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Receptor
PDB id Resolution Class Description Source Keywords
5FRE 1.9 Å EC: 7.-.-.- CHARACTERIZATION OF A NOVEL CBM FROM CLOSTRIDIUM PERFRINGENS CLOSTRIDIUM PERFRINGENS HYDROLASE CBM40
Ref.: CHARACTERIZATION OF A HIGH-AFFINITY SIALIC ACID-SPE CBM40 FROM CLOSTRIDIUM PERFRINGENS AND ENGINEERING DIVALENT FORM. BIOCHEM.J. V. 473 2109 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA B:213;
C:210;
C:211;
A:210;
A:212;
B:210;
A:211;
B:214;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
40.078 Ca [Ca+2...
1PG B:1190;
A:1190;
Invalid;
Invalid;
none;
none;
submit data
252.305 C11 H24 O6 COCCO...
ACT B:1191;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SIA GAL B:201;
A:201;
C:201;
Valid;
Valid;
Valid;
none;
none;
none;
Kd = 32 uM
454.405 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FRE 1.9 Å EC: 7.-.-.- CHARACTERIZATION OF A NOVEL CBM FROM CLOSTRIDIUM PERFRINGENS CLOSTRIDIUM PERFRINGENS HYDROLASE CBM40
Ref.: CHARACTERIZATION OF A HIGH-AFFINITY SIALIC ACID-SPE CBM40 FROM CLOSTRIDIUM PERFRINGENS AND ENGINEERING DIVALENT FORM. BIOCHEM.J. V. 473 2109 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5FRE Kd = 32 uM SIA GAL n/a n/a
2 5FRA Kd = 68 uM SIA GAL 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 250 families.
1 5FRE Kd = 32 uM SIA GAL n/a n/a
2 5FRA Kd = 68 uM SIA GAL n/a n/a
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 2V73 - SIA C11 H19 N O9 CC(=O)N[C@....
2 6ER3 - SIA GAL n/a n/a
3 6ER4 Kd = 1.7 mM SIA GAL BGC n/a n/a
4 5FRE Kd = 32 uM SIA GAL n/a n/a
5 5FRA Kd = 68 uM SIA GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA GAL; Similar ligands found: 83
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL 1 1
2 GAL SIA 0.714286 0.960784
3 SIA GAL NAG GAL 0.693878 0.943396
4 SIA 2FG 0.689655 0.890909
5 NAG SIA GAL 0.632653 0.924528
6 GAL NGA GAL SIA 0.631068 0.943396
7 SIA GAL NAG 0.63 0.909091
8 NGA GAL SIA 0.622449 0.924528
9 SIA GAL A2G 0.622449 0.924528
10 BGC SIA GAL 0.616162 0.960784
11 SIA GAL GLC 0.616162 0.960784
12 GAL BGC SIA 0.616162 0.960784
13 BGC GAL SIA 0.616162 0.960784
14 GLA GLC SIA 0.616162 0.960784
15 SIA GAL BGC 0.616162 0.960784
16 SIA 2FG NAG 0.613861 0.859649
17 SIA SIA GAL 0.612245 0.907407
18 SIA GAL NDG SIA 0.59434 0.909091
19 SIA GAL NGA 0.594059 0.924528
20 NGC MBG 0.585106 0.90566
21 NAG GAL NGC 0.575472 0.924528
22 SIA GAL NGS 0.574074 0.731343
23 SIA GAL NGA GAL 0.570093 0.924528
24 GAL SIA NGA GAL 0.570093 0.924528
25 GAL SIA NGA GAL SIA 0.570093 0.924528
26 SIA GAL NAG SIA 0.564815 0.943396
27 SIA GLA NAG FUC 0.54955 0.924528
28 SIA GAL NAG FUC 0.54955 0.924528
29 FUC NDG GAL SIA 0.54955 0.924528
30 NAG FUC SIA GAL 0.54955 0.924528
31 SIA GAL NDG FUC 0.54955 0.924528
32 NDG FUC SIA GAL 0.54955 0.924528
33 BGC SIA SIA GAL 0.539823 0.907407
34 SIA SIA GLA BGC 0.539823 0.907407
35 SIA NAG GAL 0.537736 0.909091
36 SIA GAL MAG FUC 0.535714 0.888889
37 SIA NAG 0.53125 0.909091
38 SIA GAL BGC NGA 0.530973 0.924528
39 GAL BGC SIA NGA 0.530973 0.924528
40 BGC GAL SIA NGA 0.530973 0.924528
41 BGC GAL SIA SIA GAL NGA 0.525862 0.924528
42 BGC GAL SIA NGA GAL SIA 0.525862 0.924528
43 MNA 0.52439 0.849057
44 GAL NGA GAL BGC SIA 0.521368 0.924528
45 SIA GAL BGC NGA GAL 0.521368 0.924528
46 BGC GAL SIA NGA GAL 0.521368 0.924528
47 GAL NGA SIA GAL BGC 0.521368 0.924528
48 4U2 0.519231 0.90566
49 NAG GAL SIA 0.514019 0.943396
50 MN0 GAL GLC 0.514019 0.923077
51 GAL TNR SIA 0.508929 0.909091
52 NGC GAL NGA POL AZI 0.508475 0.753846
53 SIA SIA GAL NGA GAL SIA 0.508333 0.907407
54 SLT 0.504762 0.941176
55 SIA SIA GAL NGA GAL 0.504132 0.907407
56 SIA GLA NGS FUC 0.504132 0.731343
57 SIA SIA 0.489583 0.888889
58 SLB SIA 0.489583 0.888889
59 SIA NAG GAL GAL 0.486726 0.943396
60 SLB SIA SIA 0.484536 0.888889
61 SIA SIA SIA SIA SIA SIA SIA 0.484536 0.888889
62 SIA GAL SIA GLC NGA 0.472441 0.907407
63 SIA GAL SIA BGC NGA 0.472441 0.907407
64 GAL NAG SIA GAL 0.470085 0.943396
65 SIA SIA SIA 0.460784 0.888889
66 4U1 0.459459 0.924528
67 4U0 0.45045 0.960784
68 SIA GAL BGC 16C 0.448529 0.806452
69 BGC 18C GAL SIA 0.442029 0.806452
70 SIA WIA 0.441176 0.892857
71 SIA GAL NAG GAL GLC 0.44 0.943396
72 BGC GAL NAG SIA GAL 0.44 0.943396
73 SIA GAL NAG GAL BGC 0.44 0.943396
74 SLB 0.435294 0.86
75 SIA 0.435294 0.86
76 CNP 0.428571 0.796296
77 BGC GAL CEQ SLB NGA GAL SIA SIA 0.425532 0.777778
78 MN0 0.422222 0.849057
79 SIA GAL SIA BGC NGA CEQ 0.41844 0.769231
80 MUS 0.416667 0.793103
81 NXD 0.410526 0.789474
82 SID 0.404255 0.781818
83 BND 0.401961 0.803571
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FRE; Ligand: SIA GAL; Similar sites found with APoc: 27
This union binding pocket(no: 1) in the query (biounit: 5fre.bio3) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5U5G NAP 2.57732
2 4P25 FUC GAL NAG FUC 2.57732
3 4ZW9 BGC 3.09278
4 4ZW9 GLC 3.09278
5 5A5W GUO 3.09278
6 2DW7 SRT 3.60825
7 3B9A NAG NAG NAG NAG NAG NAG 4.12371
8 5JCA FAD 4.12371
9 5J6D 6H5 4.63918
10 1XPM HMG 5.15464
11 5D48 L96 5.92105
12 5JE0 SAH 6.70103
13 5JE0 AZ8 6.70103
14 2NNQ T4B 6.87023
15 1N5S ADL 7.14286
16 3TKY N7I 7.2165
17 2HOX P1T 7.2165
18 1UNB PN1 7.73196
19 1UNB AKG 7.73196
20 1PO0 FLC 10.8247
21 5U98 1KX 11.1111
22 4XOE KGM 14.433
23 5AB1 BCD TA5 HP6 MAN 14.433
24 3ACL 3F1 15.9794
25 5GQF GAL NAG 15.9794
26 5H9Q TD2 25.8065
27 4YZ5 SLT 43.8144
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