Receptor
PDB id Resolution Class Description Source Keywords
5M17 1.03 Å EC: 3.2.1.130 STRUCTURE OF THE GH99 ENDO-ALPHA-MANNANASE FROM BACTEROIDES XYLANISOLVENS IN COMPLEX WITH MANNOSE-ALPHA-1,3-1,2-DIDEOXY BACTEROIDES XYLANISOLVENS XB1A ENDOMANNANASE ENDOMANNOSIDASE GH99 N-GLYCOSYLATION GLYCOINHIBITOR INHIBITION SHAPE CHARGE MANNOBIOSE MANNOSE GLYCOBIOLOGY 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:401;
A:402;
 Invalid;
Invalid;
 none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
ACT A:403;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
7D1 MAN B:1;
 Valid;
 none;
 Kd = 221 uM
310.299 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: 7D1 MAN; Similar ligands found: 47
No: Ligand ECFP6 Tc MDL keys Tc
1 7D1 MAN 1 1
2 MAN MAN 0.584906 0.942857
3 GLC IFM 0.525424 0.733333
4 ISX 0.483333 0.767442
5 BQZ 0.480769 0.857143
6 MAN G63 0.460317 0.66
7 RR7 GLC 0.457627 0.891892
8 GAL GLA 0.45614 0.888889
9 LG9 GLC 0.446154 0.611111
10 GCU BGC 0.444444 0.815789
11 5QP 0.442623 0.888889
12 BGC BGC BGC BGC BGC 0.442623 0.888889
13 BGC BGC BGC BGC BGC BGC 0.442623 0.888889
14 BGC BGC BGC 0.442623 0.888889
15 GLC BGC BGC BGC 0.442623 0.888889
16 BGC BGC BGC BGC BGC BGC BGC 0.442623 0.888889
17 RZM 0.440678 0.695652
18 MBG GAL 0.440678 0.842105
19 BGC GLA GAL 0.438596 0.888889
20 MBG GLA 0.438596 0.842105
21 BGC OXZ 0.435484 0.673469
22 9MR 0.435484 0.75
23 IFM BGC 0.435484 0.717391
24 NAG BMA 0.432836 0.66
25 GLC DMJ 0.428571 0.702128
26 NOJ GLC 0.428571 0.702128
27 NOY BGC 0.428571 0.64
28 MAN MNM 0.428571 0.64
29 ABL 0.421875 0.64
30 GAL FUC 0.419355 0.916667
31 MGL GAL 0.416667 0.842105
32 GYP 0.411765 0.810811
33 MBG 0.411765 0.810811
34 GLC BGC FUC GAL 0.411765 0.864865
35 BGC FUC GAL 0.411765 0.864865
36 MMA 0.411765 0.810811
37 G2F BGC BGC BGC BGC BGC 0.411765 0.825
38 AMG 0.411765 0.810811
39 GLC G6P 0.409836 0.711111
40 MAN BMA BMA 0.409091 0.891892
41 XYS GLC GLC 0.408451 0.864865
42 MAN BMA BMA BMA BMA BMA BMA 0.403226 0.888889
43 GLC GLC GLC GLC BGC GLC GLC 0.403226 0.888889
44 BGC BGC BGC BGC BGC BGC BGC BGC BGC 0.403226 0.888889
45 FUC GAL 0.403226 0.837838
46 CJX 0.4 0.653061
47 GLC 7LQ 0.4 0.837838
Similar Ligands (3D)
Ligand no: 1; Ligand: 7D1 MAN; Similar ligands found: 52
No: Ligand Similarity coefficient
1 DGO MAN 0.9990
2 MAN IFM 0.9955
3 GDQ GLC 0.9472
4 GLC GLC 0.9427
5 DGO Z61 0.9411
6 BWG 0.9393
7 ZEL MAN 0.9282
8 BGC GLC 0.9205
9 MMA MAN 0.9175
10 XMM 0.9172
11 MAN GLC 0.9170
12 IFM MAN 0.9136
13 SER MAN 0.9120
14 GLA BEZ 0.9066
15 ADN 0.8941
16 RAM GAD 0.8941
17 DMJ MAN 0.8912
18 FRU GLC 0.8901
19 XYP XDN 0.8891
20 GLC BGC 0.8883
21 2M8 0.8873
22 XYP GCU 0.8835
23 GLC Z9N 0.8835
24 BMA IFM 0.8825
25 XYA 0.8810
26 MYG 0.8807
27 MTP 0.8804
28 GLC GLA 0.8793
29 MAN MVL 0.8782
30 BMA MAN 0.8755
31 MBE 0.8749
32 SGC GLC 0.8742
33 BGC GLA 0.8740
34 FMB 0.8729
35 5AD 0.8726
36 AD3 0.8710
37 1DA 0.8709
38 BMA BMA 0.8709
39 NOS 0.8708
40 6MD 0.8706
41 TW7 GLC 0.8701
42 TBN 0.8698
43 Z4R MAN 0.8689
44 MMA LDY 0.8685
45 26A 0.8670
46 GLA GLC 0.8669
47 5ID 0.8665
48 EKH 0.8618
49 FTU 0.8592
50 3L1 0.8561
51 SNI 0.8558
52 GAL GAL 0.8541
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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