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Receptor
PDB id Resolution Class Description Source Keywords
5F7N 2.28 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A LEWIS B PENTASACCHARIDE HELICOBACTER PYLORI ADHESIN LECTIN NANOBODY COMPLEX CELL ADHESION
Ref.: STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BIN HELICOBACTER PYLORI. CELL HOST MICROBE V. 19 55 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NAG GAL FUC FUC A2G A:501;
B:501;
Valid;
Valid;
none;
none;
submit data
878.828 n/a O=C(N...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5F7N 2.28 Å NON-ENZYME: BINDING BLOOD GROUP ANTIGEN BINDING ADHESIN BABA OF HELICOBACTER PYL 17875 IN COMPLEX WITH BLOOD GROUP A LEWIS B PENTASACCHARIDE HELICOBACTER PYLORI ADHESIN LECTIN NANOBODY COMPLEX CELL ADHESION
Ref.: STRUCTURAL INSIGHTS INTO POLYMORPHIC ABO GLYCAN BIN HELICOBACTER PYLORI. CELL HOST MICROBE V. 19 55 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 510 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC 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 391 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC 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 298 families.
1 5F7N - NAG GAL FUC FUC A2G n/a n/a
2 5F9A - GLC GAL NAG GAL FUC FUC n/a n/a
3 5F8R - BGC GAL NAG GAL FUC FUC n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG GAL FUC FUC A2G; Similar ligands found: 138
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG GAL FUC FUC A2G 1 1
2 FUC GAL NAG A2G FUC 0.95 1
3 BGC FUC GAL FUC A2G 0.77907 0.959184
4 GLC FUC GAL FUC A2G 0.77907 0.959184
5 FUC GAL NAG A2G 0.770115 1
6 A2G GAL NAG FUC 0.770115 1
7 A2G GAL BGC FUC 0.730337 0.938776
8 BCW 0.702381 0.959184
9 FUC NAG GAL FUC 0.702381 0.959184
10 GAL NDG FUC 0.674699 0.938776
11 FUC NDG GAL 0.674699 0.938776
12 FUC NDG GAL FUC 0.662791 0.959184
13 FUC GAL NDG FUC 0.662791 0.959184
14 GAL NDG FUC FUC 0.662791 0.959184
15 BDZ 0.662791 0.959184
16 GAL NAG FUC FUC 0.662791 0.959184
17 FUC GAL NAG FUC 0.662791 0.959184
18 A2G GAL FUC 0.658824 0.938776
19 FUC GAL A2G 0.658824 0.938776
20 NGA GAL FUC 0.658824 0.938776
21 A2G GLA FUC 0.658824 0.938776
22 FUC GLA A2G 0.658824 0.938776
23 A2G GAL NAG FUC GAL GLC 0.637255 1
24 GLC GAL NAG GAL FUC A2G 0.637255 1
25 FUC BGC GAL NAG 0.634409 0.938776
26 BGA 0.614583 0.824561
27 NAG NGA 0.559524 0.979592
28 NAG A2G 0.559524 0.979592
29 DR3 0.549451 0.938776
30 GLA GAL NAG FUC GAL GLC 0.542857 0.938776
31 FUC GAL NAG GAL FUC 0.535354 0.959184
32 NAG AMU 0.531915 0.98
33 NAG MUB 0.531915 0.98
34 FUL GAL NAG 0.521739 0.938776
35 DR2 0.521739 0.938776
36 FUC GAL NDG 0.521739 0.938776
37 NDG GAL FUC 0.521739 0.938776
38 GAL NAG FUC 0.521739 0.938776
39 FUC GAL NAG 0.521739 0.938776
40 NAG GAL FUC 0.521739 0.938776
41 FUC BGC GAL NAG GAL 0.519231 0.938776
42 BGC GLA GAL FUC 0.516129 0.693878
43 MAG FUC GAL 0.51087 0.94
44 GLA NAG GAL FUC 0.510204 0.938776
45 GAL NAG GAL FUC 0.510204 0.938776
46 CBS 0.505747 0.979592
47 CBS CBS 0.505747 0.979592
48 NDG NAG 0.505747 0.979592
49 NAG GDL 0.505747 0.979592
50 GLC GAL NAG GAL FUC FUC 0.504673 0.959184
51 BGC GAL NAG GAL FUC FUC 0.504673 0.959184
52 NAG GAL NAG 0.494737 0.979592
53 NAG FUC 0.494253 0.897959
54 GAL NGA A2G 0.48913 0.979592
55 NAG BDP NAG BDP NAG BDP NAG 0.485437 0.98
56 NAG NAG NAG NDG 0.483516 1
57 NAG NAG NAG NAG NDG 0.483516 1
58 NAG NAG NAG NAG NAG NAG 0.483516 1
59 NAG NAG NAG NAG NAG NAG NAG NAG 0.483516 1
60 CTO 0.483516 1
61 NAG NAG NDG 0.483516 1
62 NDG NAG NAG NDG 0.483516 1
63 NAG NAG NAG NAG NAG 0.483516 1
64 NDG NAG NAG NAG 0.483516 1
65 NAG NAG NDG NAG 0.483516 1
66 NDG NAG NAG 0.483516 1
67 NAG MAN BMA 0.478723 0.918367
68 GAL NAG 0.477273 0.918367
69 NAG GAL 0.477273 0.918367
70 FUC BGC GAL 0.47191 0.693878
71 NAG AMU ALA DGL 0.469027 0.907407
72 NGA GAL BGC 0.468085 0.918367
73 GLC NAG GAL GAL FUC 0.46729 0.938776
74 FUC GAL NAG GAL BGC 0.46729 0.938776
75 GAL GLC NAG GAL FUC 0.46729 0.938776
76 NAG MU2 0.464912 0.890909
77 NAG GAL BGC 0.463918 0.918367
78 SIA GLA NAG FUC 0.46281 0.942308
79 SIA GAL NAG FUC 0.46281 0.942308
80 SIA GAL NDG FUC 0.46281 0.942308
81 NAG FUC SIA GAL 0.46281 0.942308
82 FUC NDG GAL SIA 0.46281 0.942308
83 NDG FUC SIA GAL 0.46281 0.942308
84 FUC NAG GLA GAL 0.461538 0.92
85 NAG MAN MMA 0.458333 0.92
86 FUC NAG 0.456522 0.849057
87 NAG MBG 0.455556 0.92
88 NGA GLA GAL BGC 0.455446 0.918367
89 SGA MAG FUC 0.451923 0.712121
90 A2G MBG 0.450549 0.92
91 MBG A2G 0.450549 0.92
92 MAN MAN NAG 0.44898 0.882353
93 NGA GAL 0.445652 0.862745
94 GAL GAL FUC 0.444444 0.693878
95 FUC GLA GLA 0.444444 0.693878
96 FUC GAL GLA 0.444444 0.693878
97 GLA GLA FUC 0.444444 0.693878
98 GLA GAL FUC 0.444444 0.693878
99 NAG A2G GAL 0.44 0.979592
100 FUC NAG GAL 0.438776 0.867925
101 GAL NGA 0.438202 0.918367
102 GAL A2G 0.438202 0.918367
103 A2G GAL 0.438202 0.918367
104 NAG NM9 0.434343 0.960784
105 EAG RAM RAM GLC RAM NAG RAM RAM GLC RAM 0.432432 0.98
106 NAG MAN MAN 0.43 0.918367
107 NAG MAN MAN MAN NAG 0.428571 0.979592
108 G4S MAG FUC 0.428571 0.712121
109 3QL 0.42268 0.90566
110 NAG BMA NAG MAN MAN NAG NAG 0.422414 1
111 GAL NAG GAL NAG GAL NAG 0.421569 1
112 NAG GAL GAL NAG 0.421569 0.979592
113 NAG NAG 0.421053 0.886792
114 NAG NDG 0.421053 0.886792
115 NAG MAN BMA NDG MAN NAG GAL 0.420168 1
116 NAG MAN BMA MAN NAG GAL 0.417391 0.979592
117 M5G 0.416667 0.979592
118 NAG NAG BMA MAN MAN NAG GAL NAG 0.416667 1
119 FUC GAL NAG NON FUC 0.415929 0.857143
120 BGB 0.415842 0.614035
121 GLC GAL FUC 0.414894 0.693878
122 BGC GAL FUC 0.414894 0.693878
123 FUC GAL GLC 0.414894 0.693878
124 LAT FUC 0.414894 0.693878
125 NAG MAN 0.414894 0.959184
126 8B7 0.414894 0.693878
127 MMA MAN NAG MAN NAG NAG 0.407407 0.98
128 NDG GAL 0.406593 0.918367
129 NLC 0.406593 0.918367
130 GAL NDG 0.406593 0.918367
131 NAG NAG NAG NAG 0.405941 0.924528
132 NAG NAG NAG 0.405941 0.924528
133 BMA Z4Y NAG 0.40566 0.9
134 LEC NGA 0.40566 0.765625
135 Z4S NAG NAG 0.403846 0.924528
136 WZ5 0.401786 0.92
137 FUC C4W NAG BMA MAN MAN NAG NAG 0.4 0.942308
138 FUC C4W NAG BMA MAN NAG 0.4 0.942308
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5F7N; Ligand: NAG GAL FUC FUC A2G; Similar sites found with APoc: 122
This union binding pocket(no: 1) in the query (biounit: 5f7n.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 6DEF GCP 2.04604
2 1CLU DBG 2.5
3 4FE2 AIR 2.7451
4 5OCG 9R5 3.1746
5 4UUG PXG 3.31325
6 2VDF OCT 3.33333
7 1RJW ETF 3.33333
8 5W75 SUC 3.33333
9 1U1I NAD 3.33333
10 4HXY NDP 3.88128
11 5YSI NCA 3.94737
12 5F7J ADE 4.16667
13 1UI0 URA 4.16667
14 5TS5 FAD 4.16667
15 5IFK HPA 4.16667
16 4YRI 4JH 4.16667
17 2GQS C2R 4.21941
18 4FK7 P34 4.80349
19 4CP8 MLI 5
20 4RF7 ARG 5
21 3QPB URA 5
22 5XHA FRU 5
23 3PLN U5P 5
24 3THR C2F 5
25 6CEP OXM 5
26 6CEP NAD 5
27 2FAR DTP 5
28 6GNO XDI 5.18518
29 6FA4 D1W 5.20231
30 2AG4 LP3 5.4878
31 2AG4 OLA 5.4878
32 4YQE PLQ 5.58376
33 4YQE FMN 5.58376
34 3A7R LAQ 5.83333
35 3BJE URA 5.83333
36 3I7V ATP 5.83333
37 4Y4V DAL 5.83333
38 5XDT MB3 5.84416
39 4XMF HSM 5.97826
40 4DE2 DN3 6.08365
41 2C3H GLC GLC 6.12245
42 3AB4 THR 6.17978
43 5LYH 7B8 6.21762
44 5YJS SAL 6.66667
45 4WOP CTP 6.66667
46 5G48 1FL 6.66667
47 5MRH Q9Z 6.66667
48 4LOO SB4 6.66667
49 1I7E IBS 6.79245
50 3CBC DBS 7.07071
51 4N65 FMN 7.07547
52 5KJW 53C 7.25995
53 4PTN GXV 7.28863
54 2HJR APR 7.29614
55 6EK3 OUL 7.5
56 1VA6 P2S 7.5
57 1VA6 ADP 7.5
58 4WOE ADP 7.5
59 1VKO NAD 7.5
60 5W4W 9WG 7.5
61 4WHZ 3NL 7.5
62 1JJV ATP 7.5
63 2XIQ MLC 7.5
64 6GAR FAD 7.5
65 5BVE 4VG 7.5
66 4KBA 1QM 7.5
67 1C3X 8IG 7.5
68 3CM2 X23 7.69231
69 2OFW ADX 7.69231
70 9LDT NAD 7.83133
71 9LDB NAD 7.83133
72 1USF NAP 7.86517
73 3ESS 18N 8.33333
74 2QHV OC9 8.33333
75 2QHS OCA 8.33333
76 3KVY URA 8.33333
77 5T8U LPA 8.33333
78 2WBV SIA 8.46561
79 4MOB ADP 9.03614
80 3A16 PXO 9.16667
81 2BHZ MAL 9.16667
82 3WYJ H78 9.16667
83 2E5A LAQ 9.16667
84 1VRP ADP 9.16667
85 4OYA 1VE 9.22747
86 1KGI T4A 9.44882
87 5DQ8 FLF 10
88 5ZI2 NAD 10
89 4CE5 PDG 10
90 4XSH NAI 10.6145
91 1VMK GUN 10.8333
92 3LGS ADE 10.8333
93 5G6U TRP 10.8333
94 3LL5 IP8 10.8434
95 4YJK URA 11.6667
96 5Y72 DST 11.6667
97 3PP0 03Q 12.5
98 3VKX T3 12.5
99 3A4V PYR 12.5
100 3A4V NAD 12.5
101 6C5F 7L9 12.8205
102 1SDW IYT 13.3333
103 3UYW TAU 13.5514
104 4LY9 1YY 14.1667
105 4LY9 S6P 14.1667
106 2JK0 ASP 14.1667
107 6ACS CIT 14.3411
108 1RM0 D6P 15
109 1RM0 NAI 15
110 4PAB THG 15
111 1OFL NGK GCD 15
112 5A89 FMN 15.8333
113 5A89 ADP 15.8333
114 5TV6 PML 16.6667
115 1TU3 GNP 17.7215
116 1ME8 RVP 18.3333
117 5LX6 78P 19.1667
118 2G30 ALA ALA PHE 20.8333
119 5TZO 7V7 20.8333
120 2PNC CLU 21.6667
121 5YRV 5AD 24.1667
122 3TMK T5A 31.0185
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