Receptor
PDB id Resolution Class Description Source Keywords
5BXP 1.7 Å EC: 3.2.1.140 LNBASE IN COMPLEX WITH LNB-LOGNAC 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...
LOG GAL C:1;
D:1;
 Valid;
Valid;
 none;
none;
 Ki = 7.7 uM
396.349 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 LOG GAL 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 LOG GAL 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 LOG GAL n/a n/a
6 4H04 - NAG GAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: LOG GAL; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 LOG GAL 1 1
2 LOG 0.52381 0.910714
3 MGC GAL 0.514286 0.775862
4 A2G GAL 0.514286 0.803571
5 5G0 GAL 0.5 0.794118
6 NAG GAL 0.492958 0.803571
7 TVD GAL 0.492958 0.810345
8 NAG BMA 0.472973 0.733333
9 NOK GAL 0.467532 0.71875
10 GAL A2G MBN 0.457831 0.793103
11 NAG GAL GAL 0.455696 0.803571
12 A2G SER GAL 0.451219 0.754098
13 A2G THR GAL 0.445783 0.783333
14 BGC GAL NGA GAL 0.445783 0.803571
15 NAG FUC GAL 0.444444 0.789474
16 GLC U8V 0.442857 0.614035
17 A2G MBN GAL 0.440476 0.807018
18 GAL NAG GAL 0.439024 0.803571
19 BGC GAL NAG GAL 0.435294 0.803571
20 MAN NAG GAL 0.426829 0.803571
21 A2G NPO GAL 0.425287 0.80303
22 NAG GAL BGC GAL 0.423529 0.803571
23 A2G GAL NAG 0.418605 0.793103
24 BGC GAL GLA NGA GAL 0.41573 0.803571
25 GAL NAG FUC GAL 0.41573 0.789474
26 GAL NAG GAL NAG GAL 0.413793 0.793103
27 NAG GAL NAG GAL NAG GAL 0.413793 0.810345
28 NAG GAL NAG GAL 0.413793 0.793103
29 GAL GC2 0.411765 0.630137
30 NAG GAL FUC GLA 0.411111 0.789474
31 GAL FUC GAL 0.402597 0.607143
32 NAG NAG BMA 0.402299 0.741935
33 BMA MAN NAG 0.4 0.803571
Similar Ligands (3D)
Ligand no: 1; Ligand: LOG GAL; Similar ligands found: 17
No: Ligand Similarity coefficient
1 GAL NOK 0.9521
2 NGA GAL 0.9410
3 GAL NGT 0.9388
4 NGT GAL 0.9382
5 NAG GCD 0.9208
6 4WS GAL 0.9205
7 NAG GC4 0.9156
8 GLC GAL 0.9094
9 BGC GAL 0.9042
10 NAG BDP 0.9024
11 NGA GCD 0.9024
12 NAG GAD 0.8972
13 NDG GAL 0.8947
14 ABL 0.8700
15 FRU GAL 0.8617
16 GAL GLA 0.8612
17 NOY BGC 0.8607
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: 2
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
2 4AZC NGW 32.1267
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