Receptor
PDB id Resolution Class Description Source Keywords
4EDT 2 Å EC: 2.7.7.- THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BO PPGPP AND MANGANESE STAPHYLOCOCCUS AUREUS CATALYTIC DOMAIN BACTERIAL NUCLEOTIDE NUCLEOSIDE TRIPHOSPNUCLEOSIDE POLYPHOSPHATE PROTEIN-LIGAND COMPLEX TRANSFERATRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: BINDING MECHANISM OF METAL-NTP SUBSTRATES AND STRINGENT-RESPONSE ALARMONES TO BACTERIAL DNAG-TYPE PRIMASES. STRUCTURE V. 20 1478 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BEN A:501;
Invalid;
none;
submit data
120.152 C7 H8 N2 [H]/N...
G4P A:502;
Valid;
none;
submit data
603.16 C10 H17 N5 O17 P4 c1nc2...
MN A:503;
A:504;
Part of Protein;
Part of Protein;
none;
none;
submit data
54.938 Mn [Mn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4EDK 2 Å EC: 2.7.7.- THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BO AND MANGANESE STAPHYLOCOCCUS AUREUS CATALYTIC DOMAIN NUCLEOSIDE TRIPHOSPHATE NUCLEOSIDE POLYPHPROTEIN-LIGAND COMPLEX TRANSFERASE
Ref.: BINDING MECHANISM OF METAL-NTP SUBSTRATES AND STRINGENT-RESPONSE ALARMONES TO BACTERIAL DNAG-TYPE PRIMASES. STRUCTURE V. 20 1478 2012
Members (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 4EDG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4EDK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4EDR - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
4 4EDV - 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
5 4EE1 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EDT - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
70% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4EDG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4EDK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4EDR - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
4 4EDV - 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
5 4EE1 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EDT - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4EDG - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4EDK - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
3 4EDR - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
4 4EDV - 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
5 4EE1 - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
6 4EDT - G4P C10 H17 N5 O17 P4 c1nc2c(n1[....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: G4P; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 G4P 1 1
2 0O2 0.905882 1
3 G3D 0.879518 1
4 GDP 0.715909 0.986486
5 3GP 0.674419 0.959459
6 GTP 0.655914 0.986486
7 BGO 0.638889 0.935897
8 GNH 0.634409 0.973333
9 GP3 0.630435 0.960526
10 G G 0.63 0.922078
11 GNP 0.625 0.960526
12 GSP 0.625 0.935897
13 DGI 0.606383 0.935065
14 G 0.604396 0.972973
15 5GP 0.604396 0.972973
16 G1R 0.597938 0.973333
17 GCP 0.597938 0.960526
18 GDD 0.596154 0.948052
19 GDC 0.596154 0.948052
20 GKE 0.596154 0.948052
21 GAV 0.59596 0.948052
22 GPX 0.59 0.959459
23 GPG 0.588235 0.948052
24 GMP 0.588235 0.866667
25 GDP MG 0.57732 0.910256
26 G2P 0.575758 0.948052
27 G G U 0.574074 0.947368
28 GMV 0.571429 0.960526
29 GDP BEF 0.571429 0.8875
30 GH3 0.57 0.986486
31 GGM 0.565217 0.9125
32 2GP 0.565217 0.972973
33 G2R 0.563107 0.948052
34 GFB 0.560748 0.948052
35 GDR 0.560748 0.948052
36 GP2 0.556701 0.948052
37 6CK 0.555556 0.924051
38 ALF 5GP 0.555556 0.876543
39 BEF GDP 0.554455 0.876543
40 GTP MG 0.554455 0.910256
41 DGT 0.55 0.935065
42 GCP G 0.54902 0.922078
43 G A A A 0.547009 0.910256
44 GKD 0.545455 0.948052
45 JB2 0.545455 0.948052
46 CG2 0.543103 0.924051
47 GDX 0.540541 0.960526
48 GPD 0.540541 0.9125
49 GDP AF3 0.538462 0.876543
50 GDP ALF 0.538462 0.876543
51 G G G RPC 0.538462 0.886076
52 G C 0.538462 0.8875
53 Y9Z 0.537037 0.890244
54 G5P 0.536364 0.960526
55 GTG 0.53211 0.924051
56 U A G G 0.529412 0.922078
57 G3A 0.527273 0.960526
58 U2G 0.525862 0.924051
59 APC G U 0.520661 0.897436
60 JB3 0.517241 0.935897
61 YGP 0.513761 0.888889
62 G G G C 0.512195 0.9
63 A G C C 0.508065 0.898734
64 NGD 0.5 0.948052
65 GDP 7MG 0.495575 0.898734
66 DGP 0.494845 0.922078
67 DG 0.494845 0.922078
68 G C C C 0.492188 0.911392
69 P2G 0.489796 0.894737
70 CAG 0.487805 0.869048
71 GPC 0.487805 0.86747
72 2MD 0.487603 0.879518
73 FEG 0.487395 0.86747
74 G U34 0.483333 0.876543
75 ZGP 0.483333 0.857143
76 P1G 0.48 0.883117
77 DBG 0.476562 0.935897
78 MGD 0.475806 0.879518
79 PAP 0.475248 0.918919
80 A G U 0.470588 0.876543
81 U G A 0.467153 0.876543
82 TPG 0.465116 0.829545
83 UCG 0.461538 0.923077
84 MD1 0.460938 0.879518
85 DG DG 0.459459 0.876543
86 G1G 0.456693 0.9125
87 PGD 0.449612 0.9125
88 I2C FE2 CMO CMO 0.448819 0.797753
89 IDP 0.446602 0.959459
90 CGP 0.443548 0.878049
91 G4M 0.442029 0.869048
92 G1R G1R 0.431818 0.911392
93 SGP 0.431373 0.8375
94 FE9 0.430769 0.765957
95 PGD O 0.428571 0.83908
96 DC DG 0.428571 0.855422
97 5GP 5GP 0.424528 0.894737
98 C2E 0.415094 0.933333
99 PCG 0.415094 0.945946
100 35G 0.415094 0.945946
101 AGO 0.414062 0.9
102 MGP 0.40367 0.948052
103 6G0 0.4 0.948052
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EDK; Ligand: GTP; Similar sites found: 8
This union binding pocket(no: 1) in the query (biounit: 4edk.bio1) has 21 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U18 HSM 0.001263 0.46898 1.62162
2 3JUC PCA 0.01692 0.40575 1.96078
3 4M00 SUC 0.01164 0.42519 2.43161
4 1P7T PYR 0.008815 0.42377 4.25532
5 1D8C GLV 0.008806 0.41107 4.25532
6 3P7G MAN 0.01519 0.40266 4.79452
7 4MO2 FDA 0.02111 0.40158 5.47112
8 1SQL GUN 0.01817 0.41437 15.7534
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