Receptor
PDB id Resolution Class Description Source Keywords
5NN8 2.45 Å EC: 3.2.1.20 CRYSTAL STRUCTURE OF HUMAN LYSOSOMAL ACID-ALPHA-GLUCOSIDASE, COMPLEX WITH ACARBOSE HOMO SAPIENS GLYCOSIDE HYDROLASE LYSOSOME GLYCOGEN CATABOLISM POMPE DIHYDROLASE
Ref.: STRUCTURE OF HUMAN LYSOSOMAL ACID ALPHA-GLUCOSIDASE FOR THE TREATMENT OF POMPE DISEASE. NAT COMMUN V. 8 1111 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1019;
A:1018;
A:1017;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
EDO A:1026;
A:1029;
A:1035;
A:1037;
A:1034;
A:1032;
A:1030;
A:1023;
A:1031;
A:1024;
A:1028;
A:1025;
A:1036;
A:1033;
A:1027;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
NAG NAG BMA E:1;
C:1;
Invalid;
Invalid;
none;
none;
submit data
570.545 n/a O=C(N...
NAG NAG FUC F:1;
B:1;
Invalid;
Invalid;
none;
none;
submit data
n/a n/a
CL A:1022;
A:1020;
A:1021;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
35.453 Cl [Cl-]
PGE A:1039;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
GOL A:1038;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
NAG NAG D:1;
Invalid;
none;
submit data
408.404 n/a O=C(N...
GLC GLC AC1 G:1;
Valid;
Atoms found LESS than expected: % Diff = 0;
submit data n/a n/a n/a n/a
GLC AC1 H:1;
Valid;
none;
submit data n/a n/a n/a n/a
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NN6 2 Å EC: 3.2.1.20 CRYSTAL STRUCTURE OF HUMAN LYSOSOMAL ACID-ALPHA-GLUCOSIDASE, COMPLEX WITH N-HYDROXYETHYL-1-DEOXYNOJIRIMYCIN HOMO SAPIENS GLYCOSIDE HYDROLASE LYSOSOME GLYCOGEN CATABOLISM POMPE DIHYDROLASE
Ref.: STRUCTURE OF HUMAN LYSOSOMAL ACID ALPHA-GLUCOSIDASE FOR THE TREATMENT OF POMPE DISEASE. NAT COMMUN V. 8 1111 2017
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
2 5NN8 - GLC GLC AC1 n/a n/a
3 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
4 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
2 5NN8 - GLC GLC AC1 n/a n/a
3 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
4 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3W37 - GLC GLC AC1 n/a n/a
2 3WEO Ki = 0.888 uM GLC GLC GLC GLC GLC GLC AC1 n/a n/a
3 3WEL Ki = 2.66 uM GLC GLC GLC AC1 n/a n/a
4 3L4W Ki = 1 uM MIG C8 H17 N O5 C1[C@@H]([....
5 3L4X Ki = 0.13 uM NR3 C12 H24 O12 S2 C1[C@H]([C....
6 3L4Y Ki = 0.1 uM NR4 C12 H24 O12 S2 C1[C@H]([C....
7 3CTT Ki = 0.45 uM 3CU C8 H15 N O5 C1[C@@H]([....
8 3L4V Ki = 0.19 uM KTL C12 H24 O12 S2 C1[C@H]([C....
9 2QMJ Ki = 62 uM GLC GLC AC1 n/a n/a
10 3L4T Ki = 3.8 uM BJ1 C10 H20 O10 S2 C1[C@H]([C....
11 3L4U Ki = 0.03 uM DSK C12 H25 O9 S C1[C@H]([C....
12 3L4Z Ki = 0.19 uM SSD C9 H18 O9 S2 C1[C@H]([C....
13 5NN4 Kd = 11.57 mM SC2 C5 H9 N O3 S CC(=O)N[C@....
14 5NN8 - GLC GLC AC1 n/a n/a
15 5NN6 Ki = 3 uM MIG C8 H17 N O5 C1[C@@H]([....
16 5NN5 Ki = 3.4 uM NOJ C6 H13 N O4 C1[C@@H]([....
17 3LPP Ki = 0.6 uM KTL C12 H24 O12 S2 C1[C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GLC GLC AC1; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Ligand no: 2; Ligand: GLC AC1; Similar ligands found: 0
No: Ligand ECFP6 Tc MDL keys Tc
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NN6; Ligand: MIG; Similar sites found with APoc: 7
This union binding pocket(no: 1) in the query (biounit: 5nn6.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 3MKK GLC BGC 34.5345
2 3MKK GLC BGC 34.5345
3 5DKY NOJ 38.1881
4 5HJO XD3 40.7235
5 5HJO XD3 40.7235
6 5H9O GLC 40.7235
7 5H9O GLC 40.7235
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