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Receptor
PDB id Resolution Class Description Source Keywords
3GVK 1.84 Å EC: 3.2.1.129 CRYSTAL STRUCTURE OF ENDO-NEURAMINIDASE NF MUTANT ENTEROBACTERIA PHAGE K1F ENDO NEURAMINIDASE POLYSIALIC ACID TRIPLE-BETA HELIX GLYCHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE O POLYSIALIC ACID BY THE BACTERIOPHAGE K1F TAILSPIKE ENDONF. J.MOL.BIOL. V. 397 341 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA A:916;
B:916;
C:916;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
22.99 Na [Na+]
SLB SIA A:914;
B:914;
C:914;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
598.511 n/a O=C(N...
SLB SIA SIA A:1;
A:911;
B:1;
B:911;
C:1;
C:911;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
888.759 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3GVL 1.41 Å EC: 3.2.1.129 CRYSTAL STRUCTURE OF ENDO-NEURAMINIDASENF ENTEROBACTERIA PHAGE K1F ENDO-NEURAMINIDASE POLYSIALIC ACID TRIPLE-BETA HELIX GLYCHYDROLASE
Ref.: STRUCTURAL BASIS FOR THE RECOGNITION AND CLEAVAGE O POLYSIALIC ACID BY THE BACTERIOPHAGE K1F TAILSPIKE ENDONF. J.MOL.BIOL. V. 397 341 2010
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
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 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
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 3JU4 - SLB C11 H19 N O9 CC(=O)N[C@....
2 3GVJ - SLB SIA SIA SIA SIA n/a n/a
3 3GVL - SLB SIA n/a n/a
4 3GVK - SLB SIA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SLB SIA; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA 1 1
2 SLB SIA 1 1
3 SIA SIA SIA SIA SIA SIA SIA 0.985915 1
4 SLB SIA SIA 0.985915 1
5 SIA SIA SIA 0.717647 1
6 SIA SIA GAL 0.648936 0.981132
7 SIA 0.565789 0.826923
8 SLB 0.565789 0.826923
9 SIA SIA GLA BGC 0.554545 0.981132
10 BGC SIA SIA GAL 0.554545 0.981132
11 MNA 0.544304 0.851852
12 SIA SIA GAL NGA GAL SIA 0.521368 0.981132
13 SIA SIA GAL NGA GAL 0.516949 0.981132
14 GAL SIA 0.516129 0.924528
15 SIA 2FG 0.5 0.859649
16 SIA GAL SIA GLC NGA 0.495935 0.981132
17 SIA GAL SIA BGC NGA 0.495935 0.981132
18 SIA GAL 0.489583 0.888889
19 SIA NAG 0.484536 0.910714
20 42D 0.464286 0.8
21 18D 0.464286 0.796296
22 CNP 0.45977 0.767857
23 MUS 0.456311 0.79661
24 SIA GAL NGA 0.449541 0.962264
25 SIA GAL SIA BGC NGA CEQ 0.448529 0.8
26 BGC GAL CEQ SLB NGA GAL SIA SIA 0.445255 0.83871
27 SIA GAL A2G 0.444444 0.962264
28 NGA GAL SIA 0.444444 0.962264
29 NGC 0.440476 0.811321
30 NGE 0.440476 0.811321
31 GLA GLC SIA 0.440367 0.924528
32 SIA GAL BGC 0.440367 0.924528
33 NAG SIA GAL 0.440367 0.962264
34 BGC SIA GAL 0.440367 0.924528
35 SIA GAL GLC 0.440367 0.924528
36 GAL BGC SIA 0.440367 0.924528
37 BGC GAL SIA 0.440367 0.924528
38 MN0 0.436782 0.818182
39 NAG GAL SIA 0.432432 0.944444
40 SIA GAL NAG 0.428571 0.910714
41 SIA NAG GAL 0.428571 0.910714
42 SIA 2FG NAG 0.428571 0.894737
43 GAL SIA NGA GAL SIA 0.422414 0.962264
44 SIA GAL NGA GAL 0.422414 0.962264
45 GAL SIA NGA GAL 0.422414 0.962264
46 NDG FUC SIA GAL 0.420168 0.962264
47 NAG FUC SIA GAL 0.420168 0.962264
48 SIA GAL NDG FUC 0.420168 0.962264
49 SIA GLA NAG FUC 0.420168 0.962264
50 FUC NDG GAL SIA 0.420168 0.962264
51 SIA GAL NAG FUC 0.420168 0.962264
52 SIA GAL MAG FUC 0.420168 0.962264
53 GAL TNR SIA 0.418803 0.910714
54 SID 0.417582 0.785714
55 NGC MBG 0.417476 0.907407
56 SIA GAL NAG GAL 0.417391 0.944444
57 SIA GAL NGS 0.415254 0.761194
58 SIA WIA 0.411765 0.862069
59 SIA NAG GAL GAL 0.410256 0.944444
60 GAL NGA GAL SIA 0.410256 0.944444
61 NXD 0.408602 0.793103
62 SIA GAL NAG SIA 0.40678 0.944444
63 SIA GAL NDG SIA 0.40678 0.910714
64 C5P SIA 0.406504 0.666667
65 425 0.405405 0.662338
66 NAG GAL NGC 0.401709 0.925926
67 79J 0.4 0.849057
Ligand no: 2; Ligand: SLB SIA SIA; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA SIA SIA SIA SIA SIA SIA 1 1
2 SLB SIA SIA 1 1
3 SIA SIA 0.985915 1
4 SLB SIA 0.985915 1
5 SIA SIA SIA 0.729412 1
6 SIA SIA GAL 0.659574 0.981132
7 BGC SIA SIA GAL 0.563636 0.981132
8 SIA SIA GLA BGC 0.563636 0.981132
9 SLB 0.558442 0.826923
10 SIA 0.558442 0.826923
11 MNA 0.5375 0.851852
12 SIA SIA GAL NGA GAL SIA 0.529915 0.981132
13 SIA SIA GAL NGA GAL 0.525424 0.981132
14 GAL SIA 0.510638 0.924528
15 SIA GAL SIA GLC NGA 0.504065 0.981132
16 SIA GAL SIA BGC NGA 0.504065 0.981132
17 SIA 2FG 0.494845 0.859649
18 SIA GAL 0.484536 0.888889
19 SIA NAG 0.479592 0.910714
20 42D 0.458824 0.8
21 18D 0.458824 0.796296
22 SIA GAL SIA BGC NGA CEQ 0.455882 0.8
23 CNP 0.454545 0.767857
24 BGC GAL CEQ SLB NGA GAL SIA SIA 0.452555 0.83871
25 MUS 0.451923 0.79661
26 SIA GAL NGA 0.445455 0.962264
27 NGA GAL SIA 0.440367 0.962264
28 SIA GAL A2G 0.440367 0.962264
29 GLA GLC SIA 0.436364 0.924528
30 SIA GAL BGC 0.436364 0.924528
31 BGC SIA GAL 0.436364 0.924528
32 SIA GAL GLC 0.436364 0.924528
33 GAL BGC SIA 0.436364 0.924528
34 BGC GAL SIA 0.436364 0.924528
35 NAG SIA GAL 0.436364 0.962264
36 NGE 0.435294 0.811321
37 NGC 0.435294 0.811321
38 MN0 0.431818 0.818182
39 NAG GAL SIA 0.428571 0.944444
40 SIA GAL NAG 0.424779 0.910714
41 SIA NAG GAL 0.424779 0.910714
42 SIA 2FG NAG 0.424779 0.894737
43 GAL SIA NGA GAL SIA 0.418803 0.962264
44 GAL SIA NGA GAL 0.418803 0.962264
45 SIA GAL NGA GAL 0.418803 0.962264
46 SIA GAL NAG FUC 0.416667 0.962264
47 FUC NDG GAL SIA 0.416667 0.962264
48 NAG FUC SIA GAL 0.416667 0.962264
49 SIA GAL MAG FUC 0.416667 0.962264
50 SIA GAL NDG FUC 0.416667 0.962264
51 SIA GLA NAG FUC 0.416667 0.962264
52 NDG FUC SIA GAL 0.416667 0.962264
53 GAL TNR SIA 0.415254 0.910714
54 SIA GAL NAG GAL 0.413793 0.944444
55 NGC MBG 0.413462 0.907407
56 SID 0.413043 0.785714
57 SIA GAL NGS 0.411765 0.761194
58 SIA WIA 0.407767 0.862069
59 SIA NAG GAL GAL 0.40678 0.944444
60 GAL NGA GAL SIA 0.40678 0.944444
61 NXD 0.404255 0.793103
62 SIA GAL NDG SIA 0.403361 0.910714
63 SIA GAL NAG SIA 0.403361 0.944444
64 C5P SIA 0.403226 0.666667
65 425 0.401786 0.662338
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3GVL; Ligand: SLB; Similar sites found with APoc: 10
This union binding pocket(no: 1) in the query (biounit: 3gvl.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 4ZL4 4PK 2.02703
2 6B5G CQY 2.63692
3 6B5G NAD 2.63692
4 3L41 LYS PRO SEP GLN GLU LEU 2.72727
5 1O0S NAI 3.73134
6 4R5M 4NO 4.25532
7 1FUR MLT 4.28266
8 6MB9 COA 5.47445
9 3C2O NTM 5.67164
10 3WSJ MK1 7.75862
Pocket No.: 2; Query (leader) PDB : 3GVL; Ligand: SLB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3gvl.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3GVL; Ligand: SLB; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3gvl.bio1) has 25 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3GVL; Ligand: SLB SIA; Similar sites found with APoc: 127
This union binding pocket(no: 4) in the query (biounit: 3gvl.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 1J0X NAD 1.20482
2 4IP7 FBP 1.28913
3 3WQT ANP 1.44628
4 1CDO NAD 1.60428
5 1T5C ADP 1.7192
6 2XT3 ADP 1.74419
7 4FRZ ADP 1.81347
8 3VOZ 04A 1.90476
9 3A70 NPO 1.94489
10 3BBH SFG 1.95122
11 6A20 ADP 2.28833
12 2AWN ADP 2.3622
13 1IXE COA 2.38727
14 6F3M NAD 2.3913
15 5Q0F 9FA 2.45902
16 5WB6 9ZM 2.45902
17 1V8B NAD 2.50522
18 4KIB SAH 2.52101
19 5BSH PRO 2.52708
20 3LRE ADP 2.53521
21 4EHU ANP 2.53623
22 2Z49 AMG 2.5463
23 2Z48 NGA 2.5463
24 2Z48 A2G 2.5463
25 5W7K SAH 2.5641
26 3NW7 LGV 2.60586
27 4D57 ARG AMP 2.79232
28 2HIM ASN 2.7933
29 3S1S SAH 2.83582
30 4GK9 MAN BMA MAN MAN MAN 2.86738
31 2P8O BVA 3.09278
32 4D8N 0HM 3.13901
33 5L4S 6KX 3.14465
34 5L4S NAP 3.14465
35 4L2H AR6 AR6 3.14465
36 4ZRN UPG 3.20513
37 4ZRN NAD 3.20513
38 3KO8 NAD 3.20513
39 1P0F NAP 3.21716
40 3OND NAD 3.27869
41 3OND ADN 3.27869
42 3LU1 NAD 3.2967
43 1PNO NAP 3.33333
44 1IAU ACE ILE GLU PRO ASJ 3.52423
45 2OOR TXP 3.64583
46 4B2D FBP 3.64964
47 1O0S NAI 3.73134
48 2FXU ATP 3.73333
49 3VC1 SAH 3.84615
50 3WMX NAD 3.91061
51 4RQU NAD 4
52 3MN6 ATP 4.01069
53 2VVL FAD 4.0404
54 2VVM FAD 4.0404
55 2CDC XYP 4.09836
56 2CDC NAP 4.09836
57 2W3O TYR ALA GLY SEP TPO ASP GLU ASN 4.42478
58 3AKI AH8 4.48718
59 5E50 ALA TYR ASP GLU SEP TPO ASP GLU GLU 4.5045
60 4CBU ATP 4.72441
61 4GKV NAD 4.7619
62 1D9I 00P 4.86111
63 5UR0 NAD 4.87106
64 1SL3 170 4.87805
65 1PQ7 ARG 4.91071
66 1XUJ BOZ 4.93274
67 3QH2 3NM 4.97738
68 4Y4V DAL 5.01475
69 5WS9 AMP 5.05263
70 1W0J ADP BEF 5.09804
71 5YU3 PRO 5.23256
72 5YU3 NAD 5.23256
73 1T32 OHH 5.35714
74 3COB ADP 5.42005
75 2VVG ADP 5.42857
76 1EB1 ZAL PRO MMO 5.44747
77 6BQK Z1E 5.47945
78 1GV8 GLY 5.66038
79 3AB4 THR 5.70071
80 3MMG GLU THR VAL ARG PHE GLN SER ASP 5.80913
81 2GJ8 ALF GDP 5.81395
82 3SUD SUE 5.91133
83 5O98 NAP 5.99369
84 4YCA NDP 6.12245
85 2YG3 FAD 6.40177
86 3P8N L4T 6.45161
87 5GS9 ARG 6.52819
88 5WQP NAP 6.83761
89 4QED NAP 6.85484
90 5H4S RAM 7.39437
91 2PZE ATP 7.42358
92 2ZFZ ARG 7.59494
93 4CQM NAP 7.66284
94 5L3S G 7.77027
95 5W75 SUC 7.90816
96 5FAH 5VT 8.03571
97 2ZJ1 ARJ 8.08081
98 2ZJ1 NAD 8.08081
99 3H4S ADP 8.14815
100 1A2C 34H LEU PRJ OAR 8.33333
101 2ANM CDO 8.33333
102 5WHT SIA GAL GLC 8.69565
103 5WHT SIA GAL 8.69565
104 5GM1 SAH 9.09091
105 1YF4 CYS TYR PHE GLN ASN CYS PRO ARG GLY NH2 9.86547
106 1GJC 130 9.88142
107 1SQA UI1 10.2041
108 4WEI GLC GAL 10.4693
109 1HPG BOC ALA ALA PRO GLU 10.6952
110 1PTR PRB 12
111 1GOJ ADP 12.3944
112 2B7D C1B 12.5
113 1E3W NAD 13.0268
114 2EC9 24X 13.3803
115 5L2Z 70C 13.7931
116 1XPJ TLA 14.2857
117 2O66 FLC 14.8148
118 1FKB RAP 14.9533
119 3CM2 X23 16.1538
120 4IWN GEK 20.9607
121 5A8Y VBM 24.7706
122 1TMT DPN PRO ARG 27.7778
123 3VXE DPN PRO ARG 29.4118
124 2OUA AES 32.4468
125 2XCF BBQ 39.1304
126 3KEE 30B 39.1304
127 4AX9 N5N 45.4545
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