51515
3 1EZ0 NAP 1.66453
4 4ZY1 4U5 1.91571
5 3FSM 2NC 1.97044
6 3KA2 2NC 1.97044
7 1S7G NAD 1.97628
8 6HLY G9Z 2.05279
9 4EIL NDP 2.12014
10 2XG9 NOJ GLC 2.24299
11 4OAG ADP 2.38806
12 1FQ5 0GM 2.43161
13 4M2K PLP 2.46305
14 4I8P NAD 2.5
15 3RHJ NAP 2.51451
16 2D1S SLU 2.55474
17 6MA3 JAJ 2.62794
18 3R1Z ALA GLU 2.63852
19 4R84 CSF 2.7833
20 3KJS NAP 2.87908
21 3KJS DQ1 2.87908
22 4WJT NAG 2.99401
23 3D3X ARG ILE MET GLU NH2 3.0445
24 1V25 ANP 3.14233
25 1U8X NAD 3.17797
26 1EIX BMQ 3.26531
27 5L4L 7OX 3.28947
28 3FW4 CAQ 3.37079
29 1AJS PLA 3.39806
30 6DND PLP 3.40633
31 5XWV NDP 3.42742
32 5XWV 8H6 3.42742
33 2WOX NDP 3.47648
34 5YIC 8VO 3.65854
35 1YQZ FAD 3.71319
36 3IUY AMP 3.94737
37 3U7S 017 4.0404
38 4X6I 3Y1 4.18605
39 4OR7 NAP 4.24242
40 3DG6 MUC 4.35967
41 5OE4 3UK 4.4226
42 3FV3 IVA VAL VAL STA ALA STA 4.42478
43 1H8P PC 4.58716
44 5F33 PGH 4.59016
45 6GH9 MIX 4.65753
46 1XON PIL 4.87106
47 4GID 0GH 4.89691
48 4M8X KGQ 5.05051
49 3UBQ SIA GAL 5.08475
50 5XL4 SIA 5.11364
51 3WSJ MK1 5.17241
52 3MF2 AMP 5.20231
53 4PIV NDP 5.30303
54 4Q5M ROC 5.41872
55 3PDB PMP 5.48628
56 3PD6 PMP 5.48628
57 1RVX SIA GAL NAG 5.625
58 2DPM SAM 5.6338
59 2Y4O DLL 5.64334
60 1UP7 NAD 5.7554
61 5DXV NAP 5.76923
62 1QS8 IVA VAL VAL STA ALA STA 5.77508
63 5T2Z 017 6.06061
64 1SB8 NAD 6.53409
65 1SB8 UD2 6.53409
66 4KM2 ATR 6.70391
67 4KM2 TOP 6.70391
68 1SMR PIV HIS PRO PHE HIS LPL TYR TYR SER 6.86567
69 1Q6D GLC GLC 6.86869
70 3EMY IVA VAL VAL STA ALA STA 6.99088
71 1SIV PSI 7.07071
72 1O9J NAD 7.18563
73 4EI7 GDP 7.45501
74 1CZA G6P 7.8105
75 3A5Z KAA 7.8534
76 4L1A AB1 8.08081
77 4JEM C5P 8.23529
78 2CJF RP4 8.28025
79 4USI ATP 8.44156
80 4FC7 NAP 8.66426
81 4FC7 COA 8.66426
82 4NJS G08 9.09091
83 2G37 FAD 9.48012
84 1QRP HH0 9.5092
85 4YHQ G10 10.101
86 1IDA 0PO 10.101
87 2P3C 3TL 10.101
88 3O9L LPN 10.8434
89 5M42 FMN 11.1111
90 2VUT NAD 11.6279
91 2PID YSA 12.0787
92 3S43 478 12.1212
93 2QZX IVA VAL VAL STA ALA STA 12.5731
94 3NWQ 2NC 13.1313
95 3MWS 017 13.1313
96 2FXD DR7 13.1313
97 1BB6 UMG 13.9535
98 4H2V AMP 15.4545
99 2QO4 CHD 15.873
100 3DZ6 M8E 17.9104
101 1ONI BEZ 21.0145
102 2O4N TPV 21.2121
103 2P3B 3TL 22.2222
104 6C8X BVR 22.2222
105 3FGZ BEF 25.7812
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