Receptor
PDB id Resolution Class Description Source Keywords
5BXR 1.6 Å EC: 3.2.1.140 LNBASE IN COMPLEX WITH LNB-NHACDNJ BIFIDOBACTERIUM BIFIDUM JCM 1254 TIM BARREL HYDROLASE DISTAL GUT HUMAN MILK OLIGOSACCHARIDINHIBITOR
Ref.: GAINING INSIGHT INTO THE CATALYSIS BY GH20 LACTO-N-USING SMALL MOLECULE INHIBITORS AND STRUCTURAL ANAL CHEM.COMMUN.(CAMB.) V. 51 15008 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:703;
B:704;
A:705;
B:703;
A:704;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
NOK GAL A:702;
Valid;
none;
Ki = 0.88 uM
367.375 n/a O=C(N...
GAL NOK B:701;
Valid;
none;
Ki = 0.88 uM
367.375 n/a O=C(N...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4JAW 1.8 Å EC: 3.2.1.140 CRYSTAL STRUCTURE OF LACTO-N-BIOSIDASE FROM BIFIDOBACTERIUM COMPLEXED WITH LNB-THIAZOLINE BIFIDOBACTERIUM BIFIDUM ALPHA/BETA-DOMAIN TIM BARREL BETA-TREFOIL HYDROLASE MEMBANCHORED EXTRACELLULAR
Ref.: CRYSTAL STRUCTURES OF A GLYCOSIDE HYDROLASE FAMILY LACTO-N-BIOSIDASE FROM BIFIDOBACTERIUM BIFIDUM J.BIOL.CHEM. V. 288 11795 2013
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5BXT Ki = 52 uM 4WS GAL n/a n/a
2 5BXR Ki = 0.88 uM NOK GAL n/a n/a
3 5BXS Ki = 0.52 uM GAL GC2 n/a n/a
4 4JAW Ki = 125 nM GAL NGT n/a n/a
5 5BXP Ki = 7.7 uM GAL LOG n/a n/a
6 4H04 - NAG GAL n/a n/a
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5BXT Ki = 52 uM 4WS GAL n/a n/a
2 5BXR Ki = 0.88 uM NOK GAL n/a n/a
3 5BXS Ki = 0.52 uM GAL GC2 n/a n/a
4 4JAW Ki = 125 nM GAL NGT n/a n/a
5 5BXP Ki = 7.7 uM GAL LOG n/a n/a
6 4H04 - NAG GAL n/a n/a
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5BXT Ki = 52 uM 4WS GAL n/a n/a
2 5BXR Ki = 0.88 uM NOK GAL n/a n/a
3 5BXS Ki = 0.52 uM GAL GC2 n/a n/a
4 4JAW Ki = 125 nM GAL NGT n/a n/a
5 5BXP Ki = 7.7 uM GAL LOG n/a n/a
6 4H04 - NAG GAL n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NOK GAL; Similar ligands found: 72
No: Ligand ECFP6 Tc MDL keys Tc
1 NOK GAL 1 1
2 GAL NOK 1 1
3 GLC DMJ 0.569231 0.811321
4 NAG BMA 0.542857 0.90566
5 GAL MGC 0.521739 0.785714
6 A2G GAL 0.5 0.814815
7 NDG GAL 0.5 0.814815
8 NLC 0.5 0.814815
9 8VZ 0.5 0.821429
10 GAL GC2 0.5 0.84127
11 GAL NGA 0.5 0.814815
12 GAL NDG 0.5 0.814815
13 NOJ GLC 0.5 0.811321
14 GAL A2G 0.5 0.814815
15 NAG NAG BMA 0.47561 0.875
16 NAG NDG BMA 0.47561 0.875
17 GLA GAL NAG 0.461538 0.814815
18 MAN BMA NAG 0.461538 0.814815
19 NAG GAL GAL 0.461538 0.814815
20 GAL LOG 0.460526 0.730159
21 LOG GAL 0.460526 0.730159
22 GAL NGA A2G 0.454545 0.789474
23 GAL NAG MAN 0.45 0.814815
24 GAL SER A2G 0.45 0.854545
25 MAN NAG GAL 0.45 0.814815
26 A2G SER GAL 0.45 0.854545
27 NGA SER GAL 0.45 0.854545
28 GAL TNR 0.45 0.854545
29 NOY BGC 0.449275 0.796296
30 NAG NAG BMA MAN 0.444444 0.875
31 MAN MNM 0.442857 0.796296
32 NAG GAL GAL NAG GAL 0.435294 0.803571
33 GAL A2G THR 0.433735 0.807018
34 FUC NDG GAL 0.432099 0.8
35 GAL NAG FUC 0.432099 0.8
36 FUC NAG GAL 0.432099 0.8
37 MAG FUC GAL 0.432099 0.77193
38 GAL NDG FUC 0.432099 0.8
39 NOJ NAG NAG NAG 0.430233 0.894737
40 NOJ NAG NAG 0.430233 0.910714
41 GAL NAG GAL 0.428571 0.851852
42 GAL A2G MBN 0.428571 0.803571
43 M13 0.426471 0.6
44 GAL MBG 0.426471 0.6
45 MDM 0.426471 0.6
46 RZM 0.426471 0.714286
47 GLA MBG 0.424242 0.6
48 LAT NAG GAL 0.423529 0.814815
49 GAL NAG GAL BGC 0.423529 0.814815
50 BGC GAL NAG GAL 0.423529 0.814815
51 BMA IFM 0.422535 0.727273
52 IFM BGC 0.422535 0.727273
53 IFM BMA 0.422535 0.727273
54 BMA MAN 0.42029 0.641509
55 DOM 0.42029 0.6
56 NAG GAL GAL NAG 0.418605 0.803571
57 GAL NAG GAL NAG GAL NAG 0.418605 0.789474
58 NAG NAG 0.417722 0.890909
59 GAL A2G NPO 0.413793 0.657143
60 NPO A2G GAL 0.413793 0.657143
61 GLC GAL NAG GAL 0.413793 0.814815
62 GAL BGC NAG GAL 0.411765 0.814815
63 DR5 0.405797 0.6
64 MMA MAN 0.405797 0.6
65 GAL NAG GAL FUC 0.404494 0.8
66 GAL NGA GLA BGC GAL 0.404494 0.814815
67 GLA NAG GAL FUC 0.404494 0.8
68 BGC OXZ 0.402778 0.666667
69 9MR 0.402778 0.727273
70 FUC BGC GAL 0.402597 0.611111
71 NGA GAL BGC 0.402439 0.814815
72 CG3 A2G GAL 0.4 0.647887
Ligand no: 2; Ligand: GAL NOK; Similar ligands found: 72
No: Ligand ECFP6 Tc MDL keys Tc
1 NOK GAL 1 1
2 GAL NOK 1 1
3 GLC DMJ 0.569231 0.811321
4 NAG BMA 0.542857 0.90566
5 GAL MGC 0.521739 0.785714
6 A2G GAL 0.5 0.814815
7 NDG GAL 0.5 0.814815
8 NLC 0.5 0.814815
9 8VZ 0.5 0.821429
10 GAL GC2 0.5 0.84127
11 GAL NGA 0.5 0.814815
12 GAL NDG 0.5 0.814815
13 NOJ GLC 0.5 0.811321
14 GAL A2G 0.5 0.814815
15 NAG NAG BMA 0.47561 0.875
16 NAG NDG BMA 0.47561 0.875
17 GLA GAL NAG 0.461538 0.814815
18 MAN BMA NAG 0.461538 0.814815
19 NAG GAL GAL 0.461538 0.814815
20 GAL LOG 0.460526 0.730159
21 LOG GAL 0.460526 0.730159
22 GAL NGA A2G 0.454545 0.789474
23 GAL NAG MAN 0.45 0.814815
24 GAL SER A2G 0.45 0.854545
25 MAN NAG GAL 0.45 0.814815
26 A2G SER GAL 0.45 0.854545
27 NGA SER GAL 0.45 0.854545
28 GAL TNR 0.45 0.854545
29 NOY BGC 0.449275 0.796296
30 NAG NAG BMA MAN 0.444444 0.875
31 MAN MNM 0.442857 0.796296
32 NAG GAL GAL NAG GAL 0.435294 0.803571
33 GAL A2G THR 0.433735 0.807018
34 FUC NDG GAL 0.432099 0.8
35 GAL NAG FUC 0.432099 0.8
36 FUC NAG GAL 0.432099 0.8
37 MAG FUC GAL 0.432099 0.77193
38 GAL NDG FUC 0.432099 0.8
39 NOJ NAG NAG NAG 0.430233 0.894737
40 NOJ NAG NAG 0.430233 0.910714
41 GAL NAG GAL 0.428571 0.851852
42 GAL A2G MBN 0.428571 0.803571
43 M13 0.426471 0.6
44 GAL MBG 0.426471 0.6
45 MDM 0.426471 0.6
46 RZM 0.426471 0.714286
47 GLA MBG 0.424242 0.6
48 LAT NAG GAL 0.423529 0.814815
49 GAL NAG GAL BGC 0.423529 0.814815
50 BGC GAL NAG GAL 0.423529 0.814815
51 BMA IFM 0.422535 0.727273
52 IFM BGC 0.422535 0.727273
53 IFM BMA 0.422535 0.727273
54 BMA MAN 0.42029 0.641509
55 DOM 0.42029 0.6
56 NAG GAL GAL NAG 0.418605 0.803571
57 GAL NAG GAL NAG GAL NAG 0.418605 0.789474
58 NAG NAG 0.417722 0.890909
59 GAL A2G NPO 0.413793 0.657143
60 NPO A2G GAL 0.413793 0.657143
61 GLC GAL NAG GAL 0.413793 0.814815
62 GAL BGC NAG GAL 0.411765 0.814815
63 DR5 0.405797 0.6
64 MMA MAN 0.405797 0.6
65 GAL NAG GAL FUC 0.404494 0.8
66 GAL NGA GLA BGC GAL 0.404494 0.814815
67 GLA NAG GAL FUC 0.404494 0.8
68 BGC OXZ 0.402778 0.666667
69 9MR 0.402778 0.727273
70 FUC BGC GAL 0.402597 0.611111
71 NGA GAL BGC 0.402439 0.814815
72 CG3 A2G GAL 0.4 0.647887
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JAW; Ligand: GAL NGT; Similar sites found: 26
This union binding pocket(no: 1) in the query (biounit: 4jaw.bio3) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2EPN NGT 0.00001005 0.57235 1.91388
2 5A6B OAN 0.0000875 0.42446 3.10559
3 2OVW CBI 0.005696 0.42231 3.16302
4 3P7G MAN 0.01142 0.40151 3.42466
5 4WQQ MAN 0.003808 0.42213 3.5461
6 1JZN BGC GAL 0.001283 0.44856 3.7037
7 1OBB MAL 0.01664 0.4001 3.75
8 1OJJ GLC GAL 0.002156 0.43755 4.47761
9 1OJK GLC BGC 0.002 0.42848 4.47761
10 1PWB GLC GLC 0.002373 0.40604 5.08475
11 2MSB NAG BMA MAN MAN MAN MAN MAN 0.007894 0.4092 5.21739
12 3RAB GNP 0.02482 0.40058 5.32544
13 3TNF GNP 0.007324 0.42992 5.98958
14 3KOX Z98 0.008776 0.41645 7.43802
15 5KTI TRE 6X6 0.008055 0.41175 8.05369
16 2OX9 GAL NAG FUC 0.011 0.40322 10.7143
17 1G1T SIA GAL MAG FUC 0.005336 0.42577 10.828
18 4RPM HXC 0.008852 0.41286 11.5764
19 1C7S CBS 0.002529 0.42154 16.9255
20 4AZI OAN 0.00000281 0.56683 22.3982
21 4AZ6 OAN 0.000005702 0.52369 23.2184
22 1NOW IFG 0.00003688 0.48486 23.4714
23 1JAK IFG 0.00002981 0.50613 28.9062
24 4AZC NGW 0.00000006759 0.6896 32.1267
25 3SUT OAN 0.00008897 0.49689 32.5714
26 3S6T OAN 0.001666 0.40713 34.087
Pocket No.: 2; Query (leader) PDB : 4JAW; Ligand: NGT GAL; Similar sites found: 32
This union binding pocket(no: 2) in the query (biounit: 4jaw.bio3) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2EPN NGT 0.000008805 0.5815 1.91388
2 4Z5W TYS ILE TYS THR GLN 0.01111 0.41157 2.02492
3 2GZM DGL 0.01214 0.40608 2.99625
4 5A6B OAN 0.00007579 0.40939 3.10559
5 2OVW CBI 0.002101 0.44316 3.16302
6 3P7G MAN 0.02004 0.40053 3.42466
7 4WQQ MAN 0.002418 0.43997 3.5461
8 1ZUW DGL 0.0129 0.4048 3.67647
9 1JZN BGC GAL 0.001929 0.44041 3.7037
10 2GGX NPJ 0.007879 0.42244 4.375
11 1OJJ GLC GAL 0.002464 0.4398 4.47761
12 1OJK GLC BGC 0.002373 0.41211 4.47761
13 1TLG GAL 0.001555 0.42158 4.8
14 2MSB NAG BMA MAN MAN MAN MAN MAN 0.01085 0.40528 5.21739
15 3FU7 KIA 0.01907 0.41596 5.54562
16 3TNF GNP 0.01817 0.40276 5.98958
17 3KOX Z98 0.0117 0.40257 7.43802
18 5KTI TRE 6X6 0.009981 0.40934 8.05369
19 1UA4 BGC 0.01543 0.401 8.57143
20 1UA4 GLC 0.01543 0.401 8.57143
21 1G1T SIA GAL MAG FUC 0.001077 0.46516 10.828
22 4RPM HXC 0.01267 0.4097 11.5764
23 1DZK PRZ 0.007987 0.40227 12.7389
24 4YEF 4CQ 0.01085 0.4129 13.4831
25 1C7S CBS 0.0006479 0.45663 16.9255
26 4AZI OAN 0.0000005005 0.60929 22.3982
27 4AZ6 OAN 0.000002569 0.55955 23.2184
28 1NOW IFG 0.00003971 0.4626 23.4714
29 1JAK IFG 0.000009195 0.54185 28.9062
30 4AZC NGW 0.000000006547 0.75199 32.1267
31 3SUT OAN 0.00003075 0.52472 32.5714
32 3S6T OAN 0.001638 0.41873 34.087
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