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 A:702;
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 - NAG C8 H15 N O6 CC(=O)N[C@....
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 - NAG C8 H15 N O6 CC(=O)N[C@....
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 - NAG C8 H15 N O6 CC(=O)N[C@....
3 5O1J - Z4S NAG NAG n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: Z4S NAG NAG; Similar ligands found: 118
No: Ligand ECFP6 Tc MDL keys Tc
1 Z4S NAG NAG 1 1
2 3QL 0.882353 0.981132
3 NAG NAG NAG 0.62963 0.859649
4 NAG NAG NAG NAG 0.62963 0.859649
5 NAG NAG NAG NAG NAG NAG NAG NAG 0.623377 0.924528
6 NAG NAG NDG 0.623377 0.924528
7 NAG NAG NAG NAG NDG 0.623377 0.924528
8 NAG NAG NDG NAG 0.623377 0.924528
9 CTO 0.623377 0.924528
10 NAG NAG NAG NDG 0.623377 0.924528
11 NAG NAG NAG NAG NAG NAG 0.623377 0.924528
12 NAG NAG NAG NAG NAG 0.623377 0.924528
13 NDG NAG NAG 0.623377 0.924528
14 NDG NAG NAG NAG 0.623377 0.924528
15 NDG NAG NAG NDG 0.623377 0.924528
16 NOJ NAG NAG NAG 0.619048 0.816667
17 NOJ NAG NAG 0.619048 0.8
18 AH0 NAG 0.595238 0.981481
19 CBS CBS 0.571429 0.90566
20 NAG GDL 0.571429 0.90566
21 NDG NAG 0.571429 0.90566
22 CBS 0.571429 0.90566
23 NAG AH0 0.561798 0.981481
24 A2G MBG 0.544304 0.851852
25 MBG A2G 0.544304 0.851852
26 NAG NDG 0.54321 0.824561
27 NAG NAG 0.54321 0.824561
28 NAG NAG NGT 0.527473 0.866667
29 NAG AMU NAG AMV 0.526882 0.890909
30 NAG NDG BMA 0.522727 0.842105
31 NAG NAG BMA 0.522727 0.842105
32 GAL NAG 0.518987 0.849057
33 NAG GAL 0.518987 0.849057
34 NGA GAL 0.518519 0.8
35 DLD 0.516854 0.761905
36 NAG NGA 0.5125 0.90566
37 NAG A2G 0.5125 0.90566
38 GAL NAG GAL 0.511364 0.818182
39 ALA NAG AH0 DAL 0.51 0.963636
40 NGA GAL BGC 0.505882 0.849057
41 NAA NAA AMI 0.494845 0.787879
42 AO3 0.494845 0.787879
43 6Y2 0.494624 0.720588
44 GAL NGA A2G 0.494118 0.90566
45 NAG NAG BMA MAN NAG 0.490385 0.859649
46 NAG GAL GAL NAG GAL 0.483516 0.90566
47 NAG GAL NAG 0.483146 0.90566
48 MAN MAN NAG 0.483146 0.818182
49 NAG MAN BMA 0.482759 0.849057
50 GAL NAG MAN 0.482759 0.849057
51 GAL NAG GAL BGC 0.478723 0.818182
52 TCG 0.477778 0.790323
53 NAG MBG 0.47561 0.851852
54 UMG 0.475248 0.847458
55 NAG NAG BMA MAN 0.474227 0.842105
56 NAG MAN 0.464286 0.886792
57 NAG NAG BMA BMA 0.463158 0.844828
58 NGT NAG 0.461538 0.85
59 2F8 0.459459 0.796296
60 MAG 0.459459 0.796296
61 NAG NAG BMA MAN MAN NAG NAG 0.459459 0.859649
62 NAG MAN BMA MAN NAG GAL 0.457143 0.90566
63 FUC GLA A2G 0.455556 0.867925
64 A2G GAL FUC 0.455556 0.867925
65 A2G GLA FUC 0.455556 0.867925
66 FUC GAL A2G 0.455556 0.867925
67 NGA GAL FUC 0.455556 0.867925
68 GUM 0.455446 0.847458
69 NAG GAL GAL NAG 0.451613 0.90566
70 GAL NAG GAL NAG GAL NAG 0.451613 0.924528
71 NAG NM9 0.450549 0.890909
72 NAG GAL BGC 0.450549 0.849057
73 NAG BMA NAG MAN MAN NAG NAG 0.448598 0.924528
74 GLC GAL NAG GAL 0.446809 0.849057
75 LAT NAG GAL 0.446809 0.849057
76 NAG MAN MMA 0.444444 0.851852
77 NGA GLA GAL BGC 0.442105 0.849057
78 NAG MUB 0.44086 0.907407
79 NAG AMU 0.44086 0.907407
80 A2G GAL NAG FUC 0.44 0.924528
81 FUC GAL NAG A2G 0.44 0.924528
82 FUC C4W NAG BMA 0.436893 0.875
83 FUC BGC GAL NAG GAL 0.436893 0.867925
84 NG1 0.435897 0.709677
85 GN1 0.435897 0.709677
86 SN5 SN5 0.435294 0.754386
87 FUC C4W NAG BMA MAN NAG 0.434783 0.875
88 FUC BGC GAL NAG 0.434343 0.867925
89 NA1 NAA AMI 0.433962 0.776119
90 JXD 0.431193 0.680556
91 NAG MAN MAN 0.430108 0.849057
92 GLC FUC GAL FUC A2G 0.43 0.886792
93 BGC FUC GAL FUC A2G 0.43 0.886792
94 NAG NAG BMA MAN MAN NAG GAL NAG 0.428571 0.924528
95 NAG MAN MAN MAN NAG 0.428571 0.90566
96 NDG BDP BDP NPO NDG 0.423423 0.720588
97 8VZ 0.421687 0.888889
98 MMA MAN NAG MAN NAG NAG 0.42 0.907407
99 FHY 0.42 0.892857
100 NAG MAN BMA NDG MAN NAG GAL 0.419643 0.924528
101 GYU 0.411765 0.754098
102 A2G GAL BGC FUC 0.411765 0.867925
103 FUC C4W NAG BMA MAN MAN NAG NAG 0.409836 0.875
104 NAG NAG BMA MAN MAN 0.409524 0.90566
105 NAG AMU ALA DGL 0.405405 0.844828
106 GAL NDG 0.404762 0.849057
107 NDG GAL 0.404762 0.849057
108 NLC 0.404762 0.849057
109 MLD 0.40458 0.883333
110 SN5 SN5 NGT 0.40404 0.770492
111 LEC NGA 0.40404 0.720588
112 BMA Z4Y NAG 0.40404 0.833333
113 NAG GAL FUC FUC A2G 0.403846 0.924528
114 FUC GAL NAG A2G FUC 0.403846 0.924528
115 FUC C4W NAG BMA MAN MAN NAG 0.403226 0.875
116 NAG BDP NAG BDP NAG BDP NAG 0.401961 0.907407
117 NAG MU2 0.401786 0.830508
118 FUC C4W NAG BMA MAN 0.401786 0.875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5O2N; Ligand: NAG NAG NDG 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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