Receptor
PDB id Resolution Class Description Source Keywords
5O1J 1.9 Å EC: 4.2.2.- LYTIC TRANSGLYCOSYLASE IN ACTION NEISSERIA MENINGITIDIS SEROGROUP B (STMC58) LYTIC TRANSGLYCOSYLASES ACID/BASE CATALYSIS PEPTIDOGLYCANBACTERIA HYDROLASE
Ref.: A STEP-BY-STEPIN CRYSTALLOGUIDE TO BOND CLEAVAGE AN 1,6-ANHYDRO-SUGAR PRODUCT SYNTHESIS BY A PEPTIDOGLYCAN-DEGRADING LYTIC TRANSGLYCOSYLASE. J. BIOL. CHEM. V. 293 6000 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:706;
A:707;
A:705;
A:704;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
Z4S NAG NAG B:1;
 Valid;
 none;
 submit data
609.582 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5O2N 1.51 Å EC: 4.2.2.- LYTIC TRANSGLYCOSYLASE IN ACTION NEISSERIA MENINGITIDIS LYTIC TRANSGLYCOSYLASES ACID/BASE CATALYSIS PEPTIDOGLYCANBACTERIA HYDROLASE
Ref.: A STEP-BY-STEPIN CRYSTALLOGUIDE TO BOND CLEAVAGE AN 1,6-ANHYDRO-SUGAR PRODUCT SYNTHESIS BY A PEPTIDOGLYCAN-DEGRADING LYTIC TRANSGLYCOSYLASE. J. BIOL. CHEM. V. 293 6000 2018
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5MPQ - BLG C16 H30 N3 O14 S2 CC(=O)N[C@....
2 5O2N - FLC C6 H5 O7 C(C(=O)[O-....
3 5O1J - Z4S NAG NAG n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 5MPQ - BLG C16 H30 N3 O14 S2 CC(=O)N[C@....
2 5O2N - FLC C6 H5 O7 C(C(=O)[O-....
3 5O1J - Z4S NAG NAG 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 5 families.
1 5MPQ - BLG C16 H30 N3 O14 S2 CC(=O)N[C@....
2 5O2N - FLC C6 H5 O7 C(C(=O)[O-....
3 5O1J - Z4S NAG NAG n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: Z4S NAG NAG; Similar ligands found: 90
No: Ligand ECFP6 Tc MDL keys Tc
1 Z4S NAG NAG 1 1
2 3QL 0.882353 0.981132
3 NAG NAG NAG NAG 0.62963 0.859649
4 NAG NAG NAG 0.62963 0.859649
5 NAG NAG NAG NAG NAG NAG NAG 0.62963 0.859649
6 NDG NAG NAG NAG NAG 0.623377 0.924528
7 NAG NAG NAG NAG NAG NAG NAG NAG 0.623377 0.924528
8 NAG NAG NAG NAG NAG NAG 0.623377 0.924528
9 NAG NAG NAG NAG NAG 0.623377 0.924528
10 NAG NOJ NAG 0.619048 0.8
11 NAG NOJ NAG NAG 0.619048 0.816667
12 AH0 NAG 0.595238 0.981481
13 GDL NAG 0.571429 0.90566
14 NAG AH0 0.561798 0.981481
15 MBG A2G 0.544304 0.851852
16 NAG NGT NAG 0.527473 0.866667
17 AMV NAG AMU NAG 0.526882 0.890909
18 BMA MAN NAG 0.523256 0.849057
19 NAG NAG BMA 0.522727 0.842105
20 Z3Q NGA 0.522727 0.75
21 GAL NGA 0.518519 0.8
22 A2G NAG 0.5125 0.90566
23 GAL NAG GAL 0.511628 0.849057
24 ALA NAG AH0 DAL 0.51 0.963636
25 BGC GAL NGA 0.505882 0.849057
26 NAA AMI NAA 0.494845 0.787879
27 AO3 0.494845 0.787879
28 NAG NAG BMA MAN NAG 0.494845 0.924528
29 6Y2 0.494624 0.720588
30 GAL NGA A2G 0.494118 0.90566
31 NAG NGO 0.488636 0.892857
32 MAN NAG 0.4875 0.849057
33 GAL NAG GAL NAG GAL 0.483516 0.90566
34 MAN MAN NAG 0.483146 0.818182
35 NAG GAL NAG 0.483146 0.90566
36 MAN NAG GAL 0.482759 0.849057
37 NDG NAG 0.481928 0.924528
38 NAG NAG NAG TMX 0.477778 0.790323
39 MBG NAG 0.47561 0.851852
40 UMG 0.475248 0.847458
41 NAG NAG BMA MAN 0.474227 0.842105
42 NAG NAG BMA BMA 0.463158 0.844828
43 NGT NAG 0.461538 0.85
44 MAG 0.459459 0.796296
45 2F8 0.459459 0.796296
46 NAG NAG BMA MAN MAN NAG NAG 0.459459 0.859649
47 BMA MAN MAN NAG GAL NAG 0.457143 0.90566
48 GAL FUC A2G 0.455556 0.867925
49 GUM 0.455446 0.847458
50 NAG GAL NAG GAL NAG GAL 0.451613 0.924528
51 NAG GAL NAG GAL 0.451613 0.90566
52 NM9 NAG 0.450549 0.890909
53 BGC GAL NAG 0.450549 0.849057
54 MMA MAN NAG 0.444444 0.851852
55 BGC GAL GLA NGA 0.442105 0.849057
56 AMU NAG 0.44086 0.907407
57 C4W NAG FUC BMA 0.436893 0.875
58 BGC FUC GAL NAG GAL 0.436893 0.867925
59 NG1 0.435897 0.709677
60 GN1 0.435897 0.709677
61 SN5 SN5 0.435294 0.754386
62 C4W NAG FUC BMA MAN NAG 0.434783 0.875
63 BGC FUC GAL NAG 0.434343 0.867925
64 NAA AMI NA1 0.433962 0.776119
65 JXD 0.431193 0.680556
66 BGC FUC GAL FUC A2G 0.43 0.886792
67 NAG NAG BMA MAN MAN NAG GAL NAG 0.428571 0.924528
68 MAN MAN MAN NAG NAG 0.428571 0.90566
69 BDP NPO NDG BDP NDG 0.423423 0.720588
70 TVD GAL 0.421687 0.888889
71 MMA MAN NAG MAN NAG NAG 0.42 0.907407
72 FHY 0.42 0.892857
73 NDG BMA MAN MAN NAG GAL NAG 0.419643 0.924528
74 NAG GAL GLC NAG GLC RAM 0.414141 0.90566
75 BGC GAL FUC A2G 0.411765 0.867925
76 GYU 0.411765 0.754098
77 C4W NAG FUC BMA MAN MAN NAG NAG 0.409836 0.875
78 NAG NAG MAN MAN MAN 0.409524 0.90566
79 AMU ALA NAG DGL 0.405405 0.844828
80 NAG GAL 0.404762 0.849057
81 MLD 0.40458 0.883333
82 LEC NGA 0.40404 0.720588
83 SN5 NGT SN5 0.40404 0.770492
84 BMA Z4Y NAG 0.40404 0.833333
85 NAG GAL FUC FUC A2G 0.403846 0.924528
86 NAG FUC GAL FUC A2G 0.403846 0.924528
87 C4W NAG FUC BMA MAN MAN NAG 0.403226 0.875
88 NAG BDP NAG BDP NAG BDP NAG 0.401961 0.907407
89 C4W NAG FUC BMA MAN 0.401786 0.875
90 MUB ALA NAG ZGL 0.401786 0.830508
Similar Ligands (3D)
Ligand no: 1; Ligand: Z4S NAG NAG; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5O2N; Ligand: NDG NAG NAG NAG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5o2n.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5O2N; Ligand: NAG; 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: 5o2n.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5O2N; Ligand: FLC; 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: 5o2n.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
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