Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:705;
A:703;
A:706;
A:704;
B:704;
B:703;
B:705;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
GAL NGT A:701;
Valid;
none;
Ki = 125 nM
381.402 n/a S1C2O...
NGT GAL B:702;
Valid;
none;
Ki = 125 nM
381.402 n/a S1C2O...
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: GAL NGT; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 NGT GAL 1 1
2 GAL NGT 1 1
3 BMA NGT MAN MAN 0.547619 1
4 GNL 0.492063 0.9
5 NGT 0.492063 0.9
6 NGT NAG 0.463415 0.862069
7 NAG NAG NGT 0.431818 0.847458
8 TRE 0.431034 0.66
9 SN5 NGT 0.428571 0.909091
10 GLA EGA 0.428571 0.666667
11 MDM 0.426471 0.666667
12 DR5 0.426471 0.666667
13 M13 0.426471 0.666667
14 MMA MAN 0.426471 0.666667
15 GAL MBG 0.426471 0.666667
16 LAT GLA 0.424242 0.66
17 GLA MBG 0.424242 0.666667
18 MAL MAL 0.41791 0.647059
19 LB2 0.41791 0.66
20 LBT 0.41791 0.66
21 GLC BGC 0.41791 0.66
22 B2G 0.41791 0.66
23 LAT 0.41791 0.66
24 BMA GAL 0.41791 0.66
25 GAL BGC 0.41791 0.66
26 BGC BMA 0.41791 0.66
27 MAB 0.41791 0.66
28 GLA GAL 0.41791 0.66
29 BMA BMA 0.41791 0.66
30 M3M 0.41791 0.66
31 GLC GAL 0.41791 0.66
32 N9S 0.41791 0.66
33 GAL GLC 0.41791 0.66
34 MAN GLC 0.41791 0.66
35 GLA GLA 0.41791 0.66
36 CBI 0.41791 0.66
37 MAL 0.41791 0.66
38 BGC GAL 0.41791 0.66
39 BGC GLC 0.41791 0.66
40 CBK 0.41791 0.66
41 2M4 0.402985 0.66
42 MAN MAN 0.402985 0.66
43 BGC BGC 0.402985 0.66
44 MAL EDO 0.402778 0.634615
45 SN5 SN5 NGT 0.4 0.909091
46 GLA GAL BGC 5VQ 0.4 0.641509
47 DOM 0.4 0.634615
Ligand no: 2; Ligand: NGT GAL; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 NGT GAL 1 1
2 GAL NGT 1 1
3 BMA NGT MAN MAN 0.547619 1
4 GNL 0.492063 0.9
5 NGT 0.492063 0.9
6 NGT NAG 0.463415 0.862069
7 NAG NAG NGT 0.431818 0.847458
8 TRE 0.431034 0.66
9 SN5 NGT 0.428571 0.909091
10 GLA EGA 0.428571 0.666667
11 MDM 0.426471 0.666667
12 DR5 0.426471 0.666667
13 M13 0.426471 0.666667
14 MMA MAN 0.426471 0.666667
15 GAL MBG 0.426471 0.666667
16 LAT GLA 0.424242 0.66
17 GLA MBG 0.424242 0.666667
18 MAL MAL 0.41791 0.647059
19 LB2 0.41791 0.66
20 LBT 0.41791 0.66
21 GLC BGC 0.41791 0.66
22 B2G 0.41791 0.66
23 LAT 0.41791 0.66
24 BMA GAL 0.41791 0.66
25 GAL BGC 0.41791 0.66
26 BGC BMA 0.41791 0.66
27 MAB 0.41791 0.66
28 GLA GAL 0.41791 0.66
29 BMA BMA 0.41791 0.66
30 M3M 0.41791 0.66
31 GLC GAL 0.41791 0.66
32 N9S 0.41791 0.66
33 GAL GLC 0.41791 0.66
34 MAN GLC 0.41791 0.66
35 GLA GLA 0.41791 0.66
36 CBI 0.41791 0.66
37 MAL 0.41791 0.66
38 BGC GAL 0.41791 0.66
39 BGC GLC 0.41791 0.66
40 CBK 0.41791 0.66
41 2M4 0.402985 0.66
42 MAN MAN 0.402985 0.66
43 BGC BGC 0.402985 0.66
44 MAL EDO 0.402778 0.634615
45 SN5 SN5 NGT 0.4 0.909091
46 GLA GAL BGC 5VQ 0.4 0.641509
47 DOM 0.4 0.634615
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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