Receptor
PDB id Resolution Class Description Source Keywords
6N6F 1.74 Å EC: 3.1.-.- VIBRIO CHOLERAE OLIGORIBONUCLEASE BOUND TO PGC VIBRIO CHOLERAE 3-prime -5-prime EXORIBONUCLEASE RNA BINDING PROTEIN RNA BINDING PROTCOMPLEX
Ref.: A DEDICATED DIRIBONUCLEOTIDASE RESOLVES A KEY BOTTL THE TERMINAL STEP OF RNA DEGRADATION. ELIFE V. 8 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
NA D:701;
 Part of Protein;
 none;
 submit data
22.99 Na [Na+]
G C D:603;
 Valid;
 Atoms found MORE than expected: % Diff = 1.545;
 submit data
587.419 n/a P(=O)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6N6A 1.5 Å EC: 3.1.-.- VIBRIO CHOLERAE OLIGORIBONUCLEASE BOUND TO PGG VIBRIO CHOLERAE 3-prime -5-prime EXORIBONUCLEASE RNA BINDING PROTEIN RNA BINDING PROTCOMPLEX
Ref.: A DEDICATED DIRIBONUCLEOTIDASE RESOLVES A KEY BOTTL THE TERMINAL STEP OF RNA DEGRADATION. ELIFE V. 8 2019
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 6N6E - G A n/a n/a
2 6N6D - A G n/a n/a
3 6N6A - G G n/a n/a
4 6N6G - C G n/a n/a
5 6N6C - A A n/a n/a
6 6N6H - C U n/a n/a
7 6N6F - G C n/a n/a
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 25 families.
1 6N6E - G A n/a n/a
2 6N6D - A G n/a n/a
3 6N6A - G G n/a n/a
4 6N6G - C G n/a n/a
5 6N6C - A A n/a n/a
6 6N6H - C U n/a n/a
7 6N6F - G C n/a n/a
8 6A4F - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 6A4D - 9RC C16 H18 N3 O10 P CC1=CN(C(=....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 22 families.
1 6N6E - G A n/a n/a
2 6N6D - A G n/a n/a
3 6N6A - G G n/a n/a
4 6N6G - C G n/a n/a
5 6N6C - A A n/a n/a
6 6N6H - C U n/a n/a
7 6N6F - G C n/a n/a
8 6N6K - A G n/a n/a
9 6N6I - G G n/a n/a
10 6N6J - A A n/a n/a
11 6A4F - U5P C9 H13 N2 O9 P C1=CN(C(=O....
12 6A4D - 9RC C16 H18 N3 O10 P CC1=CN(C(=....
13 6RCL - A A n/a n/a
14 6RCN - DA DA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: G C ; Similar ligands found: 99
No: Ligand ECFP6 Tc MDL keys Tc
1 G C 1 1
2 GPC 0.680328 0.927711
3 G 5MC C U 0.664336 0.939024
4 G G 6MZ C 0.647541 0.925926
5 OMC OMU OMG OMG U 0.647059 0.939024
6 CG2 0.634146 0.9625
7 6MZ C U 0.601449 0.925926
8 3GP 0.566038 0.898734
9 G3D 0.561404 0.8875
10 G 6MZ C U 0.548611 0.91358
11 G4P 0.538462 0.8875
12 ALF 5GP 0.530435 0.869048
13 GDP BEF 0.525862 0.9125
14 CDP MG 0.523364 0.858974
15 GTP MG 0.521368 0.935897
16 0O2 0.520661 0.8875
17 U2G 0.519084 0.9625
18 G 0.513514 0.911392
19 5GP 0.513514 0.911392
20 GPG 0.508197 0.91358
21 GDP 0.504348 0.9
22 GDP AF3 0.504132 0.869048
23 GDP ALF 0.504132 0.869048
24 APC G U 0.503597 0.888889
25 CSV 0.491935 0.829268
26 CSQ 0.491935 0.829268
27 GP2 0.491379 0.86747
28 GNH 0.487179 0.888889
29 GSP 0.483333 0.857143
30 GP3 0.482759 0.901235
31 2GP 0.482143 0.8875
32 CDP 0.481818 0.8375
33 CAR 0.481132 0.848101
34 C 0.481132 0.848101
35 GMP 0.481132 0.835443
36 C5P 0.481132 0.848101
37 GTP 0.478992 0.9
38 GAV 0.47541 0.86747
39 GCP 0.475 0.878049
40 G2P 0.471074 0.86747
41 M7G A2M G 0.469512 0.853933
42 GDP 7MG 0.469231 0.91358
43 GKE 0.46875 0.91358
44 GDC 0.46875 0.91358
45 GDD 0.46875 0.91358
46 CGP 0.467153 0.915663
47 GMV 0.466667 0.878049
48 7XL 0.465517 0.817073
49 G1R 0.46281 0.888889
50 GNP 0.459016 0.878049
51 9GM 0.459016 0.878049
52 CTP 0.45614 0.8375
53 HF4 0.45614 0.8375
54 C5G 0.455285 0.839506
55 UCG 0.452055 0.9375
56 2TM 0.448276 0.807229
57 CDP RB0 0.448 0.839506
58 CDM 0.447154 0.77907
59 JB2 0.443609 0.890244
60 91P 0.442029 0.939024
61 G2R 0.440945 0.86747
62 0RC 0.440678 0.797619
63 CDC 0.439024 0.744444
64 KB7 0.438017 0.809524
65 TPG 0.435374 0.824176
66 Y9Z 0.435115 0.83908
67 I2C FE2 CMO CMO 0.434483 0.853933
68 GKD 0.432836 0.91358
69 GDR 0.431818 0.890244
70 GFB 0.431818 0.890244
71 C2G 0.429752 0.82716
72 CTP C C C C 0.42963 0.858974
73 G3A 0.428571 0.901235
74 6CK 0.428571 0.869048
75 YGP 0.427481 0.903614
76 AR3 0.427184 0.759494
77 CTN 0.427184 0.759494
78 G1R G1R 0.425676 0.902439
79 G5P 0.425373 0.901235
80 NGD 0.421429 0.91358
81 BGO 0.421429 0.857143
82 GTG 0.421053 0.891566
83 GPD 0.419118 0.858824
84 GDX 0.419118 0.901235
85 ZGP 0.41844 0.829545
86 3PD UM3 0.41844 0.938272
87 C3P 0.418182 0.835443
88 CXY 0.417323 0.817073
89 P1G 0.416667 0.829268
90 JB3 0.414286 0.879518
91 CAG 0.413793 0.840909
92 PGD O 0.413333 0.853933
93 FEG 0.411348 0.83908
94 A7R 0.407407 0.875
95 2AA 0.405594 0.682692
96 KBD 0.40458 0.831325
97 GPX 0.403101 0.851852
98 2MD 0.402778 0.872093
99 P2G 0.4 0.839506
Similar Ligands (3D)
Ligand no: 1; Ligand: G C ; Similar ligands found: 2
No: Ligand Similarity coefficient
1 A U 0.9328
2 UPU 0.8647
Similar Binding Sites (Proteins are less than 50% similar to leader) APoc FAQ
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