Receptor
PDB id Resolution Class Description Source Keywords
4EDV 2.01 Å EC: 2.7.7.- THE STRUCTURE OF THE S. AUREUS DNAG RNA POLYMERASE DOMAIN BO PPPGPP 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
0O2 A:502;
Valid;
none;
submit data
683.14 C10 H18 N5 O20 P5 c1nc2...
BEN A:501;
Invalid;
none;
submit data
120.152 C7 H8 N2 [H]/N...
MN A:503;
A:504;
A:505;
Part of Protein;
Part of Protein;
Part of Protein;
none;
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: 0O2; Similar ligands found: 103
No: Ligand ECFP6 Tc MDL keys Tc
1 0O2 1 1
2 G4P 0.905882 1
3 G3D 0.797753 1
4 GTP 0.736264 0.986486
5 GP3 0.673913 0.960526
6 GDP 0.666667 0.986486
7 GSP 0.666667 0.935897
8 3GP 0.644444 0.959459
9 GH3 0.642857 0.986486
10 GNH 0.625 0.973333
11 DGT 0.622449 0.935065
12 GAV 0.62 0.948052
13 GNP 0.616162 0.960526
14 G1R 0.606061 0.973333
15 G G 0.605769 0.922078
16 GDC 0.603774 0.948052
17 GDD 0.603774 0.948052
18 GKE 0.603774 0.948052
19 G 0.595745 0.972973
20 5GP 0.595745 0.972973
21 GCP 0.59 0.960526
22 BGO 0.587719 0.935897
23 GPG 0.580952 0.948052
24 6CK 0.577982 0.924051
25 G5P 0.572727 0.960526
26 G2R 0.571429 0.948052
27 GTG 0.568807 0.924051
28 GFB 0.568807 0.948052
29 GDR 0.568807 0.948052
30 G2P 0.568627 0.948052
31 GMV 0.564356 0.960526
32 G3A 0.563636 0.960526
33 GPD 0.5625 0.9125
34 GMP 0.561798 0.866667
35 GDP MG 0.554455 0.910256
36 G G U 0.553571 0.947368
37 GKD 0.553571 0.948052
38 JB2 0.553571 0.948052
39 DGI 0.55 0.935065
40 GP2 0.55 0.948052
41 GDP BEF 0.54902 0.8875
42 GDX 0.548673 0.960526
43 GGM 0.546219 0.9125
44 Y9Z 0.545455 0.890244
45 GCP G 0.542857 0.922078
46 2GP 0.541667 0.972973
47 CG2 0.537815 0.924051
48 GPX 0.537736 0.959459
49 ALF 5GP 0.533981 0.876543
50 BEF GDP 0.533333 0.876543
51 GTP MG 0.533333 0.910256
52 G A A A 0.528926 0.910256
53 JB3 0.525424 0.935897
54 U2G 0.521008 0.924051
55 G C 0.520661 0.8875
56 GDP AF3 0.518519 0.876543
57 GDP ALF 0.518519 0.876543
58 U A G G 0.512195 0.922078
59 YGP 0.508929 0.888889
60 NGD 0.508333 0.948052
61 G G G RPC 0.508197 0.886076
62 CAG 0.508065 0.869048
63 APC G U 0.504 0.897436
64 TPG 0.496124 0.829545
65 G G G C 0.496063 0.9
66 2MD 0.495935 0.879518
67 A G C C 0.492188 0.898734
68 G1G 0.488189 0.9125
69 MGD 0.484127 0.879518
70 GPC 0.484127 0.86747
71 FEG 0.483607 0.86747
72 ZGP 0.479675 0.857143
73 GDP 7MG 0.478632 0.898734
74 G C C C 0.477273 0.911392
75 DG 0.475248 0.922078
76 DGP 0.475248 0.922078
77 DBG 0.473282 0.935897
78 P2G 0.470588 0.894737
79 G U34 0.467742 0.876543
80 MGP 0.46729 0.948052
81 6G0 0.462963 0.948052
82 P1G 0.461538 0.883117
83 PGD 0.458015 0.9125
84 MD1 0.458015 0.879518
85 A G U 0.457143 0.876543
86 U G A 0.453901 0.876543
87 G4M 0.45 0.869048
88 UCG 0.447761 0.923077
89 I2C FE2 CMO CMO 0.435115 0.797753
90 01G 0.432203 0.890244
91 DG DG 0.431034 0.876543
92 PAP 0.429907 0.918919
93 CGP 0.429688 0.878049
94 FE9 0.428571 0.765957
95 IDP 0.416667 0.959459
96 PGD O 0.416058 0.83908
97 SGP 0.415094 0.8375
98 G1R G1R 0.408759 0.911392
99 DC DG 0.40458 0.855422
100 AGO 0.401515 0.9
101 C2E 0.4 0.933333
102 35G 0.4 0.945946
103 PCG 0.4 0.945946
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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