Receptor
PDB id Resolution Class Description Source Keywords
5M3W 1.04 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-1,2-DIDEOXYA ND ALPHA-1,2-MANNOBIOSE BACTEROIDES XYLANISOLVENS XB1A ENDOMANNANASE GH99 MANNOBIOSE MANNOSE 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 MAN C:1;
 Valid;
 none;
 submit data
326.298 n/a O(C1C...
ACT A:402;
A:401;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
EDO A:403;
 Invalid;
 none;
 submit data
62.068 C2 H6 O2 C(CO)...
7D1 MAN B:1;
 Valid;
 none;
 submit data
310.299 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 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
Ligand no: 2; Ligand: 7D1 MAN; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 7D1 MAN 1 1
2 MAN MAN 0.584906 0.942857
3 GLC IFM 0.525424 0.733333
4 ISX 0.483333 0.767442
5 BQZ 0.480769 0.857143
6 MAN G63 0.460317 0.66
7 RR7 GLC 0.457627 0.891892
8 GAL GLA 0.45614 0.888889
9 LG9 GLC 0.446154 0.611111
10 GCU BGC 0.444444 0.815789
11 5QP 0.442623 0.888889
12 BGC BGC BGC BGC BGC 0.442623 0.888889
13 BGC BGC BGC BGC BGC BGC 0.442623 0.888889
14 BGC BGC BGC 0.442623 0.888889
15 GLC BGC BGC BGC 0.442623 0.888889
16 BGC BGC BGC BGC BGC BGC BGC 0.442623 0.888889
17 RZM 0.440678 0.695652
18 MBG GAL 0.440678 0.842105
19 BGC GLA GAL 0.438596 0.888889
20 MBG GLA 0.438596 0.842105
21 BGC OXZ 0.435484 0.673469
22 9MR 0.435484 0.75
23 IFM BGC 0.435484 0.717391
24 NAG BMA 0.432836 0.66
25 GLC DMJ 0.428571 0.702128
26 NOJ GLC 0.428571 0.702128
27 NOY BGC 0.428571 0.64
28 MAN MNM 0.428571 0.64
29 ABL 0.421875 0.64
30 GAL FUC 0.419355 0.916667
31 MGL GAL 0.416667 0.842105
32 GYP 0.411765 0.810811
33 MBG 0.411765 0.810811
34 GLC BGC FUC GAL 0.411765 0.864865
35 BGC FUC GAL 0.411765 0.864865
36 MMA 0.411765 0.810811
37 G2F BGC BGC BGC BGC BGC 0.411765 0.825
38 AMG 0.411765 0.810811
39 GLC G6P 0.409836 0.711111
40 MAN BMA BMA 0.409091 0.891892
41 XYS GLC GLC 0.408451 0.864865
42 MAN BMA BMA BMA BMA BMA BMA 0.403226 0.888889
43 GLC GLC GLC GLC BGC GLC GLC 0.403226 0.888889
44 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.403226 0.888889
45 FUC GAL 0.403226 0.837838
46 CJX 0.4 0.653061
47 GLC 7LQ 0.4 0.837838
Similar Ligands (3D)
Ligand no: 1; 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
Ligand no: 2; Ligand: 7D1 MAN; Similar ligands found: 52
No: Ligand Similarity coefficient
1 DGO MAN 0.9990
2 MAN IFM 0.9955
3 GDQ GLC 0.9472
4 GLC GLC 0.9427
5 DGO Z61 0.9411
6 BWG 0.9393
7 ZEL MAN 0.9282
8 BGC GLC 0.9205
9 MMA MAN 0.9175
10 XMM 0.9172
11 MAN GLC 0.9170
12 IFM MAN 0.9136
13 SER MAN 0.9120
14 GLA BEZ 0.9066
15 ADN 0.8941
16 RAM GAD 0.8941
17 DMJ MAN 0.8912
18 FRU GLC 0.8901
19 XYP XDN 0.8891
20 GLC BGC 0.8883
21 2M8 0.8873
22 XYP GCU 0.8835
23 GLC Z9N 0.8835
24 BMA IFM 0.8825
25 XYA 0.8810
26 MYG 0.8807
27 MTP 0.8804
28 GLC GLA 0.8793
29 MAN MVL 0.8782
30 BMA MAN 0.8755
31 MBE 0.8749
32 SGC GLC 0.8742
33 BGC GLA 0.8740
34 FMB 0.8729
35 5AD 0.8726
36 AD3 0.8710
37 1DA 0.8709
38 BMA BMA 0.8709
39 NOS 0.8708
40 6MD 0.8706
41 TW7 GLC 0.8701
42 TBN 0.8698
43 Z4R MAN 0.8689
44 MMA LDY 0.8685
45 26A 0.8670
46 GLA GLC 0.8669
47 5ID 0.8665
48 EKH 0.8618
49 FTU 0.8592
50 3L1 0.8561
51 SNI 0.8558
52 GAL GAL 0.8541
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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