Receptor
PDB id Resolution Class Description Source Keywords
3KVY 2.3 Å EC: 2.-.-.- TRAPPING OF AN OXOCARBENIUM ION INTERMEDIATE IN UP CRYSTALS BOS TAURUS OXOCARBENIUM ION GLYCAL PYRIMIDINE SALVAGE URIDINE PHOSPHTRANSFERASE
Ref.: GLYCAL FORMATION IN CRYSTALS OF URIDINE PHOSPHORYLA BIOCHEMISTRY V. 49 3499 2010
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
R2B A:313;
B:313;
Valid;
Valid;
none;
none;
submit data
132.115 C5 H8 O4 C1=C(...
SO4 A:310;
A:311;
B:310;
B:311;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
URA A:312;
B:312;
Valid;
Valid;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3KVY 2.3 Å EC: 2.-.-.- TRAPPING OF AN OXOCARBENIUM ION INTERMEDIATE IN UP CRYSTALS BOS TAURUS OXOCARBENIUM ION GLYCAL PYRIMIDINE SALVAGE URIDINE PHOSPHTRANSFERASE
Ref.: GLYCAL FORMATION IN CRYSTALS OF URIDINE PHOSPHORYLA BIOCHEMISTRY V. 49 3499 2010
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 236 families.
1 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3P0E - BAU C14 H16 N2 O4 c1ccc(cc1)....
2 3P0F - BAU C14 H16 N2 O4 c1ccc(cc1)....
3 3EUF - BAU C14 H16 N2 O4 c1ccc(cc1)....
4 3NBQ - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
50% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 3P0E - BAU C14 H16 N2 O4 c1ccc(cc1)....
2 3P0F - BAU C14 H16 N2 O4 c1ccc(cc1)....
3 3EUF - BAU C14 H16 N2 O4 c1ccc(cc1)....
4 3NBQ - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 5CYF - FLC C6 H5 O7 C(C(=O)[O-....
6 4TXJ - THM C10 H14 N2 O5 CC1=CN(C(=....
7 4TXM - TDR C5 H6 N2 O2 CC1=CNC(=O....
8 4TXL - URA C4 H4 N2 O2 C1=CNC(=O)....
9 4TXN - URF C4 H3 F N2 O2 C1=C(C(=O)....
10 3KVY - URA C4 H4 N2 O2 C1=CNC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: R2B; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 R2B 1 1
2 LCN 0.575758 0.875
Ligand no: 2; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3KVY; Ligand: R2B; Similar sites found: 26
This union binding pocket(no: 1) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5EWK P34 0.01232 0.40165 None
2 1CT9 GLN 0.0096 0.41207 1.61812
3 1U2Z SAH 0.01609 0.41911 2.26537
4 1ZOS MTM 0.0001406 0.42672 2.6087
5 2G2Y MLI 0.002977 0.43675 3.24675
6 3BL6 FMC 0.0002037 0.40203 4.78261
7 1PKX XMP 0.01755 0.41491 6.47249
8 4QAR ADE 0.0005515 0.41101 6.96517
9 4Y2H SAH 0.03555 0.41807 9.06149
10 4BMX ADE 0.0003394 0.50068 9.56175
11 1NW4 IMH 0.000000003503 0.60455 10.1449
12 2AC7 ADN 0.000001483 0.41654 10.6383
13 3LGS SAH 0.0002693 0.40058 14.2322
14 3LGS ADE 0.0002693 0.40058 14.2322
15 5MX4 HPA 0.001803 0.44895 16.7382
16 3QPB R1P 0.0000001822 0.57663 24.8227
17 3QPB URA 0.002275 0.44578 24.8227
18 4DA6 GA2 0.00002603 0.54917 29.249
19 3BJE R1P 0.0000006854 0.56817 30.4207
20 3BJE URA 0.001299 0.45711 30.4207
21 1JE1 GMP 0.00000001553 0.42478 31.7797
22 1Z34 2FD 0.000005155 0.50574 33.1915
23 4YJK URA 0.0008615 0.46833 33.3333
24 3U40 ADN 0.000000003473 0.60536 34.2975
25 1VHW ADN 0.000000007679 0.63222 38.7352
26 1ODJ GMP 0.000000006012 0.59987 39.1489
Pocket No.: 2; Query (leader) PDB : 3KVY; Ligand: R2B; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3KVY; Ligand: URA; Similar sites found: 47
This union binding pocket(no: 3) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1VKF CIT 0.004129 0.42098 2.12766
2 1PJS SAH 0.01805 0.40899 2.26537
3 1U2Z SAH 0.03573 0.40017 2.26537
4 4X1B MLI 0.01311 0.40009 2.26537
5 2RDE C2E 0.009798 0.41531 2.39044
6 1GAD NAD 0.02706 0.41201 2.589
7 1ZOS MTM 0.00001512 0.46083 2.6087
8 4FK7 P34 0.001787 0.44371 2.62009
9 1IYE PGU 0.009272 0.44196 2.91262
10 1D1G NDP 0.01846 0.41811 2.97619
11 2I0G I0G 0.04146 0.41925 3.11284
12 3OV6 MK0 0.02358 0.41699 3.23625
13 3VC3 C6P 0.03187 0.40569 3.23625
14 1TDF FAD 0.03734 0.42153 3.55987
15 2P4S DIH 0.00008946 0.45828 3.8835
16 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 0.008426 0.4126 3.8835
17 2XZ9 PYR 0.01065 0.40144 3.8835
18 1KC7 PPR 0.003466 0.41905 4.20712
19 3BL6 FMC 0.00001612 0.4405 4.78261
20 4GLJ RHB 0.0001342 0.40614 6.06061
21 1VMK GUN 0.000173 0.48955 6.13718
22 5ETJ IM5 0.00007874 0.43945 6.47249
23 4QAR ADE 0.00001074 0.48162 6.96517
24 5F7J ADE 0.00005299 0.41896 7.1875
25 5IFK HPA 0.00004264 0.52101 7.76699
26 2A9K NAD 0.01293 0.42129 8.96861
27 3SHR CMP 0.003427 0.40463 9.36455
28 1GZF NIR 0.007739 0.40152 9.47867
29 4BMX ADE 0.00003749 0.54963 9.56175
30 1NW4 IMH 0.000006865 0.4819 10.1449
31 1K27 MTM 0.00003399 0.42166 10.2473
32 3HQP OXL 0.00841 0.40351 11.0032
33 1G2O IMH 0.0001591 0.42859 11.9403
34 3LGS ADE 0.00002093 0.44083 14.2322
35 3LGS SAH 0.00002093 0.44083 14.2322
36 3VSE SAH 0.01665 0.40166 15.5779
37 5MX4 HPA 0.000000355 0.63167 16.7382
38 4Q3F TLA 0.01116 0.40182 18.8034
39 4WKB TDI 0.00005487 0.41397 23.3607
40 3QPB URA 0.00000002455 0.68588 24.8227
41 4DA6 GA2 0.000002289 0.60296 29.249
42 3BJE URA 0.00000000002043 0.84681 30.4207
43 1Z34 2FD 0.000009368 0.49213 33.1915
44 4YJK URA 0.00000000005933 0.82875 33.3333
45 3U40 ADN 0.000001563 0.50855 34.2975
46 1VHW ADN 0.000006261 0.51393 38.7352
47 1ODJ GMP 0.000008722 0.48276 39.1489
Pocket No.: 4; Query (leader) PDB : 3KVY; Ligand: URA; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3kvy.bio1) has 13 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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