Receptor
PDB id Resolution Class Description Source Keywords
6VCL 2.06 Å EC: 5.1.1.7 CRYSTAL STRUCTURE OF E.COLI RPPH-DAPF IN COMPLEX WITH PPPGPP F- ESCHERICHIA COLI (STRAIN K12) RNA DEGRADATION RNA BINDING PROTEIN RNA BINDING PROTEIN-ISCOMPLEX
Ref.: PRINCIPLES OF RNA AND NUCLEOTIDE DISCRIMINATION BY PROCESSING ENZYME RPPH. NUCLEIC ACIDS RES. V. 48 3776 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0O2 B:209;
 Valid;
 none;
 ic50 = 54.4 uM
683.14 C10 H18 N5 O20 P5 c1nc2...
CL B:207;
A:301;
 Invalid;
Invalid;
 none;
none;
 submit data
35.453 Cl [Cl-]
MG B:204;
B:202;
B:201;
B:203;
 Invalid;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
24.305 Mg [Mg+2...
F B:208;
 Invalid;
 none;
 submit data
18.998 F [F-]
GOL B:205;
B:206;
 Invalid;
Invalid;
 none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6VCL 2.06 Å EC: 5.1.1.7 CRYSTAL STRUCTURE OF E.COLI RPPH-DAPF IN COMPLEX WITH PPPGPP F- ESCHERICHIA COLI (STRAIN K12) RNA DEGRADATION RNA BINDING PROTEIN RNA BINDING PROTEIN-ISCOMPLEX
Ref.: PRINCIPLES OF RNA AND NUCLEOTIDE DISCRIMINATION BY PROCESSING ENZYME RPPH. NUCLEIC ACIDS RES. V. 48 3776 2020
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6VCM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 6D1V - APC G U n/a n/a
3 6VCL ic50 = 54.4 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6VCM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 6D1V - APC G U n/a n/a
3 6VCL ic50 = 54.4 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 6VCM - GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 6D1V - APC G U n/a n/a
3 6VCL ic50 = 54.4 uM 0O2 C10 H18 N5 O20 P5 c1nc2c(n1[....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0O2; Similar ligands found: 96
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 GAV 0.62 0.948052
14 GNP 0.616162 0.960526
15 9GM 0.616162 0.960526
16 G1R 0.606061 0.973333
17 GKE 0.603774 0.948052
18 GDD 0.603774 0.948052
19 GDC 0.603774 0.948052
20 G 0.595745 0.972973
21 5GP 0.595745 0.972973
22 GCP 0.59 0.960526
23 BGO 0.587719 0.935897
24 GPG 0.580952 0.948052
25 6CK 0.577982 0.924051
26 G5P 0.572727 0.960526
27 G2R 0.571429 0.948052
28 GFB 0.568807 0.948052
29 GTG 0.568807 0.924051
30 GDR 0.568807 0.948052
31 G2P 0.568627 0.948052
32 GMV 0.564356 0.960526
33 G3A 0.563636 0.960526
34 GPD 0.5625 0.9125
35 GMP 0.561798 0.866667
36 JB2 0.553571 0.948052
37 GKD 0.553571 0.948052
38 DGI 0.55 0.935065
39 GP2 0.55 0.948052
40 GDX 0.548673 0.960526
41 GGM 0.546219 0.9125
42 Y9Z 0.545455 0.890244
43 GDP BEF 0.543689 0.922078
44 2GP 0.541667 0.972973
45 GTP MG 0.538462 0.946667
46 CG2 0.537815 0.924051
47 GPX 0.537736 0.959459
48 ALF 5GP 0.533981 0.876543
49 JB3 0.525424 0.935897
50 U2G 0.521008 0.924051
51 G C 0.520661 0.8875
52 GDP ALF 0.518519 0.876543
53 GDP AF3 0.518519 0.876543
54 YGP 0.508929 0.888889
55 NGD 0.508333 0.948052
56 CAG 0.508065 0.869048
57 APC G U 0.503937 0.897436
58 QBQ 0.5 0.972973
59 TPG 0.496124 0.829545
60 2MD 0.495935 0.879518
61 G1G 0.488189 0.9125
62 KB7 0.485714 0.814815
63 GPC 0.484127 0.86747
64 MGD 0.484127 0.879518
65 FEG 0.483607 0.86747
66 ZGP 0.479675 0.857143
67 GDP 7MG 0.478632 0.898734
68 DGP 0.475248 0.922078
69 DG 0.475248 0.922078
70 DBG 0.473282 0.935897
71 P2G 0.470588 0.894737
72 MGP 0.46729 0.948052
73 6G0 0.462963 0.948052
74 P1G 0.461538 0.883117
75 MD1 0.458015 0.879518
76 PGD 0.458015 0.9125
77 KBD 0.45614 0.814815
78 G4M 0.45 0.869048
79 UCG 0.447761 0.923077
80 KBJ 0.440678 0.785714
81 AKW 0.436508 0.878049
82 CZF 0.435185 0.92
83 01G 0.432203 0.890244
84 PAP 0.429907 0.918919
85 CGP 0.429688 0.878049
86 FE9 0.428571 0.765957
87 I2C FE2 CMO CMO 0.41791 0.797753
88 IDP 0.416667 0.959459
89 PGD O 0.416058 0.83908
90 SGP 0.415094 0.8375
91 G1R G1R 0.408759 0.911392
92 AGO 0.401515 0.9
93 G 5MC C U 0.401274 0.878049
94 35G 0.4 0.945946
95 C2E 0.4 0.933333
96 PCG 0.4 0.945946
Similar Ligands (3D)
Ligand no: 1; Ligand: 0O2; 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 : 6VCL; Ligand: 0O2; 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: 6vcl.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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