Receptor
PDB id Resolution Class Description Source Keywords
4AD5 1.9 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDE XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3-DEOXYMANNOJIRIMYCA LPHA-1,2-MANNOBIOSE BACTEROIDES XYLANISOLVENS HYDROLASE ENDOMANNOSIDASE GLYCOSIDE HYDROLASE GH99 CAZYCARBOHYDRATE INTERACTION 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;
 Valid;
 none;
 submit data
326.322 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: 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
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: 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
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
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