-->
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 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[....
70% 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[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 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 GCP G 0.646465 0.933333
8 BGO 0.638889 0.935897
9 GNH 0.634409 0.973333
10 GP3 0.630435 0.960526
11 GSP 0.625 0.935897
12 GNP 0.625 0.960526
13 9GM 0.625 0.960526
14 DGI 0.606383 0.935065
15 5GP 0.604396 0.972973
16 G 0.604396 0.972973
17 G1R 0.597938 0.973333
18 GCP 0.597938 0.960526
19 GDC 0.596154 0.948052
20 GKE 0.596154 0.948052
21 GDD 0.596154 0.948052
22 GAV 0.59596 0.948052
23 G G 0.590476 0.935065
24 GPX 0.59 0.959459
25 GPG 0.588235 0.948052
26 GMP 0.588235 0.866667
27 G2P 0.575758 0.948052
28 C1Z 0.572816 1
29 GMV 0.571429 0.960526
30 GH3 0.57 0.986486
31 2GP 0.565217 0.972973
32 GGM 0.565217 0.9125
33 G2R 0.563107 0.948052
34 GDR 0.560748 0.948052
35 GFB 0.560748 0.948052
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 G A A A 0.547009 0.910256
41 GKD 0.545455 0.948052
42 JB2 0.545455 0.948052
43 CG2 0.543103 0.924051
44 GPD 0.540541 0.9125
45 GDX 0.540541 0.960526
46 GDP AF3 0.538462 0.876543
47 G G G RPC 0.538462 0.886076
48 G C 0.538462 0.8875
49 GDP ALF 0.538462 0.876543
50 ALF GDP 0.538462 0.876543
51 Y9Z 0.537037 0.890244
52 G5P 0.536364 0.960526
53 A G 0.533898 0.922078
54 GTG 0.53211 0.924051
55 U A G G 0.529412 0.922078
56 G3A 0.527273 0.960526
57 U2G 0.525862 0.924051
58 G U 0.521368 0.8875
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 DG 0.494845 0.922078
67 DGP 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 TPG 0.465116 0.829545
82 UCG 0.461538 0.923077
83 MD1 0.460938 0.879518
84 DG DG 0.459459 0.876543
85 G1G 0.456693 0.9125
86 A G U U 0.453901 0.876543
87 PGD 0.449612 0.9125
88 IDP 0.446602 0.959459
89 CGP 0.443548 0.878049
90 G4M 0.442029 0.869048
91 AKW 0.439024 0.878049
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 35G 0.415094 0.945946
99 C2E 0.415094 0.933333
100 PCG 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 with APoc: 24
This union binding pocket(no: 1) in the query (biounit: 4edk.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1U18 HSM 1.62162
2 5C9P FUC 1.82371
3 3JUC PCA 1.96078
4 6BE0 COA 2.31788
5 4M00 SUC 2.43161
6 2WPF FAD 3.03951
7 2WPF WPF 3.03951
8 4WMY 3S6 3.26797
9 5WS9 OXL 3.34347
10 5TCI MLI 3.64742
11 4G86 BNT 3.87324
12 1P7T PYR 4.25532
13 1D8C GLV 4.25532
14 4RPL 3UC 4.25532
15 2DUR MAN MAN 4.34783
16 3P7G MAN 4.79452
17 4MO2 FDA 5.47112
18 3B8I OXL 5.92335
19 1WRA PC 6.16883
20 1Q19 SSC 6.68693
21 4KFU ACP 8.01887
22 4AF5 CIT 8.42105
23 5L3S G 9.45946
24 1SQL GUN 15.7534
APoc FAQ
Feedback