Receptor
PDB id Resolution Class Description Source Keywords
6D1V 1.81 Å EC: 5.1.1.7 CRYSTAL STRUCTURE OF E. COLI RPPH-DAPF COMPLEX, MONOMER BOUN ESCHERICHIA COLI RNA DECAY RPPH DAPF ISOMERASE-HYDROLASE COMPLEX ISOMERASHYDROLASE-RNA COMPLEX
Ref.: STRUCTURAL AND KINETIC INSIGHTS INTO STIMULATION OF RPPH-DEPENDENT RNA DEGRADATION BY THE METABOLIC ENZ NUCLEIC ACIDS RES. V. 46 6841 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL B:205;
B:206;
B:204;
A:802;
A:803;
A:804;
A:801;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
CL A:806;
A:805;
B:208;
B:207;
A:807;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
MG B:203;
B:202;
B:201;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
APC G U C:1;
 Valid;
 Atoms found LESS than expected: % Diff = 0.216;
 submit data
923.341 n/a P(=O)...
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: APC G U ; Similar ligands found: 81
No: Ligand ECFP6 Tc MDL keys Tc
1 APC G U 1 1
2 G3A 0.58871 0.911392
3 G5P 0.584 0.911392
4 ATP A 0.552 0.87013
5 ATP A A A 0.552 0.87013
6 APC MG 0.534483 0.883117
7 G3D 0.528926 0.897436
8 M7G A2M G 0.521472 0.840909
9 G4P 0.520325 0.897436
10 0O2 0.503937 0.897436
11 G C 0.503597 0.888889
12 3GP 0.491379 0.909091
13 GTP MG 0.48 0.922078
14 ALF 5GP 0.475806 0.855422
15 GDP BEF 0.472 0.898734
16 PAP 0.471074 0.846154
17 A3P 0.470085 0.857143
18 GDP AF3 0.465116 0.855422
19 1YD 0.462687 0.909091
20 4BW 0.462687 0.909091
21 5GP 0.458333 0.897436
22 G 0.458333 0.897436
23 GSP 0.456693 0.843373
24 GP3 0.455285 0.911392
25 GDP ALF 0.453846 0.855422
26 GDP 0.451613 0.886076
27 GP2 0.451613 0.9
28 GCP 0.448819 0.8875
29 GNH 0.448 0.875
30 PPS 0.448 0.758621
31 G2P 0.445312 0.9
32 PO4 PO4 A A A A PO4 0.442748 0.868421
33 GTP 0.440945 0.886076
34 PAX 0.440789 0.823529
35 GMP 0.438596 0.797468
36 ADP BEF 0.438017 0.857143
37 ADP MG 0.438017 0.857143
38 G1R G1R 0.434211 0.9125
39 38V 0.434211 0.925
40 GDD 0.433824 0.876543
41 GDC 0.433824 0.876543
42 GKE 0.433824 0.876543
43 G 5MC C U 0.432749 0.857143
44 BEF ADP 0.432 0.835443
45 9BG 0.431507 0.911392
46 3AM 0.431034 0.844156
47 COA FLC 0.427632 0.747253
48 1YC 0.427536 0.883117
49 G1R 0.426357 0.875
50 GPG 0.425373 0.9
51 GDP 7MG 0.42446 0.924051
52 ATP MG 0.424 0.857143
53 ADP PO3 0.424 0.857143
54 4UR 0.423611 0.909091
55 9GM 0.423077 0.864198
56 GNP 0.423077 0.864198
57 VO4 ADP 0.421875 0.8375
58 GTA 0.421429 0.901235
59 GMV 0.418605 0.864198
60 2GP 0.418033 0.873418
61 G2R 0.41791 0.876543
62 JBT 0.417526 0.752577
63 GAV 0.416667 0.853659
64 AMP MG 0.411765 0.844156
65 BGO 0.410959 0.888889
66 ANP MG 0.410853 0.825
67 GDX 0.408451 0.8875
68 6CK 0.407143 0.855422
69 GAP 0.40625 0.8375
70 YGP 0.405797 0.845238
71 PUA 0.405229 0.831325
72 G 6MZ C 0.404762 0.844156
73 APU 0.40411 0.839506
74 Y9Z 0.402878 0.804598
75 AGS 0.401575 0.795181
76 GKD 0.401408 0.876543
77 GFB 0.4 0.876543
78 GDR 0.4 0.876543
79 ALF ADP 0.4 0.795181
80 ADP BMA 0.4 0.8375
81 GTG 0.4 0.901235
Similar Ligands (3D)
Ligand no: 1; Ligand: APC G U ; 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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