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Receptor
PDB id Resolution Class Description Source Keywords
3QT9 2.05 Å NON-ENZYME: OTHER ANALYSIS OF A NEW FAMILY OF WIDELY DISTRIBUTED METAL-INDEPEN MANNOSIDASES PROVIDES UNIQUE INSIGHT INTO THE PROCESSING OFG LYCANS, CLOSTRIDIUM PERFRINGENS CPE0426 COMPLEXED WITH ALPLI NKED 1-THIO-ALPHA-MANNOBIOSE CLOSTRIDIUM PERFRINGENS ALPHA-ALPHA SIX FOLD GLYCOSIDE HYDROLASE MANNOSIDASE HYDR
Ref.: ANALYSIS OF A NEW FAMILY OF WIDELY DISTRIBUTED METAL-INDEPENDENT {ALPHA}-MANNOSIDASES PROVIDES UNI INSIGHT INTO THE PROCESSING OF N-LINKED GLYCANS. J.BIOL.CHEM. V. 286 15586 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:428;
A:429;
A:430;
A:431;
A:432;
A:433;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
YDR A:434;
Valid;
none;
submit data
358.362 C12 H22 O10 S C([C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5M7Y 1.55 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF GH125 1,6-ALPHA-MANNOSIDASE MUTANT FROM CLOSTRIDIUM PERFRINGENS IN COMPLEX WITH 1,6-ALPHA-MANNOTRIO CLOSTRIDIUM PERFRINGENS (STRAIN 13 / TORGANISM_TAXID: 195102 GLYCOSIDE HYDROLASE MANNOSIDASE CARBOHYDRATE HYDROLASE
Ref.: COMPUTATIONAL DESIGN OF EXPERIMENT UNVEILS THE CONFORMATIONAL REACTION COORDINATE OF GH125 ALPHA-MANNOSIDASES. J. AM. CHEM. SOC. V. 139 1085 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1443 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - YDR C12 H22 O10 S C([C@@H]1[....
3 5M7I - MAN BMA n/a n/a
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1205 families.
1 5M7Y - MAN MAN MAN n/a n/a
2 3QT9 - YDR C12 H22 O10 S C([C@@H]1[....
3 5M7I - MAN BMA n/a n/a
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1039 families.
1 3QSP - BMA MAN n/a n/a
2 3QRY - DMJ C6 H13 N O4 C1[C@H]([C....
3 5M7Y - MAN MAN MAN n/a n/a
4 3QT9 - YDR C12 H22 O10 S C([C@@H]1[....
5 5M7I - MAN BMA n/a n/a
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: YDR; Similar ligands found: 26
No: Ligand ECFP6 Tc MDL keys Tc
1 YDR 1 1
2 MSX MAN 0.647059 0.918919
3 7K2 7K3 0.52381 0.723404
4 GIV 0.5 0.8
5 GAL 0.5 0.8
6 ALL 0.5 0.8
7 MAN 0.5 0.8
8 BMA 0.5 0.8
9 GXL 0.5 0.8
10 BGC 0.5 0.8
11 GLA 0.5 0.8
12 GLC 0.5 0.8
13 WOO 0.5 0.8
14 GLC SGC 0.45614 1
15 TCB 0.45614 1
16 7K2 0.451613 0.733333
17 TDG 0.428571 0.971429
18 1LL 0.428571 0.971429
19 GS1 GLC GS1 0.42623 1
20 SGC SGC BGC 0.42623 1
21 PTQ 0.419355 0.864865
22 HTG 0.416667 0.727273
23 SOG 0.409836 0.727273
24 IPT 0.403846 0.789474
25 GLC IBZ 0.4 0.761905
26 BGC IBZ 0.4 0.761905
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5M7Y; Ligand: MAN MAN MAN; Similar sites found with APoc: 28
This union binding pocket(no: 1) in the query (biounit: 5m7y.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 4RGA 3PV 1.52672
2 5Z74 SUC 1.6092
3 1Z82 G3H 2.08955
4 1Z82 G3P 2.08955
5 3QVP FAD 2.29885
6 2JF4 VDM 2.29885
7 3HQR OGA 2.43902
8 5BX3 NOJ 2.52874
9 1GAH ACR 2.75862
10 1NSA BEN 3.03797
11 1V7W NDG 3.21839
12 1V7W NAG 3.21839
13 1GPE FAD 3.21839
14 2DC1 CIT 3.38983
15 5CKS 52L 3.7037
16 5GOP SUC 4.98915
17 4ZLF CEZ 5.05747
18 5N6N SUC 5.41667
19 1LF9 ACR 5.97701
20 1M3U KPL 6.43939
21 1ULV ACR 7.12644
22 4NZ6 DLY 8.30671
23 1W1A NDG 8.56031
24 1QIN GIP 8.74317
25 2F6D ACR 8.96552
26 5W1E PHB 9.42529
27 5ANU 58T 10.7595
28 1MID LAP 16.4835
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