Receptor
PDB id Resolution Class Description Source Keywords
3DR7 1.7 Å EC: 7.-.-.- GDP-PEROSAMINE SYNTHASE FROM CAULOBACTER CRESCENTUS WITH BOU DEOXYPEROSAMINE CAULOBACTER CRESCENTUS PEROSAMINE PYRIDOXAL PHOSPHATE O-ANTIGEN LIPOPOLYSACCHARIASPARTATE AMINOTRANSFERASE DEOXYSUGAR TRANSFERASE
Ref.: ACCOMMODATION OF GDP-LINKED SUGARS IN THE ACTIVE SI GDP-PEROSAMINE SYNTHASE BIOCHEMISTRY V. 47 10685 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:1040;
D:1041;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
GPD A:500;
A:501;
D:500;
D:501;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
572.358 C16 H26 N6 O13 P2 C[C@@...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DR4 1.6 Å EC: 7.-.-.- GDP-PEROSAMINE SYNTHASE K186A MUTANT FROM CAULOBACTER CRESCENTUS WITH BOUND SUGAR LIGAND CAULOBACTER CRESCENTUS PEROSAMINE DEOXYSUGAR PYRIDOXAL PHOSPHATE ASPARTATE AMINOTRANSFERASE O-ANTIGEN
Ref.: ACCOMMODATION OF GDP-LINKED SUGARS IN THE ACTIVE SITE OF GDP-PEROSAMINE SYNTHASE BIOCHEMISTRY V. 47 10685 2008
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 311 families.
1 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
2 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
3 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
2 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
3 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 212 families.
1 5U21 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
2 5U23 - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
3 5U24 - 7SG C24 H35 N4 O19 P3 Cc1c(c(c(c....
4 1O69 - X04 C8 H11 N2 O6 P Cc1c(c(c(c....
5 1O61 - PLP C8 H10 N O6 P Cc1c(c(c(c....
6 3FRK - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
7 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
8 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(c....
9 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
10 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
11 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
12 2OGA - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GPD; Similar ligands found: 95
No: Ligand ECFP6 Tc MDL keys Tc
1 GPD 1 1
2 GDR 0.764706 0.9625
3 GFB 0.764706 0.9625
4 JB2 0.759615 0.9625
5 GP3 0.715789 0.925926
6 6CK 0.707547 0.915663
7 GDC 0.704762 0.938272
8 GDD 0.704762 0.938272
9 GKE 0.704762 0.938272
10 GTP 0.704082 0.925
11 JB3 0.702703 0.950617
12 G1R 0.69697 0.9375
13 GDP 0.690722 0.925
14 GSP 0.69 0.880952
15 GDX 0.688073 0.95
16 GNH 0.683673 0.91358
17 GKD 0.678899 0.938272
18 G2R 0.673077 0.914634
19 GCP 0.663366 0.925926
20 9GM 0.656863 0.902439
21 GNP 0.656863 0.902439
22 G 0.639175 0.9125
23 5GP 0.639175 0.9125
24 GMV 0.637255 0.902439
25 GAV 0.628571 0.891566
26 Y9Z 0.627273 0.928571
27 GTG 0.621622 0.915663
28 GP2 0.607843 0.914634
29 GPG 0.605505 0.914634
30 YGP 0.603604 0.882353
31 G3A 0.60177 0.925926
32 G5P 0.596491 0.925926
33 G2P 0.59434 0.914634
34 G4M 0.58209 0.885057
35 ALF 5GP 0.575472 0.827586
36 NGD 0.570248 0.914634
37 0O2 0.5625 0.9125
38 GDP AF3 0.558559 0.827586
39 GDP ALF 0.558559 0.827586
40 ALF GDP 0.558559 0.827586
41 FEG 0.544715 0.951807
42 2MD 0.544 0.852273
43 CAG 0.543307 0.863636
44 KB7 0.542056 0.811765
45 GMP 0.541667 0.814815
46 G4P 0.540541 0.9125
47 ZGP 0.540323 0.917647
48 G3D 0.536364 0.9125
49 U2G 0.532258 0.892857
50 GH3 0.531532 0.925
51 MGD 0.53125 0.852273
52 TPG 0.530303 0.826087
53 GDP 7MG 0.529412 0.891566
54 PGD 0.526718 0.882353
55 G G 0.525424 0.902439
56 CG2 0.52381 0.892857
57 FE9 0.519084 0.802083
58 MD1 0.515152 0.873563
59 DGT 0.513514 0.902439
60 DBG 0.496296 0.903614
61 KBD 0.495726 0.811765
62 3GP 0.495238 0.876543
63 DGI 0.490909 0.902439
64 KBJ 0.479339 0.825581
65 A G 0.469697 0.890244
66 2GP 0.46729 0.888889
67 GCP G 0.466667 0.853659
68 U A G G 0.466165 0.890244
69 G1R G1R 0.463768 0.903614
70 BGO 0.461538 0.926829
71 G A A A 0.458647 0.879518
72 GPX 0.457627 0.876543
73 R7I 0.45614 0.9
74 R5I 0.45614 0.9
75 MGP 0.45614 0.914634
76 G1G 0.455882 0.904762
77 6G0 0.452174 0.914634
78 GGM 0.451128 0.904762
79 AKW 0.450382 0.872093
80 PGD O 0.45 0.815217
81 DGP 0.449541 0.890244
82 DG 0.449541 0.890244
83 IDP 0.446429 0.9
84 JBT 0.430939 0.842105
85 GPC 0.430657 0.840909
86 G2Q 0.429752 0.914634
87 G U 0.425373 0.858824
88 P2G 0.419643 0.841463
89 G C 0.419118 0.858824
90 GTA 0.418605 0.915663
91 ADQ 0.413223 0.853659
92 01G 0.412698 0.883721
93 P1G 0.412281 0.853659
94 DG DG 0.41129 0.870588
95 IMP 0.401786 0.8875
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 4
This union binding pocket(no: 1) in the query (biounit: 3dr4.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 32.9923
2 5W71 PLP 48.0818
3 5W70 9YM 48.0818
4 5W70 9YM 48.0818
Pocket No.: 2; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 3dr4.bio1) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 32.9923
2 5K8B PDG 32.9923
3 5W71 PLP 48.0818
4 5W70 9YM 48.0818
5 5W70 9YM 48.0818
Pocket No.: 3; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 10
This union binding pocket(no: 3) in the query (biounit: 3dr4.bio2) has 39 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 32.9923
2 5K8B PDG 32.9923
3 5K8B PDG 32.9923
4 5K8B PDG 32.9923
5 3B8X G4M 47.4359
6 3B8X G4M 47.4359
7 5W71 PLP 48.0818
8 5W70 9YM 48.0818
9 5W70 9YM 48.0818
10 4K2M O1G 48.3376
Pocket No.: 4; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 3dr4.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 5K8B PDG 32.9923
2 5K8B PDG 32.9923
3 5W71 PLP 48.0818
4 5W70 9YM 48.0818
5 5W70 9YM 48.0818
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