Receptor
PDB id Resolution Class Description Source Keywords
5KIJ 1.65 Å EC: 3.2.1.24 CRYSTAL STRUCTURE OF THE CLASS I HUMAN ENDOPLASMIC RETICULUM ALPHA-MANNOSIDASE AND MAN9GLCNAC2-PA COMPLEX HOMO SAPIENS ALPHA/ALPHA-BARREL CATION REPLACEMENT PROTEIN-GLYCAN INTERHYDROLASE
Ref.: SUBSTRATE RECOGNITION AND CATALYSIS BY GH47 ALPHA-MANNOSIDASES INVOLVED IN ASN-LINKED GLYCAN MA IN THE MAMMALIAN SECRETORY PATHWAY. PROC. NATL. ACAD. SCI. V. 113 E7890 2016 U.S.A.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BU1 A:705;
A:717;
A:704;
A:716;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
90.121 C4 H10 O2 C(CCO...
NAG BMA MAN MAN MAN MAN MAN MAN MAN A:706;
Valid;
Atoms found MORE than expected: % Diff = 1.097;
submit data
1502.34 n/a O=C(N...
LA A:701;
Valid;
none;
submit data
138.905 La [La+3...
SO4 A:702;
A:703;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
1PS A:715;
Invalid;
none;
submit data
201.243 C8 H11 N O3 S c1cc[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1FO3 1.75 Å EC: 3.2.1.24 CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA1,2-MANNOSIDASE IN COMPLEX WITH KIFUNENSINE HOMO SAPIENS ALPHA-ALPHA7 BARREL HYDROLASE
Ref.: STRUCTURAL BASIS FOR CATALYSIS AND INHIBITION OF N-GLYCAN PROCESSING CLASS I ALPHA 1,2-MANNOSIDASES. J.BIOL.CHEM. V. 275 41287 2000
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
2 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
3 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
4 5KK7 - SMD C13 H24 O10 S CO[C@@H]1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
2 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
3 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
4 5KK7 - SMD C13 H24 O10 S CO[C@@H]1[....
5 1X9D Kd = 110 uM SMD C13 H24 O10 S CO[C@@H]1[....
50% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5KKB - BMA NAG MAN MAN MAN MAN MAN MAN MAN n/a n/a
2 2RI9 Ki = 0.6 mM MMA LDY n/a n/a
3 5KIJ - NAG BMA MAN MAN MAN MAN MAN MAN MAN n/a n/a
4 1FO2 ic50 = 20 uM DMJ C6 H13 N O4 C1[C@H]([C....
5 1FO3 ic50 = 0.2 uM KIF C8 H12 N2 O6 C([C@@H]1[....
6 5KK7 - SMD C13 H24 O10 S CO[C@@H]1[....
7 1DL2 - NDG NAG NDG BMA MAN MAN MAN MAN n/a n/a
8 1G6I - DMJ C6 H13 N O4 C1[C@H]([C....
9 1X9D Kd = 110 uM SMD C13 H24 O10 S CO[C@@H]1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: NAG BMA MAN MAN MAN MAN MAN MAN MAN; Similar ligands found: 76
No: Ligand ECFP6 Tc MDL keys Tc
1 NAG BMA MAN MAN MAN MAN MAN MAN MAN 1 1
2 NAG NAG BMA MAN MAN MAN MAN 0.786408 0.942308
3 NAG NAG BMA MAN MAN NAG NAG 0.733333 0.924528
4 BMA NAG MAN MAN MAN MAN MAN MAN MAN 0.676471 0.918367
5 NAG NAG BMA MAN MAN MAN MAN MAN MAN MAN 0.669725 0.865385
6 NAG NAG BMA MAN NAG 0.635514 0.924528
7 NAG MAN GAL BMA NAG MAN NAG GAL 0.626168 0.849057
8 NAG MAN GAL BMA NDG MAN NAG GAL 0.626168 0.849057
9 MAN BMA NAG NAG MAN NAG GAL GAL 0.626168 0.849057
10 NAG MAN MAN MAN NAG GAL NAG GAL 0.626168 0.849057
11 M5G 0.607143 0.865385
12 NAG BMA 0.602273 0.979592
13 NAG MAN BMA NDG MAN NAG GAL 0.598214 0.849057
14 NAG NAG BMA MAN 0.598039 0.942308
15 MAN MAN MAN BMA MAN MAN MAN 0.594059 0.68
16 MAN MAN MAN BMA MAN 0.589474 0.673469
17 NAG BMA MAN MAN MAN MAN 0.588235 0.918367
18 NAG MAN GAL MAN MAN NAG GAL 0.584906 0.865385
19 AML MAN MAN MAN MAN MAN MAN MAN MAN 0.571429 0.618182
20 NAG BMA MAN MAN MAN MAN MAN 0.56 0.641509
21 NAG NAG BMA 0.555556 0.942308
22 NAG NDG BMA 0.555556 0.942308
23 NAG BMA NAG MAN MAN NAG NAG 0.548673 0.849057
24 NAG NAG BMA MAN MAN 0.513514 0.865385
25 MAN MAN NAG MAN NAG 0.513514 0.865385
26 NAG MAN MAN MAN NAG 0.509434 0.865385
27 WZ5 0.504505 0.882353
28 NAG NAG BMA BMA 0.485981 0.907407
29 KDO MAN MAN MAN MAN MAN 0.471545 0.673077
30 MAN MAN BMA MAN 0.469388 0.673469
31 MAN MAN MAN MAN 0.469388 0.673469
32 ASN NAG NAG BMA MAN MAN NAG NAG 0.469231 0.839286
33 MAN BMA MAN MAN MAN 0.464646 0.673469
34 M5S 0.464646 0.673469
35 NAG NAG 0.464646 0.923077
36 1GN ACY GAL ACY 1GN BGC GAL BGC 0.460177 0.865385
37 FUC GAL NAG A2G 0.460177 0.907407
38 ACY 1GN GAL 1GN BGC ACY GAL BGC 0.460177 0.865385
39 NAG MAN BMA 0.457143 0.918367
40 NAG MAN MAN 0.457143 0.918367
41 MAN BMA NAG 0.455446 0.918367
42 GLA GAL NAG 0.455446 0.918367
43 NAG GAL GAL 0.455446 0.918367
44 OPM MAN MAN 0.446602 0.666667
45 GAL BGC NAG GAL 0.443396 0.918367
46 FUC GAL NAG GAL BGC 0.439655 0.9
47 WZ4 0.436508 0.833333
48 NAG GAL GAL NAG GAL 0.435185 0.865385
49 MAN MAN MAN GLC 0.434343 0.673469
50 GLC GAL NAG GAL 0.431193 0.918367
51 BMA NGT MAN MAN 0.429825 0.65
52 NAG NAG NAG NAG NAG NAG NAG 0.428571 0.907407
53 BMA MAN MAN 0.427083 0.673469
54 BGC GAL NAG GAL FUC FUC 0.425 0.882353
55 GLC GAL NAG GAL FUC FUC 0.425 0.882353
56 MAN MMA MAN 0.424242 0.68
57 GAL NAG GAL NAG GAL NAG 0.422018 0.849057
58 NAG GAL GAL NAG 0.422018 0.865385
59 MMA MAN NAG MAN NAG NAG 0.421053 0.833333
60 GAL NAG GAL BGC 0.412844 0.918367
61 BGC GAL NAG GAL 0.412844 0.918367
62 LAT NAG GAL 0.412844 0.918367
63 MAN MAN MAN MAN MAN MAN MAN MAN 0.410256 0.6
64 GAL NDG 0.408163 0.918367
65 NDG GAL 0.408163 0.918367
66 NLC 0.408163 0.918367
67 MAN NAG GAL 0.40566 0.918367
68 GAL NAG MAN 0.40566 0.918367
69 NBG BGC BGC XYS BGC XYS XYS 0.405172 0.92
70 GAL NAG GAL 0.40367 0.959184
71 DR2 0.401869 0.9
72 FUL GAL NAG 0.401869 0.9
73 FUC GAL NAG 0.401869 0.9
74 NDG GAL FUC 0.401869 0.9
75 FUC GAL NDG 0.401869 0.9
76 FUC BGC GAL NAG GAL 0.4 0.9
Ligand no: 2; Ligand: LA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 LA 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1FO3; Ligand: KIF; Similar sites found: 2
This union binding pocket(no: 1) in the query (biounit: 1fo3.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5TVM PUT 0.02111 0.42 8.23529
2 5NE5 KIF 0.0000000001053 0.56167 46.085
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