Receptor
PDB id Resolution Class Description Source Keywords
1VD3 1.8 Å EC: 3.1.27.1 RIBONUCLEASE NT IN COMPLEX WITH 2'-UMP NICOTIANA GLUTINOSA HYDROLASE RIBONUCLEASE NUCLEIC ACID RNA
Ref.: CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NT IN COMPLEX WITH NUCLEOTIDE MONOPHOSPHATES TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U2P A:214;
 Valid;
 none;
 submit data
324.181 C9 H13 N2 O9 P C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1VD3 1.8 Å EC: 3.1.27.1 RIBONUCLEASE NT IN COMPLEX WITH 2'-UMP NICOTIANA GLUTINOSA HYDROLASE RIBONUCLEASE NUCLEIC ACID RNA
Ref.: CRYSTAL STRUCTURE OF THE NICOTIANA GLUTINOSA RIBONUCLEASE NT IN COMPLEX WITH NUCLEOTIDE MONOPHOSPHATES TO BE PUBLISHED
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1VD1 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 1VCZ - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
3 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
2 1VD1 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
3 1VCZ - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
4 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1UCA - U2P C9 H13 N2 O9 P C1=CN(C(=O....
2 1V9H - U5P C9 H13 N2 O9 P C1=CN(C(=O....
3 1UCC - U3P C9 H13 N2 O9 P C1=CN(C(=O....
4 1J1F - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
5 1UCD - URA C4 H4 N2 O2 C1=CNC(=O)....
6 1J1G - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
7 1IYB - 5GP C10 H14 N5 O8 P c1nc2c(n1[....
8 1VD3 - U2P C9 H13 N2 O9 P C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: U2P; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 U2P 1 1
2 UA3 0.68254 0.953846
3 U3P 0.68254 0.953846
4 UMF 0.621212 0.897059
5 URI 0.590164 0.848485
6 CJB 0.587302 0.80597
7 C2P 0.565217 0.941176
8 DKX 0.537313 0.782609
9 U5P 0.528571 0.939394
10 U 0.528571 0.939394
11 UPU 0.5125 0.925373
12 PUP 0.511628 0.926471
13 UDP 0.506667 0.954545
14 UM3 0.492958 0.897059
15 UPA 0.49 0.828947
16 UTP 0.487179 0.954545
17 44P 0.486486 0.913043
18 U5F 0.481013 0.954545
19 U2G 0.480392 0.810127
20 UDP GAL 0.477273 0.898551
21 GDU 0.476744 0.926471
22 UPG 0.476744 0.926471
23 UFM 0.476744 0.926471
24 2KH 0.4625 0.926471
25 N3E 0.461538 0.743243
26 U2F 0.460674 0.875
27 UPF 0.460674 0.875
28 URM 0.45977 0.913043
29 660 0.45977 0.913043
30 Y6W 0.454545 0.875
31 UVC 0.452055 0.869565
32 UNP 0.451219 0.926471
33 UDP UDP 0.448718 0.895522
34 UFG 0.444444 0.875
35 UTP U U U 0.443182 0.880597
36 DUR 0.441176 0.797101
37 U4S 0.44 0.716216
38 DU 0.434211 0.884058
39 UMP 0.434211 0.884058
40 U3S 0.428571 0.716216
41 U2S 0.428571 0.72973
42 CSQ 0.427083 0.837838
43 CSV 0.427083 0.837838
44 3UC 0.425532 0.875
45 AWU 0.422222 0.898551
46 UUA 0.42029 0.757576
47 UD2 0.418367 0.913043
48 UD1 0.418367 0.913043
49 UDH 0.41573 0.851351
50 UPP 0.41573 0.898551
51 APU 0.415094 0.84
52 2TU 0.414286 0.760563
53 UDX 0.413043 0.898551
54 UAD 0.413043 0.898551
55 UDM 0.412371 0.9
56 DUD 0.407407 0.898551
57 UGA 0.404255 0.911765
58 UGB 0.404255 0.911765
59 USQ 0.404255 0.78481
60 C3P 0.402597 0.898551
61 G3N 0.4 0.873239
62 UGF 0.4 0.861111
Similar Ligands (3D)
Ligand no: 1; Ligand: U2P; Similar ligands found: 10
No: Ligand Similarity coefficient
1 OVE 0.9328
2 2AM 0.9288
3 T3P 0.9038
4 2GP 0.8907
5 DRM 0.8757
6 A04 0.8694
7 DAN 0.8604
8 6KN 0.8599
9 CTN 0.8588
10 5DX 0.8581
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1VD3; Ligand: U2P; 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: 1vd3.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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