Receptor
PDB id Resolution Class Description Source Keywords
3b8x 1.7 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE H188N MUTANT WITH BOUND GDP-PEROSAMINE ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE COLITOSE PEROSAMINE O-ANTIGENPYRIDOXAL PHOSPHATE TRANSFERASE
Ref.: GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMO SUGAR SUBSTRATE IN THE ACTIVE SITE. J.BIOL.CHEM. V. 283 4295 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:674;
A:675;
A:676;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
G4M A:500;
B:500;
 Valid;
Valid;
 none;
none;
 submit data
819.499 C24 H36 N7 O19 P3 Cc1c(...
NA A:669;
A:671;
A:672;
A:673;
B:666;
B:667;
B:668;
B:670;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
none;
none;
none;
none;
 submit data
22.99 Na [Na+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3B8X 1.7 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF GDP-4-KETO-6-DEOXYMANNOSE-3-DEHYDRATASE H188N MUTANT WITH BOUND GDP-PEROSAMINE ESCHERICHIA COLI ASPARTATE AMINOTRANSFERASE COLITOSE PEROSAMINE O-ANTIGENPYRIDOXAL PHOSPHATE TRANSFERASE
Ref.: GDP-4-KETO-6-DEOXY-D-MANNOSE 3-DEHYDRATASE, ACCOMMO SUGAR SUBSTRATE IN THE ACTIVE SITE. J.BIOL.CHEM. V. 283 4295 2008
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 62 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 59 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 47 families.
1 3GR9 - AKG C5 H6 O5 C(CC(=O)O)....
2 2GMU - PDG C13 H19 N2 O9 P Cc1c(c(c(c....
3 3B8X - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
4 2GMS - P0P C8 H12 N O7 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: G4M; Similar ligands found: 65
No: Ligand ECFP6 Tc MDL keys Tc
1 G4M 1 1
2 JB3 0.656489 0.928571
3 GDR 0.637795 0.916667
4 GFB 0.637795 0.916667
5 JB2 0.623077 0.916667
6 GKE 0.604651 0.916667
7 GDC 0.604651 0.916667
8 GDD 0.604651 0.916667
9 GDX 0.593985 0.904762
10 GPD 0.58209 0.885057
11 6CK 0.571429 0.873563
12 G1R 0.555556 0.892857
13 GP3 0.552846 0.904762
14 GKD 0.551471 0.916667
15 GDP 0.548387 0.880952
16 GTP 0.547619 0.880952
17 9GM 0.539062 0.860465
18 GNP 0.539062 0.860465
19 GSP 0.539062 0.840909
20 GNH 0.531746 0.870588
21 GCP 0.53125 0.860465
22 5GP 0.520325 0.869048
23 G 0.520325 0.869048
24 G2R 0.518797 0.872093
25 Y9Z 0.510949 0.886364
26 G3A 0.503597 0.904762
27 G5P 0.5 0.904762
28 GMV 0.5 0.860465
29 GTG 0.496403 0.895349
30 YGP 0.492754 0.863636
31 GPG 0.492647 0.916667
32 G2P 0.492424 0.872093
33 GAV 0.485075 0.850575
34 GP2 0.476923 0.872093
35 CAG 0.473684 0.846154
36 GDP BEF 0.473684 0.827586
37 2MD 0.473333 0.815217
38 GTP MG 0.470149 0.847059
39 GDP AF3 0.467153 0.791209
40 ALF 5GP 0.466165 0.791209
41 FEG 0.463087 0.908046
42 ZGP 0.46 0.876405
43 GDP ALF 0.456522 0.791209
44 NGD 0.453333 0.894118
45 U2G 0.453333 0.873563
46 0O2 0.45 0.869048
47 JBT 0.449495 0.864583
48 2QR 0.447205 0.831461
49 FE9 0.44586 0.752475
50 MD1 0.443038 0.815217
51 G4P 0.442029 0.869048
52 KB7 0.440298 0.816092
53 GDP 7MG 0.438356 0.872093
54 G3D 0.437956 0.869048
55 CG2 0.437909 0.873563
56 TPG 0.4375 0.829787
57 MGD 0.435897 0.815217
58 PGD 0.433962 0.842697
59 GMP 0.430894 0.797619
60 G1R G1R 0.419753 0.905882
61 DBG 0.419753 0.883721
62 KBD 0.41958 0.837209
63 I2C FE2 CMO CMO 0.409938 0.78125
64 KBJ 0.408163 0.808989
65 3GP 0.401515 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: G4M; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 3b8x.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 35.641
2 3DR4 G4M 47.4359
Pocket No.: 2; Query (leader) PDB : 3B8X; Ligand: G4M; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3b8x.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 35.641
2 3DR4 G4M 47.4359
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