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Receptor
PDB id Resolution Class Description Source Keywords
5WZN 2.1 Å EC: 3.2.1.49 ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM B GALNAC COMPLEX BIFIDOBACTERIUM BIFIDUM GLYCOSIDE HYDROLASE HYDROLASE
Ref.: THE FIRST CRYSTAL STRUCTURE OF A FAMILY 129 GLYCOSI HYDROLASE FROM A PROBIOTIC BACTERIUM REVEALS CRITIC RESIDUES AND METAL COFACTORS J. BIOL. CHEM. V. 292 12126 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
A2G B:702;
A:702;
Valid;
Valid;
none;
none;
submit data
221.208 C8 H15 N O6 CC(=O...
CA B:703;
A:703;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
ZN B:701;
A:701;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5WZN 2.1 Å EC: 3.2.1.49 ALPHA-N-ACETYLGALACTOSAMINIDASE NAGBB FROM BIFIDOBACTERIUM B GALNAC COMPLEX BIFIDOBACTERIUM BIFIDUM GLYCOSIDE HYDROLASE HYDROLASE
Ref.: THE FIRST CRYSTAL STRUCTURE OF A FAMILY 129 GLYCOSI HYDROLASE FROM A PROBIOTIC BACTERIUM REVEALS CRITIC RESIDUES AND METAL COFACTORS J. BIOL. CHEM. V. 292 12126 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 5WZN - A2G C8 H15 N O6 CC(=O)N[C@....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5WZN - A2G C8 H15 N O6 CC(=O)N[C@....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5WZN - A2G C8 H15 N O6 CC(=O)N[C@....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: A2G; Similar ligands found: 105
No: Ligand ECFP6 Tc MDL keys Tc
1 NGA 1 1
2 NAG 1 1
3 A2G 1 1
4 BM3 1 1
5 HSQ 1 1
6 NDG 1 1
7 BGN 0.638298 0.888889
8 SIZ 0.630435 0.906977
9 YX1 0.625 0.65
10 STZ 0.612245 0.65
11 4QY 0.591837 0.735849
12 BMX 0.591837 0.735849
13 16G 0.591837 0.735849
14 9C1 0.58 0.886364
15 SNG 0.5625 0.866667
16 NGS 0.54902 0.661017
17 NDG NAG 0.54386 0.833333
18 CBS 0.54386 0.833333
19 NAG GDL 0.54386 0.833333
20 CBS CBS 0.54386 0.833333
21 ASG 0.538462 0.661017
22 BG8 0.537037 0.906977
23 MAG 0.530612 0.909091
24 2F8 0.530612 0.909091
25 NDG GAL 0.517857 0.888889
26 NLC 0.517857 0.888889
27 GAL NDG 0.517857 0.888889
28 NAG A2G 0.517241 0.833333
29 4V5 0.517241 0.829787
30 NAG NGA 0.517241 0.833333
31 4UZ 0.508475 0.808511
32 NAG NAG NAG NAG NDG 0.508197 0.816327
33 NDG NAG NAG NAG 0.508197 0.816327
34 NAG NAG NDG 0.508197 0.816327
35 NAG NAG NDG NAG 0.508197 0.816327
36 CTO 0.508197 0.816327
37 NDG NAG NAG NDG 0.508197 0.816327
38 NAG NAG NAG NDG 0.508197 0.816327
39 NDG NAG NAG 0.508197 0.816327
40 NAG NAG NAG NAG NAG 0.508197 0.816327
41 NAG NAG NAG NAG NAG NAG 0.508197 0.816327
42 NAG NAG NAG NAG NAG NAG NAG NAG 0.508197 0.816327
43 MQG 0.5 0.698113
44 NBG 0.5 0.951219
45 GAL NGA 0.491228 0.888889
46 A2G GAL 0.491228 0.888889
47 GAL A2G 0.491228 0.888889
48 AMU 0.490909 0.930233
49 NG1 0.490566 0.754717
50 GN1 0.490566 0.754717
51 NAG GAL 0.474576 0.888889
52 GAL NAG 0.474576 0.888889
53 NAG FUC 0.474576 0.866667
54 NAG GAL NAG 0.455882 0.833333
55 3YW 0.448276 0.930233
56 GLA GAL NAG 0.446154 0.888889
57 MAN BMA NAG 0.446154 0.888889
58 NGA GAL 0.428571 0.869565
59 FUC GAL NAG 0.426471 0.869565
60 GAL NAG FUC 0.426471 0.869565
61 DR2 0.426471 0.869565
62 NAG GAL FUC 0.426471 0.869565
63 NDG GAL FUC 0.426471 0.869565
64 FUC GAL NDG 0.426471 0.869565
65 FUL GAL NAG 0.426471 0.869565
66 G6S NAG 0.426471 0.645161
67 TNR 0.42623 0.833333
68 GYU 0.42623 0.740741
69 GAL NGA A2G 0.424242 0.833333
70 NAG BDP 0.421875 0.851064
71 NAG MBG 0.419355 0.851064
72 NGA GAL BGC 0.41791 0.888889
73 NAG NDG 0.415385 0.784314
74 NAG NAG 0.415385 0.784314
75 AZC 0.415094 0.795918
76 SN5 SN5 0.412698 0.705882
77 A2G MBG 0.412698 0.851064
78 MBG A2G 0.412698 0.851064
79 HS2 0.411765 0.8125
80 5AX 0.411765 0.866667
81 NAG MAN BMA 0.411765 0.888889
82 6ZC 0.409091 0.655738
83 LEC 0.409091 0.655738
84 TCG 0.408451 0.689655
85 GAL BGC NAG GAL 0.408451 0.888889
86 NAG MAN 0.40625 0.851064
87 WOO 0.404762 0.7
88 MAN 0.404762 0.7
89 GAL 0.404762 0.7
90 BGC 0.404762 0.7
91 BMA 0.404762 0.7
92 GLA 0.404762 0.7
93 ALL 0.404762 0.7
94 GLC 0.404762 0.7
95 GXL 0.404762 0.7
96 GIV 0.404762 0.7
97 NAG AMU 0.402778 0.8
98 NAG MUB 0.402778 0.8
99 NAG A2G GAL 0.402778 0.833333
100 A2G GAL FUC 0.4 0.869565
101 FUC GLA A2G 0.4 0.869565
102 DR3 0.4 0.869565
103 A2G GLA FUC 0.4 0.869565
104 NGA GAL FUC 0.4 0.869565
105 FUC GAL A2G 0.4 0.869565
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5WZN; Ligand: A2G; Similar sites found with APoc: 29
This union binding pocket(no: 1) in the query (biounit: 5wzn.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 5WP4 SAH 1.222
2 2F2H XTG 1.40625
3 4IGQ OGA 1.94444
4 4IA6 EIC 2.03046
5 3WQQ NDP 2.45902
6 3WQQ IB3 2.45902
7 2Y88 2ER 2.45902
8 3VBK COA 2.92683
9 4TVD BGC 2.96875
10 2FHF GLC GLC GLC GLC 3.125
11 5LY2 OGA 3.14961
12 2YBP 2HG 3.14961
13 1OVD FMN 3.53698
14 1OVD ORO 3.53698
15 5GM5 CBI 3.63636
16 1NYW DAU 4.06091
17 2WVZ KIF 4.21875
18 5XVS NAG 4.22164
19 3WY2 BGC 4.46097
20 2RDE C2E 5.17928
21 3B8X G4M 5.38462
22 1W6S PQQ 5.40541
23 3K0T BGC 7.69231
24 5XLY C2E 8.27068
25 5A57 5G0 GAL 9.6875
26 3IE3 N11 10.5263
27 3IE3 GSH 10.5263
28 1BGQ RDC 11.1111
29 1LWJ ACG 11.3379
Pocket No.: 2; Query (leader) PDB : 5WZN; Ligand: A2G; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 5wzn.bio2) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 2J4D FAD 1.52381
2 2HZY DHJ 1.66271
3 1JQD SAH 2.05479
4 1RP7 TZD 2.5
5 2OS2 OGA 3.14961
6 2Q8E OGA 3.40909
7 2P5B OGA 3.40909
8 3C3N FMN 4.16667
9 2B8T THM 4.93274
10 2X34 UQ8 9.39227
11 2X32 OTP 9.49721
12 4XCL AGS 11.1969
13 5MB4 NAG 16.4589
14 5FWE OGA 33.3333
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