Receptor
PDB id Resolution Class Description Source Keywords
6HMG 1.27 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) 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...
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
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
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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