Receptor
PDB id Resolution Class Description Source Keywords
1X9D 1.41 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA-1,2-MANNOSIDASE IN COMPLEX WITH THIO-DISACCHARIDE SUBSTRATE ANALOGUE HOMO SAPIENS MANNOSIDASE SUBSTRATE ANALOGUE GLYCOSYL HYDROLASE
Ref.: MECHANISM OF CLASS 1 (GLYCOSYLHYDROLASE FAMILY 47) {ALPHA}-MANNOSIDASES INVOLVED IN N-GLYCAN PROCESSING AND ENDOPLASMIC RETICULUM QUALITY CONTROL. J.BIOL.CHEM. V. 280 16197 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BU1 A:1004;
Invalid;
none;
submit data
90.121 C4 H10 O2 C(CCO...
CA A:1001;
Part of Protein;
none;
submit data
40.078 Ca [Ca+2...
SMD A:1003;
Valid;
none;
Kd = 110 uM
372.389 C13 H24 O10 S CO[C@...
SO4 A:1002;
Invalid;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1X9D 1.41 Å EC: 3.2.1.113 CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA-1,2-MANNOSIDASE IN COMPLEX WITH THIO-DISACCHARIDE SUBSTRATE ANALOGUE HOMO SAPIENS MANNOSIDASE SUBSTRATE ANALOGUE GLYCOSYL HYDROLASE
Ref.: MECHANISM OF CLASS 1 (GLYCOSYLHYDROLASE FAMILY 47) {ALPHA}-MANNOSIDASES INVOLVED IN N-GLYCAN PROCESSING AND ENDOPLASMIC RETICULUM QUALITY CONTROL. J.BIOL.CHEM. V. 280 16197 2005
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 1X9D Kd = 110 uM 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: SMD; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 SMD 1 1
2 GLC SSG SGC SGC MA3 0.637931 1
3 BGC SSG SSG SGC MA3 0.637931 1
4 BGC SGC SGC GTM 0.637931 1
5 WZ1 0.625 1
6 WZ2 0.537313 1
7 TDG 0.520833 0.894737
8 1LL 0.520833 0.894737
9 GLC SGC 0.508772 0.921053
10 TCB 0.508772 0.921053
11 GLC SGC SGC MGL 0.5 1
12 GLC MA1 0.491525 0.894737
13 GTM BGC BGC 0.485714 1
14 SGC SGC BGC 0.47541 0.921053
15 MA2 MA3 0.467742 0.9
16 GLC SSG SSG SGC 0.460317 0.894737
17 MMA 0.45098 0.842105
18 GYP 0.45098 0.842105
19 MBG 0.45098 0.842105
20 AMG 0.45098 0.842105
21 BGC BGC SGC MGL 0.44 1
22 MGL SGC GLC GLC 0.44 1
23 IPT 0.433962 0.775
24 G0S LYS PRO LEU NH2 0.433962 0.820513
25 TM6 0.432432 0.947368
26 BGC SGC BGC SGC BGC SGC BGC SGC 0.432432 0.947368
27 TM5 0.421053 0.947368
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1X9D; Ligand: SMD; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 1x9d.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1WCQ DAN 0.008729 0.41724 1.48699
2 1EUS DAN 0.008964 0.4214 2.19178
3 4UCC ZKW 0.01568 0.4076 2.57511
4 5H06 MAL 0.009005 0.42075 2.97398
5 4YZ5 SLT 0.01407 0.40278 2.97398
6 2FV1 GAD NDG 0.005045 0.42898 3.44828
7 2CXG GLC GLC 0.004837 0.44236 7.80669
8 2C3H GLC GLC 0.01699 0.4044 20.4082
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