Receptor
PDB id Resolution Class Description Source Keywords
6VCN 1.9 Å EC: 3.6.1.- CRYSTAL STRUCTURE OF E.COLI RPPH IN COMPLEX WITH PPCPG 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
G2P A:201;
 Valid;
 none;
 submit data
521.208 C11 H18 N5 O13 P3 c1nc2...
SO4 A:203;
A:202;
A:205;
A:204;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
96.063 O4 S [O-]S...
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: G2P; Similar ligands found: 116
No: Ligand ECFP6 Tc MDL keys Tc
1 G2P 1 1
2 GP2 0.839506 1
3 G 0.777778 0.948052
4 5GP 0.777778 0.948052
5 GDP 0.77381 0.961039
6 GCP 0.758621 0.987013
7 GTP 0.747126 0.961039
8 GP3 0.741176 0.936709
9 GNH 0.724138 0.948718
10 GAV 0.714286 0.925
11 GNP 0.711111 0.936709
12 9GM 0.711111 0.936709
13 G1R 0.7 0.948718
14 GSP 0.692308 0.91358
15 GTP MG 0.692308 0.923077
16 GMV 0.688889 0.936709
17 ALF 5GP 0.688889 0.857143
18 GDP BEF 0.681319 0.9
19 GDP AF3 0.680851 0.857143
20 G2R 0.673684 0.974359
21 GPG 0.649485 0.925
22 GDP ALF 0.645833 0.857143
23 GMP 0.641975 0.846154
24 Y9Z 0.64 0.892857
25 GDD 0.64 0.925
26 GDC 0.64 0.925
27 GKE 0.64 0.925
28 G5P 0.637255 0.936709
29 YGP 0.63 0.869048
30 G3A 0.627451 0.936709
31 GTG 0.617647 0.902439
32 GDR 0.617647 0.925
33 GFB 0.617647 0.925
34 6CK 0.61165 0.902439
35 GDP 7MG 0.605769 0.878049
36 GKD 0.6 0.925
37 JB2 0.6 0.925
38 KB7 0.595745 0.797619
39 GPD 0.59434 0.914634
40 GDX 0.59434 0.936709
41 G3D 0.587629 0.948052
42 3GP 0.577778 0.910256
43 G4P 0.575758 0.948052
44 0O2 0.568627 0.948052
45 JB3 0.567568 0.91358
46 NGD 0.5625 0.925
47 U2G 0.5625 0.902439
48 KBD 0.553398 0.797619
49 APC 0.553191 0.923077
50 CG2 0.552632 0.902439
51 FEG 0.548673 0.870588
52 2MD 0.547826 0.860465
53 ZGP 0.54386 0.860465
54 2GP 0.543478 0.923077
55 CAG 0.533898 0.850575
56 MGD 0.533898 0.860465
57 KBJ 0.53271 0.790698
58 GH3 0.519608 0.961039
59 PGD 0.516393 0.891566
60 MD1 0.516393 0.882353
61 GPX 0.509615 0.910256
62 FE9 0.508197 0.752577
63 DBG 0.508065 0.91358
64 TPG 0.508065 0.833333
65 DGI 0.50505 0.936709
66 DGT 0.5 0.936709
67 P2G 0.5 0.85
68 G1R G1R 0.496 0.890244
69 I2C FE2 CMO CMO 0.495935 0.782609
70 G4M 0.492424 0.872093
71 PGD O 0.492063 0.822222
72 P1G 0.489796 0.8625
73 DGP 0.489583 0.924051
74 DG 0.489583 0.924051
75 QBQ 0.485149 0.948052
76 IDP 0.484848 0.935065
77 AKW 0.483051 0.858824
78 BGO 0.483051 0.890244
79 NYZ 0.48 0.974359
80 IMP 0.479167 0.922078
81 ACQ 0.475248 0.910256
82 G C 0.471074 0.86747
83 38V 0.460938 0.974684
84 G7M 0.459184 0.9125
85 GGM 0.459016 0.869048
86 G1G 0.452381 0.891566
87 MGP 0.451923 0.925
88 6G0 0.447619 0.925
89 APC G U 0.445312 0.9
90 RBY 0.441176 0.898734
91 ADV 0.441176 0.898734
92 SGP 0.44 0.797619
93 AP2 0.438776 0.923077
94 A12 0.438776 0.923077
95 R7I 0.438095 0.910256
96 R5I 0.438095 0.910256
97 C2E 0.436893 0.886076
98 PCG 0.436893 0.897436
99 35G 0.436893 0.897436
100 GPC 0.436508 0.848837
101 6YZ 0.433962 0.910256
102 5GP 5GP 0.432692 0.85
103 O02 0.423077 0.9125
104 CZF 0.419048 0.897436
105 M7G A2M G 0.418301 0.802198
106 GTA 0.411765 0.902439
107 G2Q 0.410714 0.974359
108 ACP 0.407767 0.910256
109 ADP 0.405941 0.884615
110 MGQ 0.405405 0.901235
111 UCG 0.402985 0.878049
112 AMP 0.402062 0.858974
113 A 0.402062 0.858974
114 93A 0.401961 0.804598
115 AMZ 0.4 0.883117
116 C2R 0.4 0.871795
Similar Ligands (3D)
Ligand no: 1; Ligand: G2P; Similar ligands found: 2
No: Ligand Similarity coefficient
1 ATP 0.8852
2 ANP 0.8610
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
APoc FAQ
Feedback