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
470.404 n/a O=C([...
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 250 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 217 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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 272 families.
1 2V73 - SIA C11 H19 N O9 CC(=O)N[C@....
2 5FRE Kd = 32 uM SIA GAL n/a n/a
3 5FRA Kd = 68 uM SIA GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SIA GAL; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 SIA GAL 1 1
2 SIA SIA GAL 0.835294 0.943396
3 5N6 GAL 0.817073 0.961538
4 SIA 2FG 0.790123 0.925926
5 SIA GAL A2G 0.725275 0.961538
6 NGA GAL SIA 0.725275 0.961538
7 BGC SIA GAL 0.717391 1
8 GAL BGC SIA 0.717391 1
9 SIA BGC GAL 0.717391 1
10 SIA GAL GLC 0.717391 1
11 SIA GAL BGC 0.717391 1
12 GLA GLC SIA 0.717391 1
13 BGC GAL SIA 0.717391 1
14 NAG SIA GAL 0.698925 0.961538
15 SIA GAL NAG 0.698925 0.961538
16 GAL SIA NGA GAL SIA 0.676768 0.961538
17 GAL NGA GAL SIA 0.66 0.961538
18 SIA GAL NGA GAL 0.66 0.961538
19 SIA GAL NGA 0.65625 0.961538
20 NGC MBG 0.651685 0.942308
21 SIA 2FG NAG 0.642857 0.892857
22 SIA GAL NAG SIA 0.637255 0.943396
23 NAG GAL NGC 0.633663 0.961538
24 SIA GAL NGS 0.631068 0.78125
25 GAL SIA NGA GAL 0.627451 0.961538
26 SIA SIA GLA BGC 0.622642 0.943396
27 BGC SIA SIA GAL 0.622642 0.943396
28 SIA GAL NDG SIA 0.621359 0.909091
29 FUC NDG GAL SIA 0.619048 0.961538
30 SIA GAL NDG FUC 0.619048 0.961538
31 SIA GLA NAG FUC 0.619048 0.961538
32 NAG FUC SIA GAL 0.619048 0.961538
33 NDG FUC SIA GAL 0.619048 0.961538
34 SIA GAL NAG FUC 0.619048 0.961538
35 SIA CMO 0.61039 0.867925
36 BGC GAL SIA SIA GAL NGA 0.605505 0.961538
37 GAL BGC GAL SIA NGA SIA 0.605505 0.961538
38 GAL SIA 0.602273 0.980392
39 MN0 GAL GLC 0.6 0.960784
40 SIA SIA GAL NGA GAL SIA 0.598214 0.943396
41 SIA GAL MAG FUC 0.588785 0.924528
42 SIA SIA GAL NGA GAL 0.578947 0.943396
43 SLT 0.575758 0.98
44 SIA GAL BGC NGA 0.568807 0.961538
45 GAL BGC SIA NGA 0.568807 0.961538
46 BGC GAL SIA NGA 0.568807 0.961538
47 SIA NAG GAL GAL 0.566038 0.943396
48 SIA GLA NGS FUC 0.565217 0.78125
49 4U2 0.56 0.942308
50 GAL NGA SIA GAL BGC 0.557522 0.961538
51 SIA GAL BGC NGA GAL 0.557522 0.961538
52 BGC GAL SIA NGA GAL 0.557522 0.961538
53 GAL NGA GAL BGC SIA 0.557522 0.961538
54 GAL NAG SIA GAL 0.545455 0.943396
55 SIA GAL NAG GAL 0.545455 0.943396
56 NGC GAL NGA POL AZI 0.54386 0.78125
57 MNA 0.5375 0.849057
58 SIA NAG GAL 0.533333 0.909091
59 BGC GAL SIA NGA GAL SIA 0.528 0.819672
60 NAG GAL SIA 0.52381 0.943396
61 SLB SIA 0.516129 0.924528
62 SIA SIA 0.516129 0.924528
63 Z3Q GAL 5N6 0.513043 0.806452
64 SLB SIA SIA SIA SIA 0.510638 0.924528
65 SIA SIA SIA SLB 0.510638 0.924528
66 SLB SIA SIA 0.510638 0.924528
67 SIA SIA SIA SIA SIA SIA SIA 0.510638 0.924528
68 SIA NAG 0.510417 0.875
69 SIA GAL SIA BGC NGA 0.504065 0.943396
70 SIA GAL SIA GLC NGA 0.504065 0.943396
71 GAL TNR SIA 0.495495 0.925926
72 SIA GAL BGC 16C 0.48855 0.806452
73 4U0 0.485981 0.960784
74 SIA SIA SIA 0.484848 0.924528
75 BGC 18C GAL SIA 0.481203 0.806452
76 BGC GAL CEQ SLB NGA GAL SIA SIA 0.474074 0.833333
77 SIA GAL NAG GAL BGC 0.471074 0.943396
78 BGC GAL NAG SIA GAL 0.471074 0.943396
79 SIA GAL NAG GAL GLC 0.471074 0.943396
80 4U1 0.46789 0.924528
81 SIA 0.463415 0.86
82 SLB 0.463415 0.86
83 SIA WIA 0.45 0.892857
84 CNP 0.438202 0.796296
85 SIA GAL SIA BGC NGA CEQ 0.434783 0.769231
86 MN0 0.431818 0.849057
87 SID 0.413043 0.781818
88 MUS 0.411215 0.793103
89 NXD 0.404255 0.789474
90 C5P SIA 0.403226 0.684932
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FRE; Ligand: SIA GAL; Similar sites found: 23
This union binding pocket(no: 1) in the query (biounit: 5fre.bio3) has 11 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5U5G NAP 0.03702 0.40706 2.57732
2 4P25 FUC GAL NAG FUC 0.0194 0.40302 2.57732
3 4CSS CWX 0.006603 0.44354 3.06748
4 4ZW9 GLC 0.02647 0.40603 3.09278
5 4ZW9 BGC 0.02647 0.40603 3.09278
6 5A5W GUO 0.04197 0.40449 3.09278
7 2DW7 SRT 0.01992 0.40374 3.60825
8 3B9A NAG NAG NAG NAG NAG NAG 0.02086 0.42152 4.12371
9 4UAL 3FV 0.0247 0.42713 5.15464
10 1XPM HMG 0.01543 0.42143 5.15464
11 5JE0 SAH 0.03943 0.40574 6.70103
12 5JE0 AZ8 0.03943 0.40574 6.70103
13 2NNQ T4B 0.04802 0.41303 6.87023
14 1N5S ADL 0.02075 0.40372 7.14286
15 2HOX P1T 0.01845 0.40856 7.2165
16 1SWG BTN 0.03121 0.40193 9.375
17 1PO0 FLC 0.01691 0.40498 10.8247
18 5U98 1KX 0.03126 0.4278 11.1111
19 5AB1 BCD TA5 HP6 MAN 0.001804 0.44628 14.433
20 4XOE KGM 0.002356 0.44351 14.433
21 3ACL 3F1 0.008921 0.43002 15.9794
22 5GQF GAL NAG 0.00512 0.4265 15.9794
23 4YZ5 SLT 0.000000003555 0.68667 43.8144
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