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 23 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 21 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 20 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 (2D)
Ligand no: 1; Ligand: G4P; Similar ligands found: 95
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 GSP 0.625 0.935897
11 GNP 0.625 0.960526
12 9GM 0.625 0.960526
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 GKE 0.596154 0.948052
20 GDC 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 G2P 0.575758 0.948052
26 C1Z 0.572816 1
27 GMV 0.571429 0.960526
28 GH3 0.57 0.986486
29 GDP BEF 0.565657 0.922078
30 2GP 0.565217 0.972973
31 GGM 0.565217 0.9125
32 G2R 0.563107 0.948052
33 GFB 0.560748 0.948052
34 GDR 0.560748 0.948052
35 GTP MG 0.56 0.946667
36 GP2 0.556701 0.948052
37 6CK 0.555556 0.924051
38 ALF 5GP 0.555556 0.876543
39 DGT 0.55 0.935065
40 JB2 0.545455 0.948052
41 GKD 0.545455 0.948052
42 CG2 0.543103 0.924051
43 GPD 0.540541 0.9125
44 GDX 0.540541 0.960526
45 GDP ALF 0.538462 0.876543
46 GDP AF3 0.538462 0.876543
47 G C 0.538462 0.8875
48 Y9Z 0.537037 0.890244
49 G5P 0.536364 0.960526
50 GTG 0.53211 0.924051
51 G3A 0.527273 0.960526
52 U2G 0.525862 0.924051
53 APC G U 0.520325 0.897436
54 JB3 0.517241 0.935897
55 YGP 0.513761 0.888889
56 NGD 0.5 0.948052
57 GDP 7MG 0.495575 0.898734
58 DG 0.494845 0.922078
59 DGP 0.494845 0.922078
60 KB7 0.490196 0.814815
61 P2G 0.489796 0.894737
62 CAG 0.487805 0.869048
63 GPC 0.487805 0.86747
64 2MD 0.487603 0.879518
65 FEG 0.487395 0.86747
66 ZGP 0.483333 0.857143
67 P1G 0.48 0.883117
68 DBG 0.476562 0.935897
69 MGD 0.475806 0.879518
70 PAP 0.475248 0.918919
71 TPG 0.465116 0.829545
72 UCG 0.461538 0.923077
73 MD1 0.460938 0.879518
74 KBD 0.459459 0.814815
75 G1G 0.456693 0.9125
76 PGD 0.449612 0.9125
77 IDP 0.446602 0.959459
78 CGP 0.443548 0.878049
79 KBJ 0.443478 0.785714
80 G4M 0.442029 0.869048
81 AKW 0.439024 0.878049
82 QBQ 0.433962 0.972973
83 G1R G1R 0.431818 0.911392
84 SGP 0.431373 0.8375
85 FE9 0.430769 0.765957
86 I2C FE2 CMO CMO 0.430769 0.797753
87 PGD O 0.428571 0.83908
88 5GP 5GP 0.424528 0.894737
89 35G 0.415094 0.945946
90 C2E 0.415094 0.933333
91 PCG 0.415094 0.945946
92 AGO 0.414062 0.9
93 G 5MC C U 0.411765 0.878049
94 MGP 0.40367 0.948052
95 6G0 0.4 0.948052
Similar Ligands (3D)
Ligand no: 1; Ligand: G4P; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4EDK; Ligand: GTP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4edk.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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