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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 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: 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 GSP 0.666667 0.935897
7 GDP 0.666667 0.986486
8 3GP 0.644444 0.959459
9 C1Z 0.643564 1
10 GH3 0.642857 0.986486
11 GNH 0.625 0.973333
12 DGT 0.622449 0.935065
13 GCP G 0.621359 0.933333
14 GAV 0.62 0.948052
15 9GM 0.616162 0.960526
16 GNP 0.616162 0.960526
17 G1R 0.606061 0.973333
18 GDD 0.603774 0.948052
19 GKE 0.603774 0.948052
20 GDC 0.603774 0.948052
21 5GP 0.595745 0.972973
22 G 0.595745 0.972973
23 GCP 0.59 0.960526
24 BGO 0.587719 0.935897
25 GPG 0.580952 0.948052
26 6CK 0.577982 0.924051
27 G5P 0.572727 0.960526
28 G2R 0.571429 0.948052
29 G G 0.568807 0.935065
30 GDR 0.568807 0.948052
31 GTG 0.568807 0.924051
32 GFB 0.568807 0.948052
33 G2P 0.568627 0.948052
34 GMV 0.564356 0.960526
35 G3A 0.563636 0.960526
36 GPD 0.5625 0.9125
37 GMP 0.561798 0.866667
38 GKD 0.553571 0.948052
39 JB2 0.553571 0.948052
40 GP2 0.55 0.948052
41 DGI 0.55 0.935065
42 GDX 0.548673 0.960526
43 GGM 0.546219 0.9125
44 Y9Z 0.545455 0.890244
45 2GP 0.541667 0.972973
46 CG2 0.537815 0.924051
47 GPX 0.537736 0.959459
48 ALF 5GP 0.533981 0.876543
49 G A A A 0.528926 0.910256
50 JB3 0.525424 0.935897
51 U2G 0.521008 0.924051
52 G C 0.520661 0.8875
53 GDP ALF 0.518519 0.876543
54 GDP AF3 0.518519 0.876543
55 ALF GDP 0.518519 0.876543
56 A G 0.516393 0.922078
57 U A G G 0.512195 0.922078
58 YGP 0.508929 0.888889
59 NGD 0.508333 0.948052
60 G G G RPC 0.508197 0.886076
61 CAG 0.508065 0.869048
62 G U 0.504132 0.8875
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 MD1 0.458015 0.879518
84 PGD 0.458015 0.9125
85 A G U 0.457143 0.876543
86 G4M 0.45 0.869048
87 UCG 0.447761 0.923077
88 A G U U 0.441379 0.876543
89 AKW 0.436508 0.878049
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 PCG 0.4 0.945946
102 C2E 0.4 0.933333
103 35G 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 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
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