Receptor
PDB id Resolution Class Description Source Keywords
6HMH 1.03 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH ALPHA-GLC-1,3-(1,2-ANHYDRO-CAG LUCOSAMINE) AND ALPHA-1,2-MANNOBIOSE BACTEROIDES XYLANISOLVENS XB1A HYDROLASE
Ref.: FROM 1,4-DISACCHARIDE TO 1,3-GLYCOSYL CARBASUGAR: S OF A BESPOKE INHIBITOR OF FAMILY GH99 ENDO-ALPHA-MANNOSIDASE. ORG.LETT. V. 20 7488 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:401;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
GDQ GLC A:403;
Valid;
none;
submit data
322.334 n/a O(C1C...
MAN MAN B:1;
Valid;
none;
submit data
326.298 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: GDQ GLC; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 GDQ GLC 1 1
2 BQZ 0.509091 0.638298
3 MAN MNM 0.5 0.773585
4 IFM BGC 0.484375 0.82
5 NOY BGC 0.476923 0.773585
6 RZM 0.467742 0.8
7 MBG GLA 0.466667 0.64
8 9MR 0.461538 0.78
9 RR7 GLC 0.460317 0.673469
10 GAL GLA 0.459016 0.666667
11 5QP 0.446154 0.666667
12 BGC GLA GAL 0.442623 0.666667
13 ISX 0.439394 0.76
14 BGC OXZ 0.439394 0.709091
15 NOJ GLC 0.432836 0.877551
16 GLC IFM 0.432836 0.8
17 GLC DMJ 0.432836 0.877551
18 FUC GAL 0.430769 0.632653
19 CJX 0.426471 0.788462
20 BGC BGC BGC BGC BGC BGC 0.424242 0.666667
21 GLC BGC BGC BGC 0.424242 0.666667
22 BGC BGC BGC 0.424242 0.666667
23 BGC BGC BGC BGC BGC BGC BGC 0.424242 0.666667
24 BGC BGC BGC BGC BGC 0.424242 0.666667
25 MGL GAL 0.421875 0.64
26 MBG GAL 0.421875 0.64
27 MAN G63 0.42029 0.826923
28 GLC GLC GLC GLC BGC GLC GLC 0.409091 0.666667
29 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.409091 0.666667
30 MAN BMA BMA BMA BMA BMA BMA 0.409091 0.666667
31 BMA MAN MAN 0.408451 0.666667
32 MAN MAN 0.40625 0.666667
33 GCU BGC 0.405797 0.653061
34 GLC 7LQ 0.405797 0.632653
35 ABL 0.405797 0.773585
36 G2I 0.405405 0.764706
37 G3I 0.405405 0.764706
38 FRU BMA 0.402985 0.615385
Ligand no: 2; Ligand: MAN MAN; Similar ligands found: 76
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MAN 1 1
2 GAL FUC 0.686275 0.970588
3 7D1 MAN 0.584906 0.942857
4 GLC IFM 0.571429 0.727273
5 BQZ 0.5 0.909091
6 ISX 0.5 0.761905
7 GAL GLA 0.5 0.941176
8 XYP IOB BGC 0.486111 0.780488
9 3CU GLC 0.483333 0.615385
10 RZM 0.482143 0.688889
11 MBG GLA 0.481481 0.888889
12 MAN G63 0.47541 0.6875
13 G2F BGC BGC BGC BGC BGC 0.46875 0.868421
14 MAN BMA BMA 0.467742 0.942857
15 NOJ GLC 0.466667 0.733333
16 XYS GLC GLC 0.462687 0.914286
17 LG9 GLC 0.460317 0.603774
18 GYP 0.458333 0.857143
19 MMA 0.458333 0.857143
20 AMG 0.458333 0.857143
21 MBG 0.458333 0.857143
22 GLC BGC BGC BGC 0.457627 0.941176
23 BGC BGC BGC BGC BGC BGC BGC 0.457627 0.941176
24 BGC BGC BGC BGC BGC BGC 0.457627 0.941176
25 BGC BGC BGC BGC BGC 0.457627 0.941176
26 BGC BGC BGC 0.457627 0.941176
27 MBG GAL 0.45614 0.888889
28 MGL GAL 0.45614 0.888889
29 BGC GLA GAL 0.454545 0.941176
30 IFM BGC 0.45 0.711111
31 RR7 GLC 0.448276 0.888889
32 XYS XYS AHR 0.447761 0.864865
33 XYP XYP AHR 0.447761 0.864865
34 MAN MAN BMA 0.446154 0.942857
35 NAG BMA 0.446154 0.6875
36 NAG GAL 0.444444 0.695652
37 BDF GLC 0.444444 0.916667
38 MAN MNM 0.442623 0.666667
39 NOY BGC 0.442623 0.666667
40 GLC DMJ 0.442623 0.733333
41 GLC GLC GLC GLC BGC GLC GLC 0.440678 0.941176
42 MAN BMA BMA BMA BMA BMA BMA 0.440678 0.941176
43 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.440678 0.941176
44 CJX 0.435484 0.680851
45 5QP 0.433333 0.941176
46 FRU GLC 0.433333 0.794872
47 BGC OXZ 0.42623 0.666667
48 9MR 0.42623 0.744186
49 XYP XYP AHR XYP 0.424658 0.864865
50 BGC FUC GAL 0.424242 0.914286
51 GLC BGC FUC GAL 0.424242 0.914286
52 GLC G6P 0.423729 0.744186
53 AHR FUB 0.423077 0.805556
54 A2G GAL 0.421875 0.695652
55 FUC GAL 0.416667 0.885714
56 XYS AHR XYP XYP XYP 0.416667 0.864865
57 BMA MAN MAN 0.415385 0.941176
58 GLC 7LQ 0.412698 0.885714
59 BGC XGP 0.412698 0.744186
60 GCU BGC 0.412698 0.861111
61 ABL 0.412698 0.666667
62 XYP XYP XYP AHR 0.410959 0.864865
63 MAN IPD MAN 0.409836 0.744186
64 DGO MAN 0.409836 0.914286
65 FRU BMA 0.409836 0.794872
66 GLC U8V 0.409836 0.864865
67 GAL FUC GAL 0.409091 0.914286
68 XYP XYP XYP AHR XYP 0.407895 0.864865
69 GDQ GLC 0.40625 0.666667
70 BGC GAL GLA 0.40625 0.941176
71 GLC GLC GLC 0.405797 0.942857
72 IPD MAN 0.403226 0.697674
73 GLC EDO GLC 0.403226 0.888889
74 GAL SO4 GAL 0.402985 0.627451
75 G2F SHG BGC BGC 0.4 0.842105
76 MGC GAL 0.4 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: GDQ GLC; Similar ligands found: 35
No: Ligand Similarity coefficient
1 GLC GLC 0.9660
2 BGC GLC 0.9615
3 MAN IFM 0.9586
4 DGO MAN 0.9501
5 7D1 MAN 0.9472
6 FRU GLC 0.9399
7 MAN GLC 0.9311
8 DGO Z61 0.9295
9 TW7 GLC 0.9174
10 GLA BEZ 0.9115
11 SGC GLC 0.9070
12 GAL FUC 0.9051
13 GLC BGC 0.9035
14 BDF GLC 0.8986
15 ZEL MAN 0.8981
16 MYG 0.8974
17 BGC BGC 0.8923
18 GLC Z9N 0.8889
19 XYP GCU 0.8877
20 GAL GAL 0.8867
21 OTU 0.8864
22 DSQ 0.8850
23 RAM GAD 0.8809
24 BGC GLA 0.8739
25 ADN 0.8738
26 NOS 0.8724
27 MTP 0.8684
28 FMB 0.8677
29 TOP 0.8677
30 AX8 0.8645
31 FMC 0.8627
32 GLC GLA 0.8624
33 IFM BMA 0.8622
34 DBM 0.8584
35 PRH 0.8561
Ligand no: 2; Ligand: MAN MAN; Similar ligands found: 31
No: Ligand Similarity coefficient
1 MMA MAN 0.9802
2 DMJ MAN 0.9768
3 ZEL MAN 0.9637
4 MAN GLC 0.9624
5 MAN IFM 0.9559
6 BMA MAN 0.9430
7 GLC GLC 0.9325
8 MSX MAN 0.9314
9 IFM MAN 0.9292
10 MMA LDY 0.9235
11 GLC FRU 0.9233
12 DGO Z61 0.9199
13 Z5L MAN 0.9176
14 BMA GLA 0.9175
15 MAN MVL 0.9160
16 BGC GLC 0.9156
17 GLA GLC 0.9115
18 GLC GLA 0.9098
19 GMH GMH 0.9093
20 XMM 0.9053
21 TW7 GLC 0.8865
22 BGC GLA 0.8855
23 BMA MVL 0.8770
24 SER MAN 0.8766
25 MVL BMA 0.8669
26 GLA BEZ 0.8637
27 RNK 0.8586
28 EGA GLA 0.8573
29 DTK 0.8572
30 BGC BGC 0.8559
31 SGC GLC 0.8509
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
APoc FAQ
Feedback