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
n/a n/a
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: NOK GAL; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 NOK GAL 1 1
2 GLC DMJ 0.552239 0.833333
3 NAG BMA 0.549296 0.888889
4 MAN G63 0.536232 0.888889
5 NOJ GLC 0.507246 0.833333
6 GAL GC2 0.493827 0.828125
7 A2G GAL 0.486111 0.8
8 TVD GAL 0.486111 0.807018
9 NAG GAL 0.486111 0.8
10 MGC GAL 0.486111 0.77193
11 LOG GAL 0.467532 0.71875
12 NAG NAG BMA 0.464286 0.859649
13 MAN MNM 0.444444 0.803571
14 MAN NAG GAL 0.439024 0.8
15 RZM 0.434783 0.701754
16 GAL NAG GAL 0.433735 0.8
17 NAG GAL GAL 0.432099 0.8
18 IFM BGC 0.430556 0.75
19 A2G SER GAL 0.428571 0.875
20 NOY BGC 0.424658 0.803571
21 A2G THR GAL 0.423529 0.810345
22 NAG FUC GAL 0.421687 0.785714
23 NAG NOJ NAG NAG 0.420455 0.896552
24 NAG NOJ NAG 0.420455 0.912281
25 NAG NAG BMA MAN 0.419355 0.859649
26 GCU BGC 0.418919 0.6
27 GLC U8V 0.416667 0.607143
28 GAL NAG GAL NAG GAL 0.409091 0.789474
29 BGC GAL NGA GAL 0.406977 0.8
30 NAG GAL FUC GLA 0.406593 0.785714
31 2F8 0.405797 0.75
32 MAG 0.405797 0.75
33 A2G NPO GAL 0.404494 0.647887
34 GAL A2G MBN 0.402299 0.789474
35 A2G MBN GAL 0.402299 0.77193
36 NAG GAL BGC GAL 0.402299 0.8
37 3CU GLC 0.4 0.693548
Ligand no: 2; Ligand: GAL NOK; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Ligands (3D)
Ligand no: 1; Ligand: NOK GAL; Similar ligands found: 26
No: Ligand Similarity coefficient
1 GAL NOK 0.9990
2 GAL NGT 0.9788
3 NGT GAL 0.9775
4 4WS GAL 0.9530
5 NGA GAL 0.9463
6 BGC GAL 0.9310
7 GLC GAL 0.9310
8 NAG GC4 0.9256
9 NAG GCD 0.9217
10 BGC BGC 0.9151
11 NDG GAL 0.9131
12 FRU GAL 0.9100
13 NGA GCD 0.9097
14 GLC BGC 0.9064
15 SHG BGC 0.9010
16 BMA GAL 0.8971
17 NAG GAD 0.8951
18 NAG BDP 0.8894
19 ABL 0.8840
20 GCS GCS 0.8823
21 BMA BGC 0.8749
22 BGC Z9D 0.8749
23 PA1 GCS 0.8714
24 MGL GAL 0.8627
25 GAL GLA 0.8602
26 GAL GAL 0.8559
Ligand no: 2; Ligand: GAL NOK; Similar ligands found: 30
No: Ligand Similarity coefficient
1 GAL NOK 1.0000
2 NOK GAL 0.9990
3 GAL NGT 0.9782
4 NGT GAL 0.9779
5 NAG GAL 0.9750
6 GAL GC2 0.9536
7 LOG GAL 0.9521
8 4WS GAL 0.9471
9 NGA GAL 0.9463
10 GLC GAL 0.9310
11 BGC GAL 0.9310
12 NAG GC4 0.9256
13 NAG GCD 0.9217
14 BGC BGC 0.9151
15 NDG GAL 0.9131
16 GLC BGC 0.9064
17 FRU GAL 0.9055
18 SHG BGC 0.9010
19 BMA GAL 0.8971
20 NAG GAD 0.8951
21 NAG BDP 0.8934
22 NOY BGC 0.8907
23 BGC Z9D 0.8884
24 ABL 0.8824
25 GCS GCS 0.8823
26 IFM BGC 0.8766
27 PA1 GCS 0.8739
28 MGL GAL 0.8716
29 9MR 0.8582
30 GAL GLA 0.8575
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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