Receptor
PDB id Resolution Class Description Source Keywords
4AD3 2 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDE XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3-DEOXYMANNOJIRIMYC BACTEROIDES XYLANISOLVENS HYDROLASE GLYCOSIDE HYDROLASE GH99 CAZY ENZYME-CARBOHYDRINTERACTION MANNOSE GLYCOSIDASE INHIBITION
Ref.: STRUCTURAL AND MECHANISTIC INSIGHT INTO N-GLYCAN PR BY ENDO-ALPHA-MANNOSIDASE. PROC.NATL.ACAD.SCI.USA V. 109 781 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GLC DMJ A:500;
B:500;
C:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 24 uM
326.322 n/a O(C1C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5LYR 1.14 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-NOEUROMYCIN BACTEROIDES XYLANISOLVENS XB1A ENDOMANNANASE ENDOMANNOSIDASE GH99 NOEUROMYCIN HYDROLASE N- GLYCOSYLATION GLYCOSYLATION INHIBITOR INHIBITION SHAPE CHARHYDROLASE
Ref.: CONTRIBUTION OF SHAPE AND CHARGE TO THE INHIBITION FAMILY GH99 ENDO-ALPHA-1,2-MANNANASE. J. AM. CHEM. SOC. V. 139 1089 2017
Members (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5M03 - MAN MAN n/a n/a
2 6HMH - GDQ GLC n/a n/a
3 5MC8 - DGO MAN n/a n/a
4 6HMG - GDQ GLC n/a n/a
5 6FAR - MAN MVL n/a n/a
6 5LYR Kd = 0.013 uM MAN MNM n/a n/a
7 4AD5 - MAN MAN n/a n/a
8 4V27 Kd = 217 nM MAN IFM n/a n/a
9 5M5D Kd = 111 uM DGO MAN n/a n/a
10 5M3W - 7D1 MAN n/a n/a
11 4AD2 Kd = 625 nM GLC IFM n/a n/a
12 4AD3 Kd = 24 uM GLC DMJ n/a n/a
13 5M17 Kd = 221 uM 7D1 MAN n/a n/a
14 6FAM - MAN G63 n/a n/a
15 4V28 - MAN 4MU MAN n/a n/a
16 4AD4 - MAN MAN n/a n/a
17 5MEL - GLC 7LQ n/a n/a
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5M03 - MAN MAN n/a n/a
2 6HMH - GDQ GLC n/a n/a
3 5MC8 - DGO MAN n/a n/a
4 6HMG - GDQ GLC n/a n/a
5 6FAR - MAN MVL n/a n/a
6 5LYR Kd = 0.013 uM MAN MNM n/a n/a
7 4AD5 - MAN MAN n/a n/a
8 4V27 Kd = 217 nM MAN IFM n/a n/a
9 5M5D Kd = 111 uM DGO MAN n/a n/a
10 5M3W - 7D1 MAN n/a n/a
11 4AD2 Kd = 625 nM GLC IFM n/a n/a
12 4AD3 Kd = 24 uM GLC DMJ n/a n/a
13 5M17 Kd = 221 uM 7D1 MAN n/a n/a
14 6FAM - MAN G63 n/a n/a
15 4V28 - MAN 4MU MAN n/a n/a
16 4AD4 - MAN MAN n/a n/a
17 5MEL - GLC 7LQ n/a n/a
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5M03 - MAN MAN n/a n/a
2 6HMH - GDQ GLC n/a n/a
3 5MC8 - DGO MAN n/a n/a
4 6HMG - GDQ GLC n/a n/a
5 6FAR - MAN MVL n/a n/a
6 5LYR Kd = 0.013 uM MAN MNM n/a n/a
7 4AD5 - MAN MAN n/a n/a
8 4V27 Kd = 217 nM MAN IFM n/a n/a
9 5M5D Kd = 111 uM DGO MAN n/a n/a
10 5M3W - 7D1 MAN n/a n/a
11 4AD2 Kd = 625 nM GLC IFM n/a n/a
12 4AD3 Kd = 24 uM GLC DMJ n/a n/a
13 5M17 Kd = 221 uM 7D1 MAN n/a n/a
14 6FAM - MAN G63 n/a n/a
15 4V28 - MAN 4MU MAN n/a n/a
16 4AD4 - MAN MAN n/a n/a
17 5MEL - GLC 7LQ n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GLC DMJ; Similar ligands found: 57
No: Ligand ECFP6 Tc MDL keys Tc
1 GLC DMJ 1 1
2 MAN G63 0.627119 0.9375
3 NOJ GLC 0.62069 1
4 NOK GAL 0.552239 0.833333
5 IFM BGC 0.55 0.893617
6 BQZ 0.5 0.666667
7 MAN MNM 0.492063 0.84
8 NOY BGC 0.492063 0.84
9 MBG GLA 0.482759 0.666667
10 RR7 GLC 0.47541 0.702128
11 GAL GLA 0.474576 0.695652
12 MAN MAN BMA 0.470588 0.73913
13 NOJ BGC 0.46875 1
14 5QP 0.460317 0.733333
15 MBG GAL 0.459016 0.666667
16 RZM 0.459016 0.833333
17 MGL GAL 0.459016 0.666667
18 BGC GLA GAL 0.457627 0.695652
19 9MR 0.453125 0.851064
20 BGC OXZ 0.453125 0.769231
21 MAN BMA BMA 0.447761 0.73913
22 EDG AHR 0.442623 0.875
23 MAN MAN 0.442623 0.733333
24 CJX 0.439394 0.857143
25 BGC BGC BGC BGC BGC BGC BGC 0.4375 0.695652
26 BGC BGC BGC BGC BGC BGC 0.4375 0.695652
27 GLC BGC BGC BGC 0.4375 0.695652
28 BGC BGC BGC BGC BGC 0.4375 0.695652
29 BGC BGC BGC 0.4375 0.695652
30 GDQ GLC 0.432836 0.877551
31 GLC EDO GLC 0.430769 0.702128
32 7D1 MAN 0.428571 0.702128
33 GLC IFM 0.424242 0.87234
34 GLC GLC GLC GLC BGC GLC GLC 0.421875 0.695652
35 FUC GAL 0.421875 0.659574
36 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.421875 0.695652
37 MAN BMA BMA BMA BMA BMA BMA 0.421875 0.695652
38 3CU GLC 0.41791 0.811321
39 GCU BGC 0.41791 0.680851
40 IDC 0.416667 0.639344
41 MVL BMA 0.416667 0.639344
42 MAN IPD MAN 0.415385 0.611111
43 FRU BMA 0.415385 0.64
44 H1M MAN MAN 0.413333 0.66
45 GPM GLC 0.411765 0.6
46 MMA MAN MAN 0.408451 0.666667
47 G2F BGC BGC BGC BGC BGC 0.408451 0.66
48 NAG BMA 0.408451 0.788462
49 MMA 0.407407 0.638298
50 GYP 0.407407 0.638298
51 MBG 0.407407 0.638298
52 AMG 0.407407 0.638298
53 MGC GAL 0.405797 0.703704
54 BGC 5VQ GAL GLA 0.405797 0.64
55 AHR FUB 0.403509 0.604167
56 LG9 GLC 0.4 0.796296
57 BMA MAN MAN 0.4 0.695652
Similar Ligands (3D)
Ligand no: 1; Ligand: GLC DMJ; Similar ligands found: 39
No: Ligand Similarity coefficient
1 GLC 7LQ 0.9692
2 GLC GLC 0.9533
3 MAN IFM 0.9514
4 MAN GLC 0.9511
5 DGO MAN 0.9476
6 FRU GLC 0.9333
7 BGC GLC 0.9284
8 ZEL MAN 0.9243
9 DGO Z61 0.9239
10 GLA BEZ 0.9158
11 MMA MAN 0.9115
12 RAM GAD 0.9109
13 GLC Z9N 0.9045
14 BGC BGC 0.9041
15 XYP GCU 0.8994
16 GAL FUC 0.8941
17 MYG 0.8934
18 GLC BGC 0.8920
19 TW7 GLC 0.8895
20 MA1 GLC 0.8891
21 BDF GLC 0.8858
22 MAN MVL 0.8826
23 IFM BMA 0.8807
24 BMA IFM 0.8807
25 SGC GLC 0.8806
26 GLC GLA 0.8752
27 NOS 0.8747
28 GMH GMH 0.8732
29 GLF B8D 0.8721
30 ADN 0.8711
31 GLC FRU 0.8705
32 6MD 0.8697
33 MTP 0.8696
34 XYP XYP 0.8694
35 AD3 0.8672
36 FMB 0.8612
37 LOX XYP 0.8573
38 GCS GCS 0.8534
39 FTU 0.8526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5LYR; Ligand: MAN MNM; 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: 5lyr.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
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