Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:1260;
B:1261;
Invalid;
Invalid;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
G4M A:500;
B:500;
C:500;
D:500;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
819.499 C24 H36 N7 O19 P3 Cc1c(...
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: G4M; Similar ligands found: 67
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 GDD 0.604651 0.916667
7 GDC 0.604651 0.916667
8 GKE 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 GNP 0.539062 0.860465
18 GSP 0.539062 0.840909
19 GNH 0.531746 0.870588
20 GCP 0.53125 0.860465
21 G 0.520325 0.869048
22 5GP 0.520325 0.869048
23 G2R 0.518797 0.872093
24 Y9Z 0.510949 0.886364
25 G3A 0.503597 0.904762
26 GMV 0.5 0.860465
27 G5P 0.5 0.904762
28 GTG 0.496403 0.895349
29 YGP 0.492754 0.863636
30 GPG 0.492647 0.916667
31 G2P 0.492424 0.872093
32 GAV 0.485075 0.850575
33 GP2 0.476923 0.872093
34 CAG 0.473684 0.846154
35 2MD 0.473333 0.815217
36 GDP MG 0.469697 0.818182
37 GDP AF3 0.467153 0.791209
38 GTP MG 0.466667 0.818182
39 GDP BEF 0.466165 0.8
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 BEF GDP 0.455882 0.791209
45 U2G 0.453333 0.873563
46 NGD 0.453333 0.894118
47 GCP G 0.452555 0.827586
48 0O2 0.45 0.869048
49 JBT 0.449495 0.864583
50 2QR 0.447205 0.831461
51 FE9 0.44586 0.752475
52 MD1 0.443038 0.815217
53 G4P 0.442029 0.869048
54 GDP 7MG 0.438356 0.872093
55 G3D 0.437956 0.869048
56 CG2 0.437909 0.873563
57 TPG 0.4375 0.829787
58 G G 0.43662 0.870588
59 MGD 0.435897 0.815217
60 PGD 0.433962 0.842697
61 GMP 0.430894 0.797619
62 G1R G1R 0.419753 0.905882
63 DBG 0.419753 0.883721
64 I2C FE2 CMO CMO 0.40625 0.78125
65 G A A A 0.405063 0.882353
66 U A G G 0.402516 0.870588
67 3GP 0.401515 0.857143
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
Feedback