Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MAN MNM A:403;
 Valid;
 none;
 Kd = 0.013 uM
326.322 n/a O(C1C...
ACT A:402;
A:401;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
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 MNM; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 MAN MNM 1 1
2 NOY BGC 0.62069 1
3 BQZ 0.528302 0.638298
4 IFM BGC 0.52459 0.82
5 NOJ GLC 0.516129 0.84
6 GLC IFM 0.516129 0.836735
7 9MR 0.5 0.78
8 GDQ GLC 0.5 0.773585
9 GLC DMJ 0.492063 0.84
10 MBG GLA 0.482759 0.673469
11 MAN G63 0.476923 0.792453
12 GAL GLA 0.474576 0.702128
13 MGL GAL 0.459016 0.673469
14 RZM 0.459016 0.730769
15 BGC GLA GAL 0.457627 0.702128
16 BGC OXZ 0.453125 0.709091
17 ISX 0.453125 0.795918
18 RR7 GLC 0.451613 0.673469
19 NOK GAL 0.444444 0.803571
20 FUC GAL 0.444444 0.666667
21 MAN MAN 0.442623 0.666667
22 BGC BGC BGC 0.4375 0.702128
23 BGC BGC BGC BGC BGC BGC 0.4375 0.702128
24 GLC BGC BGC BGC 0.4375 0.702128
25 5QP 0.4375 0.632653
26 BGC BGC BGC BGC BGC 0.4375 0.702128
27 BGC BGC BGC BGC BGC BGC BGC 0.4375 0.702128
28 G3I 0.43662 0.8
29 G2I 0.43662 0.8
30 MBG GAL 0.435484 0.673469
31 7D1 MAN 0.428571 0.64
32 NAG BMA 0.428571 0.759259
33 MAN MAN BMA 0.428571 0.673469
34 MAN BMA BMA 0.426471 0.673469
35 MGC GAL 0.426471 0.807692
36 A2G GAL 0.426471 0.84
37 GLC GLC GLC GLC BGC GLC GLC 0.421875 0.702128
38 MAN BMA BMA BMA BMA BMA BMA 0.421875 0.702128
39 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.421875 0.702128
40 BMA MAN MAN 0.42029 0.702128
41 ABL 0.41791 0.843137
42 GCU BGC 0.41791 0.6875
43 CJX 0.41791 0.788462
44 GLC 7LQ 0.41791 0.632653
45 FRU BMA 0.415385 0.615385
46 MAN IPD MAN 0.415385 0.618182
47 GLC EDO GLC 0.409091 0.673469
48 G2F BGC BGC BGC BGC BGC 0.408451 0.634615
49 MMA MAN MAN 0.408451 0.673469
50 TVD GAL 0.405797 0.777778
51 NAG GAL 0.405797 0.84
52 AHR FUB 0.403509 0.612245
53 LG9 GLC 0.4 0.677966
Similar Ligands (3D)
Ligand no: 1; Ligand: MAN MNM; Similar ligands found: 31
No: Ligand Similarity coefficient
1 DGO MAN 0.9715
2 MAN IFM 0.9713
3 ZEL MAN 0.9461
4 MMA MAN 0.9387
5 GLC GLC 0.9332
6 MAN GLC 0.9296
7 DGO Z61 0.9246
8 XMM 0.9230
9 BGC GLC 0.9137
10 FRU GLC 0.9078
11 MAN MVL 0.9027
12 GMH GMH 0.9019
13 GLA BEZ 0.8943
14 RAM GAD 0.8906
15 OTU 0.8905
16 Z4R MAN 0.8896
17 IFM BMA 0.8863
18 BMA IFM 0.8863
19 2M8 0.8841
20 MYG 0.8732
21 MTP 0.8731
22 26A 0.8716
23 ADN 0.8683
24 XYA 0.8682
25 XYP GCU 0.8647
26 AD3 0.8645
27 MMA LDY 0.8626
28 BMA BMA 0.8613
29 5AD 0.8610
30 NOS 0.8558
31 TBN 0.8526
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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