Receptor
PDB id Resolution Class Description Source Keywords
6FAM 1.13 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-2- A MINODEOXYMANNOJIRIMYCIN BACTEROIDES XYLANISOLVENS XB1A COMPLEX GH99 HYDROLASE
Ref.: EXPLORATION OF STRATEGIES FOR MECHANISM-BASED INHIB DESIGN FOR FAMILY GH99 ENDO-ALPHA-1,2-MANNANASES. CHEMISTRY V. 24 7464 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT A:501;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
MAN G63 A:502;
 Valid;
 none;
 submit data
326.346 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 G63; Similar ligands found: 37
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN G63 1 1
2 GLC DMJ 0.627119 0.9375
3 NOJ GLC 0.548387 0.9375
4 NOK GAL 0.536232 0.888889
5 BQZ 0.482143 0.625
6 MAN MNM 0.476923 0.792453
7 NOY BGC 0.476923 0.792453
8 MAN MAN 0.47541 0.6875
9 IFM BGC 0.461538 0.84
10 7D1 MAN 0.460317 0.66
11 GAL GLA 0.459016 0.653061
12 RZM 0.444444 0.784314
13 MBG GLA 0.442623 0.627451
14 BGC GLA GAL 0.442623 0.653061
15 RR7 GLC 0.4375 0.66
16 GLC IFM 0.432836 0.82
17 CJX 0.426471 0.88
18 3CU GLC 0.426471 0.767857
19 5QP 0.424242 0.6875
20 BGC BGC BGC BGC BGC 0.424242 0.653061
21 BGC BGC BGC BGC BGC BGC BGC 0.424242 0.653061
22 GLC BGC BGC BGC 0.424242 0.653061
23 BGC BGC BGC BGC BGC BGC 0.424242 0.653061
24 BGC BGC BGC 0.424242 0.653061
25 MGL GAL 0.421875 0.627451
26 MBG GAL 0.421875 0.627451
27 GDQ GLC 0.42029 0.826923
28 9MR 0.41791 0.8
29 BGC OXZ 0.41791 0.727273
30 G2F BGC BGC BGC BGC BGC 0.416667 0.622642
31 MAN BMA BMA 0.414286 0.693878
32 FUC GAL 0.409091 0.62
33 MAN BMA BMA BMA BMA BMA BMA 0.409091 0.653061
34 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.409091 0.653061
35 GLC GLC GLC GLC BGC GLC GLC 0.409091 0.653061
36 GCU BGC 0.405797 0.64
37 FRU BMA 0.402985 0.603774
Similar Ligands (3D)
Ligand no: 1; Ligand: MAN G63; Similar ligands found: 29
No: Ligand Similarity coefficient
1 MAN IFM 0.9709
2 DGO MAN 0.9704
3 GLC 7LQ 0.9466
4 ZEL MAN 0.9452
5 MMA MAN 0.9335
6 GLC GLC 0.9335
7 MAN GLC 0.9311
8 DGO Z61 0.9255
9 XMM 0.9202
10 FRU GLC 0.9067
11 BGC GLC 0.9067
12 GMH GMH 0.9005
13 MAN MVL 0.9001
14 GLA BEZ 0.8938
15 RAM GAD 0.8875
16 2M8 0.8851
17 Z4R MAN 0.8830
18 BMA IFM 0.8822
19 IFM BMA 0.8822
20 DMJ MAN 0.8777
21 MTP 0.8744
22 ADN 0.8741
23 MYG 0.8707
24 BDF GLC 0.8698
25 XYA 0.8668
26 XYP GCU 0.8667
27 SER MAN 0.8652
28 MMA LDY 0.8561
29 FMB 0.8504
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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