Receptor
PDB id Resolution Class Description Source Keywords
5M5D 1.07 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-D-GLUCAL BACTEROIDES XYLANISOLVENS XB1A ENDOMANNANASE GH99 INHIBITOR D-GLUCAL 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
EDO A:404;
A:401;
A:405;
A:403;
A:402;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
ACT A:406;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
DGO MAN B:1;
 Valid;
 none;
 Kd = 111 uM
308.283 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: DGO MAN; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 DGO MAN 1 1
2 GLC 7LQ 0.52459 0.970588
3 BQZ 0.490566 0.882353
4 DGO Z61 0.483871 0.944444
5 MBG GLA 0.473684 0.864865
6 BGC GLA GAL 0.448276 0.914286
7 GAL GLA 0.440678 0.914286
8 MGL GAL 0.42623 0.864865
9 MBG GAL 0.42623 0.864865
10 RZM 0.42623 0.673913
11 RR7 GLC 0.419355 0.864865
12 FUC GAL 0.412698 0.861111
13 MAN BMA BMA BMA BMA BMA BMA 0.412698 0.914286
14 GLC GLC GLC GLC BGC GLC GLC 0.412698 0.914286
15 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.412698 0.914286
16 MAN MAN 0.409836 0.914286
17 GCU BGC 0.409091 0.837838
18 5QP 0.40625 0.861111
19 BGC BGC BGC BGC BGC BGC 0.40625 0.914286
20 GLC BGC BGC BGC 0.40625 0.914286
21 BGC BGC BGC BGC BGC BGC BGC 0.40625 0.914286
22 BGC BGC BGC 0.40625 0.914286
23 FRU BMA 0.40625 0.775
24 MAN IPD MAN 0.40625 0.767442
25 BGC BGC BGC BGC BGC 0.40625 0.914286
26 ISX 0.4 0.744186
27 GLC EDO GLC 0.4 0.864865
28 9MR 0.4 0.727273
29 IFM BGC 0.4 0.695652
30 IPD MAN 0.4 0.72093
31 BGC OXZ 0.4 0.653061
Similar Ligands (3D)
Ligand no: 1; Ligand: DGO MAN; Similar ligands found: 39
No: Ligand Similarity coefficient
1 7D1 MAN 0.9990
2 MAN IFM 0.9921
3 GLC IFM 0.9757
4 MAN MNM 0.9715
5 MAN G63 0.9704
6 GDQ GLC 0.9501
7 GLC DMJ 0.9476
8 GLC GLC 0.9332
9 MAN GLC 0.9298
10 BGC GLC 0.9279
11 XMM 0.9183
12 ZEL MAN 0.9161
13 NOJ GLC 0.9075
14 MMA MAN 0.9074
15 SER MAN 0.9036
16 GLA BEZ 0.9035
17 FRU GLC 0.8963
18 GLC BGC 0.8948
19 DMJ MAN 0.8918
20 XYP XDN 0.8861
21 XYA 0.8853
22 MTP 0.8820
23 XYP GCU 0.8815
24 2M8 0.8788
25 NOS 0.8787
26 MYG 0.8751
27 BGC GLA 0.8747
28 ADN 0.8744
29 GLC GLA 0.8741
30 1DA 0.8715
31 MBE 0.8698
32 FMB 0.8696
33 M3N 0.8686
34 XYP XYS 0.8684
35 5AD 0.8680
36 A 0.8677
37 26A 0.8651
38 XYS XYS 0.8608
39 SNI 0.8593
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