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 O(C1C...
NGT GAL B:702;
 Valid;
 none;
 Ki = 125 nM
381.402 n/a O(C1C...
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: 42
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 NGT 0.492063 0.9
5 GNL 0.492063 0.9
6 NGT NAG 0.463415 0.862069
7 BQZ 0.435484 0.6
8 NAG NAG NGT 0.431818 0.847458
9 TRE 0.431034 0.66
10 SN5 NGT 0.428571 0.909091
11 GLA EGA 0.428571 0.666667
12 GAL MBG 0.426471 0.666667
13 MDM 0.426471 0.666667
14 MMA MAN 0.426471 0.666667
15 M13 0.426471 0.666667
16 DR5 0.426471 0.666667
17 GLA MBG 0.424242 0.666667
18 LAT GLA 0.424242 0.66
19 CBK 0.41791 0.66
20 N9S 0.41791 0.66
21 LAT 0.41791 0.66
22 MAB 0.41791 0.66
23 GAL BGC 0.41791 0.66
24 M3M 0.41791 0.66
25 CBI 0.41791 0.66
26 B2G 0.41791 0.66
27 GLC GAL 0.41791 0.66
28 BGC GAL 0.41791 0.66
29 MAN GLC 0.41791 0.66
30 NGR 0.41791 0.66
31 GLA GLA 0.41791 0.66
32 MAL 0.41791 0.66
33 LB2 0.41791 0.66
34 BMA GAL 0.41791 0.66
35 LBT 0.41791 0.66
36 BGC BMA 0.41791 0.66
37 GLA GAL 0.41791 0.66
38 2M4 0.402985 0.66
39 MAL EDO 0.402778 0.634615
40 GLA GAL BGC 5VQ 0.4 0.641509
41 DOM 0.4 0.634615
42 SN5 SN5 NGT 0.4 0.909091
Ligand no: 2; Ligand: NGT GAL; Similar ligands found: 42
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 NGT 0.492063 0.9
5 GNL 0.492063 0.9
6 NGT NAG 0.463415 0.862069
7 BQZ 0.435484 0.6
8 NAG NAG NGT 0.431818 0.847458
9 TRE 0.431034 0.66
10 SN5 NGT 0.428571 0.909091
11 GLA EGA 0.428571 0.666667
12 GAL MBG 0.426471 0.666667
13 MDM 0.426471 0.666667
14 MMA MAN 0.426471 0.666667
15 M13 0.426471 0.666667
16 DR5 0.426471 0.666667
17 GLA MBG 0.424242 0.666667
18 LAT GLA 0.424242 0.66
19 CBK 0.41791 0.66
20 N9S 0.41791 0.66
21 LAT 0.41791 0.66
22 MAB 0.41791 0.66
23 GAL BGC 0.41791 0.66
24 M3M 0.41791 0.66
25 CBI 0.41791 0.66
26 B2G 0.41791 0.66
27 GLC GAL 0.41791 0.66
28 BGC GAL 0.41791 0.66
29 MAN GLC 0.41791 0.66
30 NGR 0.41791 0.66
31 GLA GLA 0.41791 0.66
32 MAL 0.41791 0.66
33 LB2 0.41791 0.66
34 BMA GAL 0.41791 0.66
35 LBT 0.41791 0.66
36 BGC BMA 0.41791 0.66
37 GLA GAL 0.41791 0.66
38 2M4 0.402985 0.66
39 MAL EDO 0.402778 0.634615
40 GLA GAL BGC 5VQ 0.4 0.641509
41 DOM 0.4 0.634615
42 SN5 SN5 NGT 0.4 0.909091
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4JAW; Ligand: GAL NGT; 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: 4jaw.bio3) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4JAW; Ligand: NGT GAL; Similar sites found with APoc: 1
This union binding pocket(no: 2) in the query (biounit: 4jaw.bio3) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4AZC NGW 32.1267
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