Receptor
PDB id Resolution Class Description Source Keywords
2GMU 1.9 Å EC: 4.-.-.- CRYSTAL STRUCTURE OF E COLI GDP-4-KETO-6-DEOXY-D-MANNOSE-3-D COMPLEXED WITH PLP-GLUTAMATE KETIMINE INTERMEDIATE ESCHERICHIA COLI O55:H7 COLITOSE DEOXYSUGAR ASPARTATE AMINOTRANSFERASE PLP O-ANTTRANSFERASE
Ref.: THE STRUCTURE OF GDP-4-KETO-6-DEOXY-D-MANNOSE-3-DEH A UNIQUE COENZYME B6-DEPENDENT ENZYME. PROTEIN SCI. V. 15 2093 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:601;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
PDG A:500;
B:501;
 Valid;
Valid;
 none;
none;
 submit data
378.272 C13 H19 N2 O9 P Cc1c(...
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: PDG; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 PGU 1 1
2 PDG 1 1
3 QLP 0.865672 0.938462
4 N5F 0.84058 0.983871
5 PY5 0.820895 0.9375
6 7XF 0.797101 0.967742
7 LPI 0.785714 0.895522
8 PPD 0.779412 0.967213
9 PY6 0.774648 0.909091
10 PLS 0.764706 0.935484
11 ORX 0.763889 0.952381
12 C6P 0.753623 0.935484
13 PE1 0.753425 0.952381
14 PL4 0.733333 0.952381
15 76U 0.702703 0.952381
16 0PR 0.688312 0.920635
17 PDA 0.685714 0.888889
18 PP3 0.685714 0.888889
19 PDD 0.685714 0.888889
20 2BK 0.666667 0.888889
21 TLP 0.666667 0.888889
22 2BO 0.666667 0.888889
23 AQ3 0.658537 0.878788
24 ILP 0.653333 0.890625
25 EA5 0.649351 0.953125
26 IN5 0.619718 0.857143
27 PLG 0.619718 0.935484
28 KAM 0.609756 0.921875
29 IK2 0.608108 0.892308
30 CBA 0.589744 0.848485
31 PPE 0.589744 0.983871
32 PLA 0.584416 0.907692
33 PMG 0.582278 0.938462
34 P1T 0.573333 0.892308
35 5PA 0.558442 0.921875
36 33P 0.545455 0.84375
37 PSZ 0.53012 0.785714
38 PXP 0.529412 0.774194
39 HEY 0.518072 0.9375
40 3LM 0.511905 0.826087
41 PMH 0.5 0.688312
42 PMP 0.5 0.83871
43 DN9 0.494382 0.884058
44 RW2 0.494253 0.865672
45 PXG 0.494253 0.846154
46 7TS 0.493976 0.696203
47 GT1 0.492958 0.69697
48 DCS 0.488095 0.75
49 PL2 0.488095 0.823529
50 PL6 0.481928 0.825397
51 CKT 0.469136 0.859375
52 9YM 0.454545 0.820895
53 PL8 0.43956 0.819444
54 CAN PLP 0.433333 0.893939
55 1D0 0.431579 0.838235
56 7B9 0.430108 0.855072
57 PLR 0.428571 0.68254
58 PPG 0.423913 0.892308
59 PLP 2KZ 0.423529 0.815385
60 F0G 0.421687 0.75
61 KOU 0.416667 0.8125
62 0JO 0.409639 0.731343
63 Z98 0.409091 0.846154
64 RMT 0.404255 0.779412
65 OJQ 0.402299 0.670886
66 PUS 0.402174 0.702703
67 FEV 0.4 0.705882
68 P0P 0.4 0.725806
Similar Ligands (3D)
Ligand no: 1; Ligand: PDG; Similar ligands found: 17
No: Ligand Similarity coefficient
1 KET 0.9479
2 SEP PLP 0.9386
3 3QP 0.9308
4 PLP 0A0 0.9191
5 ASP PLP 0.9136
6 PLP PHE 0.9112
7 GLU PLP 0.9000
8 PM9 0.8946
9 TYR PLP 0.8918
10 GBC PLP 0.8903
11 GAB PLP 0.8887
12 P3B 0.8856
13 PLP 2ML 0.8811
14 6DF 0.8779
15 LEU PLP 0.8737
16 4LM 0.8696
17 EJ1 0.8648
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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