Receptor
PDB id Resolution Class Description Source Keywords
4ad2 2.1 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNOSIDASE FROM BACTEROIDE XYLANISOLVENS IN COMPLEX WITH GLUCOSE-1,3-ISOFAGOMINE BACTEROIDES XYLANISOLVENS HYDROLASE ENDOMANNOSIDASE GLYCOSIDE HYDROLASE GH99 CAZY CARBOHYDRATE 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 IFM A:500;
B:500;
C:500;
D:500;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 Kd = 625 nM
310.323 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 IFM; Similar ligands found: 25
No: Ligand ECFP6 Tc MDL keys Tc
1 GLC IFM 1 1
2 MAN MAN 0.571429 0.727273
3 IFM BGC 0.55 0.977273
4 7D1 MAN 0.525424 0.733333
5 ISX 0.52459 0.953488
6 MAN MNM 0.516129 0.836735
7 NOY BGC 0.46875 0.836735
8 9MR 0.453125 0.931818
9 BQZ 0.446429 0.697674
10 NOJ GLC 0.446154 0.87234
11 3CU GLC 0.439394 0.709091
12 GLC 7LQ 0.439394 0.688889
13 MAN G63 0.432836 0.82
14 GDQ GLC 0.432836 0.8
15 GAL GLA 0.42623 0.727273
16 GLC DMJ 0.424242 0.87234
17 LG9 GLC 0.42029 0.727273
18 IFM MAN 0.41791 0.977273
19 FRU GLC 0.415385 0.666667
20 5QP 0.415385 0.688889
21 RZM 0.412698 0.791667
22 BGC GLA GAL 0.409836 0.727273
23 MBG GLA 0.409836 0.695652
24 RR7 GLC 0.40625 0.733333
25 FUC GAL 0.4 0.688889
Similar Ligands (3D)
Ligand no: 1; Ligand: GLC IFM; Similar ligands found: 60
No: Ligand Similarity coefficient
1 MAN IFM 0.9834
2 DGO MAN 0.9757
3 GLC GLC 0.9533
4 DGO Z61 0.9422
5 MAN GLC 0.9409
6 BGC GLC 0.9295
7 XYP GCU 0.9200
8 GLA BEZ 0.9136
9 MYG 0.9117
10 XMM 0.9095
11 ZEL MAN 0.9088
12 RAM GAD 0.9070
13 GLC Z9N 0.9056
14 GLC BGC 0.9051
15 SGC GLC 0.9015
16 XYP XYS 0.8995
17 BGC BGC 0.8981
18 XXX 0.8979
19 DS8 0.8952
20 GAL FUC 0.8948
21 TW7 GLC 0.8906
22 NOS 0.8883
23 GLC GLA 0.8874
24 GAT 0.8868
25 MTP 0.8863
26 MMA MAN 0.8854
27 6MD 0.8846
28 EBQ 0.8841
29 TOP 0.8837
30 GLC FRU 0.8831
31 FMB 0.8812
32 XYS XYS 0.8808
33 ADN 0.8798
34 DSQ 0.8795
35 GAL GAL 0.8785
36 XYP XYP 0.8784
37 Z9N GLC 0.8756
38 GLF B8D 0.8755
39 XYA 0.8750
40 DBM 0.8745
41 BGC GLA 0.8743
42 XDN XYP 0.8723
43 AD3 0.8705
44 TBN 0.8694
45 P2C 0.8688
46 2M8 0.8680
47 BDF GLC 0.8667
48 5AD 0.8665
49 FTU 0.8660
50 ID8 0.8642
51 26A 0.8633
52 IMH 0.8631
53 MAN MVL 0.8624
54 LOX XYP 0.8622
55 UA2 0.8612
56 BMA BMA 0.8607
57 147 0.8580
58 5ID 0.8572
59 FM2 0.8520
60 8OX 0.8515
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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