Receptor
PDB id Resolution Class Description Source Keywords
4S2X 1.5 Å EC: 3.6.1.- STRUCTURE OF E. COLI RPPH BOUND TO RNA AND TWO MAGNESIUM ION ESCHERICHIA COLI NUDIX HYDROLASE RNA PYROPHOSPHOHYDROLASE HYDROLASE-RNA COM
Ref.: STRUCTURES OF RNA COMPLEXES WITH THE ESCHERICHIA CO PYROPHOSPHOHYDROLASE RPPH UNVEIL THE BASIS FOR SPEC 5'-END-DEPENDENT MRNA DECAY. J.BIOL.CHEM. V. 290 9487 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:202;
A:201;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
SO4 A:203;
A:204;
 Invalid;
Invalid;
 none;
none;
 submit data
96.063 O4 S [O-]S...
APC G U B:1;
 Valid;
 Atoms found LESS than expected: % Diff = 0.27;
 submit data
923.341 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6VCQ 1.6 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF E.COLI RPPH IN COMPLEX WITH GTP ESCHERICHIA COLI (STRAIN K12) RNA DEGRADATION RNA BINDING PROTEIN
Ref.: PRINCIPLES OF RNA AND NUCLEOTIDE DISCRIMINATION BY PROCESSING ENZYME RPPH. NUCLEIC ACIDS RES. V. 48 3776 2020
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 28 families.
1 6VCQ ic50 = 1578 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4S2X - APC G U n/a n/a
3 4S2Y - APC G U n/a n/a
4 6VCR - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
5 6VCO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
6 6VCN - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
7 6VCP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 6VCQ ic50 = 1578 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4S2X - APC G U n/a n/a
3 4S2Y - APC G U n/a n/a
4 6VCR - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
5 6VCO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
6 6VCN - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
7 6VCP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
50% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 23 families.
1 6VCQ ic50 = 1578 uM GTP C10 H16 N5 O14 P3 c1nc2c(n1[....
2 4S2X - APC G U n/a n/a
3 4S2Y - APC G U n/a n/a
4 6VCR - CTP C9 H16 N3 O14 P3 C1=CN(C(=O....
5 6VCO - APC C11 H18 N5 O12 P3 c1nc(c2c(n....
6 6VCN - G2P C11 H18 N5 O13 P3 c1nc2c(n1[....
7 6VCP - UTP C9 H15 N2 O15 P3 C1=CN(C(=O....
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 : 6VCQ; 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: 6vcq.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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