Receptor
PDB id Resolution Class Description Source Keywords
5M03 1.05 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-NOEUROMYCINA LPHA-MANNOBIOSE BACTEROIDES XYLANISOLVENS XB1A ENDOMANNANASE ENDOMANNOSIDASE GH99 NOEUROMYCIN HYDROLASE N- GLYCOSYLATION GLYCOSYLATION INHIBITOR INHIBITION SHAPE CHARMANNOBIOSE HYDROLASE
Ref.: CONTRIBUTION OF SHAPE AND CHARGE TO THE INHIBITION FAMILY GH99 ENDO-ALPHA-1,2-MANNANASE. J. AM. CHEM. SOC. V. 139 1089 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MAN MNM A:402;
 Valid;
 none;
 submit data
326.322 n/a O(C1C...
ACT A:401;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
MAN MAN B:1;
 Valid;
 Atoms found MORE than expected: % Diff = 1.478;
 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: MAN MNM; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MNM 1 1
2 NOY BGC 0.62069 1
3 BQZ 0.528302 0.638298
4 IFM BGC 0.52459 0.82
5 NOJ GLC 0.516129 0.84
6 GLC IFM 0.516129 0.836735
7 9MR 0.5 0.78
8 GDQ GLC 0.5 0.773585
9 GLC DMJ 0.492063 0.84
10 MBG GLA 0.482759 0.673469
11 MAN G63 0.476923 0.792453
12 GAL GLA 0.474576 0.702128
13 MGL GAL 0.459016 0.673469
14 RZM 0.459016 0.730769
15 BGC GLA GAL 0.457627 0.702128
16 BGC OXZ 0.453125 0.709091
17 ISX 0.453125 0.795918
18 RR7 GLC 0.451613 0.673469
19 NOK GAL 0.444444 0.803571
20 FUC GAL 0.444444 0.666667
21 MAN MAN 0.442623 0.666667
22 BGC BGC BGC 0.4375 0.702128
23 BGC BGC BGC BGC BGC BGC 0.4375 0.702128
24 GLC BGC BGC BGC 0.4375 0.702128
25 5QP 0.4375 0.632653
26 BGC BGC BGC BGC BGC 0.4375 0.702128
27 BGC BGC BGC BGC BGC BGC BGC 0.4375 0.702128
28 G3I 0.43662 0.8
29 G2I 0.43662 0.8
30 MBG GAL 0.435484 0.673469
31 7D1 MAN 0.428571 0.64
32 NAG BMA 0.428571 0.759259
33 MAN MAN BMA 0.428571 0.673469
34 MAN BMA BMA 0.426471 0.673469
35 MGC GAL 0.426471 0.807692
36 A2G GAL 0.426471 0.84
37 GLC GLC GLC GLC BGC GLC GLC 0.421875 0.702128
38 MAN BMA BMA BMA BMA BMA BMA 0.421875 0.702128
39 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.421875 0.702128
40 BMA MAN MAN 0.42029 0.702128
41 ABL 0.41791 0.843137
42 GCU BGC 0.41791 0.6875
43 CJX 0.41791 0.788462
44 GLC 7LQ 0.41791 0.632653
45 FRU BMA 0.415385 0.615385
46 MAN IPD MAN 0.415385 0.618182
47 GLC EDO GLC 0.409091 0.673469
48 G2F BGC BGC BGC BGC BGC 0.408451 0.634615
49 MMA MAN MAN 0.408451 0.673469
50 TVD GAL 0.405797 0.777778
51 NAG GAL 0.405797 0.84
52 AHR FUB 0.403509 0.612245
53 LG9 GLC 0.4 0.677966
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: MAN MNM; Similar ligands found: 31
No: Ligand Similarity coefficient
1 DGO MAN 0.9715
2 MAN IFM 0.9713
3 ZEL MAN 0.9461
4 MMA MAN 0.9387
5 GLC GLC 0.9332
6 MAN GLC 0.9296
7 DGO Z61 0.9246
8 XMM 0.9230
9 BGC GLC 0.9137
10 FRU GLC 0.9078
11 MAN MVL 0.9027
12 GMH GMH 0.9019
13 GLA BEZ 0.8943
14 RAM GAD 0.8906
15 OTU 0.8905
16 Z4R MAN 0.8896
17 IFM BMA 0.8863
18 BMA IFM 0.8863
19 2M8 0.8841
20 MYG 0.8732
21 MTP 0.8731
22 26A 0.8716
23 ADN 0.8683
24 XYA 0.8682
25 XYP GCU 0.8647
26 AD3 0.8645
27 MMA LDY 0.8626
28 BMA BMA 0.8613
29 5AD 0.8610
30 NOS 0.8558
31 TBN 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
APoc FAQ
Feedback