Receptor
PDB id Resolution Class Description Source Keywords
1UCC 1.77 Å EC: 3.1.27.1 CRYSTAL STRUCTURE OF THE RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS COMPLEXED WITH 3'-UMP. MOMORDICA CHARANTIA ALPHA PLUS BETA HYDROLASE
Ref.: CRYSTAL STRUCTURES OF THE RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS, COMPLEXED WITH 2'-UMP OR 3'-UMP, REVEAL STRUCTURAL BASIS FOR URIDINE SPECIFICITY BIOCHEM.BIOPHYS.RES.COMMUN. V. 275 572 2000
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
U3P A:300;
 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
1UCD 1.3 Å EC: 3.1.27.1 CRYSTAL STRUCTURE OF RIBONUCLEASE MC1 FROM BITTER GOURD SEEDS COMPLEXED WITH 5'-UMP MOMORDICA CHARANTIA ALPHA PLUS BETA HYDROLASE
Ref.: STRUCTURE OF RNASE MC1 FROM BITTER GOURD SEEDS IN COMPLEX WITH 5'UMP TO BE PUBLISHED
Members (6)
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[....
70% Homology Family (6)
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[....
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: U3P; Similar ligands found: 67
No: Ligand ECFP6 Tc MDL keys Tc
1 U3P 1 1
2 UA3 1 1
3 U2P 0.68254 0.953846
4 UPU 0.680556 0.939394
5 URI 0.644068 0.833333
6 CJB 0.639344 0.791045
7 PUP 0.625 0.940298
8 UMF 0.621212 0.910448
9 DKX 0.584615 0.742857
10 U 0.573529 0.953846
11 U5P 0.573529 0.953846
12 C3P 0.565217 0.940298
13 UDP 0.547945 0.939394
14 44P 0.527778 0.898551
15 UTP 0.526316 0.939394
16 CSQ 0.522222 0.849315
17 CSV 0.522222 0.849315
18 U5F 0.519481 0.939394
19 APU 0.515152 0.851351
20 UFM 0.511905 0.911765
21 UPG 0.511905 0.911765
22 URM 0.511905 0.898551
23 UTP U U U 0.511905 0.923077
24 GDU 0.511905 0.911765
25 660 0.511905 0.898551
26 U4S 0.5 0.726027
27 2KH 0.5 0.911765
28 UPF 0.494253 0.861111
29 U2F 0.494253 0.861111
30 UVC 0.492958 0.882353
31 UM3 0.492958 0.939394
32 Y6W 0.488372 0.861111
33 UNP 0.4875 0.911765
34 UDP UDP 0.486842 0.909091
35 U2S 0.486486 0.739726
36 U3S 0.486486 0.726027
37 N3E 0.480519 0.753425
38 UDP GAL 0.477273 0.884058
39 UFG 0.477273 0.861111
40 UDM 0.473118 0.885714
41 UPP 0.465116 0.884058
42 UUA 0.462687 0.742424
43 3UC 0.456522 0.861111
44 AWU 0.454545 0.884058
45 UDH 0.448276 0.837838
46 UD2 0.447917 0.898551
47 UD1 0.447917 0.898551
48 UDX 0.444444 0.884058
49 UAD 0.444444 0.884058
50 DUR 0.441176 0.782609
51 U1S 0.435294 0.723684
52 UGB 0.434783 0.897059
53 2TU 0.434783 0.746479
54 USQ 0.434783 0.772152
55 UGA 0.434783 0.897059
56 UMP 0.434211 0.897059
57 DU 0.434211 0.897059
58 G3N 0.430108 0.859155
59 UGF 0.430108 0.847222
60 12V 0.415842 0.873239
61 HWU 0.415842 0.873239
62 FZK 0.413793 0.753086
63 DUD 0.407407 0.884058
64 EPZ 0.40566 0.885714
65 C2P 0.402597 0.898551
66 EPU 0.401869 0.873239
67 EEB 0.401869 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: U3P; Similar ligands found: 29
No: Ligand Similarity coefficient
1 T3P 0.9522
2 3AM 0.9267
3 ZAR 0.9097
4 A3G 0.9079
5 103 0.9068
6 AZZ 0.9050
7 3GP 0.8988
8 J84 0.8862
9 62V 0.8753
10 NKI 0.8745
11 M0Y 0.8737
12 2AM 0.8731
13 CU8 0.8727
14 6EL 0.8718
15 2GE 0.8716
16 KW7 0.8701
17 72E 0.8670
18 OVE 0.8664
19 9FG 0.8657
20 FT2 0.8645
21 EF2 0.8639
22 40N 0.8628
23 TGW 0.8627
24 BC5 0.8620
25 CTN 0.8605
26 DFL 0.8566
27 SGP 0.8561
28 VM7 0.8560
29 IAG 0.8532
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1UCD; Ligand: U5P; 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: 1ucd.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1UCD; Ligand: URA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1ucd.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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