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@@...
View in 3D viewer
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 250 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 217 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 166 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 1O61 - PLP C8 H10 N O6 P Cc1c(c(c(c....
5 3FRK - TQP C24 H35 N4 O19 P3 Cc1c(c(c(c....
6 3NU7 - PMP C8 H13 N2 O5 P Cc1c(c(c(c....
7 3NUB - UD0 C25 H34 N5 O22 P3 Cc1c(c(c(c....
8 3BN1 - AKG C5 H6 O5 C(CC(=O)O)....
9 3DR4 - G4M C24 H36 N7 O19 P3 Cc1c(c(c(c....
10 3DR7 - GPD C16 H26 N6 O13 P2 C[C@@H]1[C....
11 1MDZ - PLP C8 H10 N O6 P Cc1c(c(c(c....
12 2OGA - PGU C13 H19 N2 O9 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: GPD; Similar ligands found: 91
No: Ligand ECFP6 Tc MDL keys Tc
1 GPD 1 1
2 GFB 0.764706 0.9625
3 GDR 0.764706 0.9625
4 JB2 0.759615 0.9625
5 GP3 0.715789 0.925926
6 6CK 0.707547 0.915663
7 GKE 0.704762 0.938272
8 GDC 0.704762 0.938272
9 GDD 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 GNP 0.656863 0.902439
21 5GP 0.639175 0.9125
22 G 0.639175 0.9125
23 GMV 0.637255 0.902439
24 GAV 0.628571 0.891566
25 Y9Z 0.627273 0.928571
26 GTG 0.621622 0.915663
27 GP2 0.607843 0.914634
28 GPG 0.605505 0.914634
29 YGP 0.603604 0.882353
30 G3A 0.60177 0.925926
31 G5P 0.596491 0.925926
32 GDP MG 0.596154 0.857143
33 G2P 0.59434 0.914634
34 GDP BEF 0.590476 0.837209
35 GCP G 0.583333 0.86747
36 G4M 0.58209 0.885057
37 ALF 5GP 0.575472 0.827586
38 GTP MG 0.574074 0.857143
39 BEF GDP 0.574074 0.827586
40 NGD 0.570248 0.914634
41 0O2 0.5625 0.9125
42 GDP AF3 0.558559 0.827586
43 GDP ALF 0.558559 0.827586
44 FEG 0.544715 0.951807
45 2MD 0.544 0.852273
46 G G 0.54386 0.890244
47 CAG 0.543307 0.863636
48 GMP 0.541667 0.814815
49 G4P 0.540541 0.9125
50 ZGP 0.540323 0.917647
51 G3D 0.536364 0.9125
52 U2G 0.532258 0.892857
53 GH3 0.531532 0.925
54 MGD 0.53125 0.852273
55 TPG 0.530303 0.826087
56 GDP 7MG 0.529412 0.891566
57 PGD 0.526718 0.882353
58 CG2 0.52381 0.892857
59 FE9 0.519084 0.802083
60 MD1 0.515152 0.873563
61 DGT 0.513514 0.902439
62 I2C FE2 CMO CMO 0.503817 0.835165
63 DBG 0.496296 0.903614
64 3GP 0.495238 0.876543
65 DGI 0.490909 0.902439
66 2GP 0.46729 0.888889
67 U A G G 0.466165 0.890244
68 G1R G1R 0.463768 0.903614
69 BGO 0.461538 0.926829
70 G A A A 0.458647 0.879518
71 GPX 0.457627 0.876543
72 MGP 0.45614 0.914634
73 G1G 0.455882 0.904762
74 6G0 0.452174 0.914634
75 GGM 0.451128 0.904762
76 PGD O 0.45 0.815217
77 DGP 0.449541 0.890244
78 DG 0.449541 0.890244
79 IDP 0.446429 0.9
80 JBT 0.430939 0.842105
81 GPC 0.430657 0.840909
82 G2Q 0.429752 0.914634
83 G G U 0.429688 0.890244
84 P2G 0.419643 0.841463
85 G C 0.419118 0.858824
86 GTA 0.418605 0.915663
87 ADQ 0.413223 0.853659
88 01G 0.412698 0.883721
89 P1G 0.412281 0.853659
90 DG DG 0.41129 0.870588
91 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3dr4.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found: 39
This union binding pocket(no: 2) in the query (biounit: 3dr4.bio1) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JE5 PMP 0.03534 0.40748 1.27877
2 4XZ6 TMO 0.00854 0.42393 1.47493
3 3EI9 PL6 0.003487 0.42573 1.79028
4 5IWQ PLP 0.01751 0.41965 1.79028
5 4ZM4 PLP 0.000638 0.48738 2.04604
6 4ZM4 P3B 0.01298 0.40941 2.04604
7 5DDW 5B6 0.004011 0.42939 2.30179
8 4ADC PLP 0.007404 0.4116 2.30179
9 4X1Z FUC GAL NDG 0.04111 0.4077 2.40964
10 4RKC PMP 0.0005787 0.48948 3.06905
11 5CDH TLA 0.0364 0.40908 3.27381
12 1UU1 PMP HSA 0.01494 0.40375 3.28358
13 4BA5 PXG 0.00008095 0.52589 3.32481
14 4UHO PLP 0.004387 0.46467 4.60358
15 3I7V ATP 0.04525 0.40454 5.97015
16 4IY7 KOU 0.0003465 0.48125 6.13811
17 4IY7 0JO 0.0003605 0.48046 6.13811
18 4ZSY RW2 0.001718 0.44588 7.67263
19 1ZN7 HSX 0.04655 0.40116 10.5556
20 2R2N PMP 0.001626 0.47202 10.7417
21 4R5Z PMP 0.01279 0.40399 11.7166
22 4P83 U5P 0.03247 0.40942 12.0879
23 2OAT PFM 0.01136 0.4184 13.0435
24 5X30 4LM 0.0001414 0.50885 13.555
25 5X30 7XF 0.0002166 0.4952 13.555
26 4RJD TFP 0.02072 0.42646 13.6364
27 4WXG 2BO 0.003465 0.42585 13.8107
28 1GCK ASP PLP 0.003715 0.43426 14.026
29 1DJ9 KAM 0.001142 0.47022 15.8854
30 5G4J EXT 0.008176 0.42183 16.8798
31 5K8B PDG 0.0000000004136 0.53627 32.9923
32 1B9I PXG 0.000000005376 0.50588 44.8454
33 3B8X G4M 0.000000000008823 0.66589 47.4359
34 4ZAH T5K 0.000000006089 0.64608 47.8261
35 5W70 9YM 0.000000003448 0.50151 48.0818
36 5W71 PLP 0.0000000004806 0.49953 48.0818
37 5W71 9YM 0.000003323 0.49893 48.0818
38 4K2M O1G 0.0000000042 0.51121 48.3376
39 2FNU PMP UD1 0.00000000003998 0.65522 49.8667
Pocket No.: 3; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found: 3
This union binding pocket(no: 3) in the query (biounit: 3dr4.bio2) has 39 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1JQN DCO 0.03592 0.40367 2.04604
2 3R75 PYR 0.03244 0.41737 3.58056
3 3MBI HSX 0.02873 0.416 7.66551
Pocket No.: 4; Query (leader) PDB : 3DR4; Ligand: G4M; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3dr4.bio2) has 36 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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