Receptor
PDB id Resolution Class Description Source Keywords
3L0N 1.74 Å EC: 4.1.1.23 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE IN COMPLEX WITH 6-MERCAPTO-UMP HOMO SAPIENS DECARBOXYLASE MULTIFUNCTIONAL ENZYME PYRIMIDINE BIOSYNTHESIS
Ref.: LYS314 IS A NUCLEOPHILE IN NON-CLASSICAL REACTIONS OF OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE CHEMISTRY V. 15 6619 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
S5P A:257;
B:257;
 Valid;
Valid;
 none;
none;
 ic50 = 1680 uM
356.246 C9 H13 N2 O9 P S C1=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3MI2 1.2 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARB COMPLEXED WITH PYRAZOFURIN MONOPHOSPHATE HOMO SAPIENS UMP SYNTHASE OROTIDINE 5-prime -MONOPHOSPHATE DECARBOXYLASE PYRAMONOPHOSPHATE LYASE
Ref.: STRUCTURAL DETERMINANTS FOR THE INHIBITORY LIGANDS OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE. BIOORG.MED.CHEM. V. 18 4032 2010
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3EWZ ic50 = 79 uM CNU C10 H12 N3 O9 P C1=C(C(=O)....
2 3EX2 ic50 ~ 200 uM 6CN C10 H12 N3 O9 P C1=C(N(C(=....
3 2QCG - 5BU C9 H12 Br N2 O9 P C1=C(C(=O)....
4 3MI2 Ki = 0.00000079 M PFU C9 H14 N3 O9 P C([C@@H]1[....
5 3L0N ic50 = 1680 uM S5P C9 H13 N2 O9 P S C1=C(N(C(=....
6 2QCL - OMP C10 H13 N2 O11 P C1=C(N(C(=....
7 3L0K ic50 = 24 uM 6AU C11 H15 N2 O10 P CC(=O)C1=C....
8 3EWY - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EX1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
10 3EX4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
11 2QCF - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
12 2QCM - JW5 C10 H15 N2 O10 P C1=C(N(C(=....
13 2QCH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 3EWX - BMP C9 H13 N2 O10 P C1=C(N(C(=....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3EWZ ic50 = 79 uM CNU C10 H12 N3 O9 P C1=C(C(=O)....
2 3EX2 ic50 ~ 200 uM 6CN C10 H12 N3 O9 P C1=C(N(C(=....
3 2QCG - 5BU C9 H12 Br N2 O9 P C1=C(C(=O)....
4 3MI2 Ki = 0.00000079 M PFU C9 H14 N3 O9 P C([C@@H]1[....
5 3L0N ic50 = 1680 uM S5P C9 H13 N2 O9 P S C1=C(N(C(=....
6 2QCL - OMP C10 H13 N2 O11 P C1=C(N(C(=....
7 3L0K ic50 = 24 uM 6AU C11 H15 N2 O10 P CC(=O)C1=C....
8 3EWY - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EX1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
10 3EX4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
11 2QCF - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
12 2QCM - JW5 C10 H15 N2 O10 P C1=C(N(C(=....
13 2QCH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 3EWX - BMP C9 H13 N2 O10 P C1=C(N(C(=....
15 4HKP - TKW C9 H14 N3 O9 P C1=C(C(=NC....
50% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3EWZ ic50 = 79 uM CNU C10 H12 N3 O9 P C1=C(C(=O)....
2 3EX2 ic50 ~ 200 uM 6CN C10 H12 N3 O9 P C1=C(N(C(=....
3 2QCG - 5BU C9 H12 Br N2 O9 P C1=C(C(=O)....
4 3MI2 Ki = 0.00000079 M PFU C9 H14 N3 O9 P C([C@@H]1[....
5 3L0N ic50 = 1680 uM S5P C9 H13 N2 O9 P S C1=C(N(C(=....
6 2QCL - OMP C10 H13 N2 O11 P C1=C(N(C(=....
7 3L0K ic50 = 24 uM 6AU C11 H15 N2 O10 P CC(=O)C1=C....
8 3EWY - U5P C9 H13 N2 O9 P C1=CN(C(=O....
9 3EX1 - U5P C9 H13 N2 O9 P C1=CN(C(=O....
10 3EX4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
11 2QCF - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
12 2QCM - JW5 C10 H15 N2 O10 P C1=C(N(C(=....
13 2QCH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 3EWX - BMP C9 H13 N2 O10 P C1=C(N(C(=....
15 1DQX Ki = 9 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3GDT - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
17 3GDL - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 4HKP - TKW C9 H14 N3 O9 P C1=C(C(=NC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: S5P; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 S5P 1 1
2 U6M 0.707692 0.902778
3 BMP 0.692308 0.943662
4 NUP 0.681818 0.917808
5 JW5 0.671642 0.890411
6 6AU 0.642857 0.902778
7 OMP 0.642857 0.902778
8 6CN 0.642857 0.878378
9 O7E 0.613333 0.878378
10 O7M 0.608108 0.878378
11 BMQ 0.573529 0.849315
12 U5P 0.535211 0.901408
13 U 0.535211 0.901408
14 FNU 0.534247 0.87013
15 UP6 0.513889 0.802632
16 8OP 0.5125 0.775
17 8GM 0.4875 0.825
18 H2U 0.479452 0.826667
19 5FU 0.466667 0.866667
20 CNU 0.455696 0.878378
21 5BU 0.454545 0.866667
22 2OM 0.448718 0.837838
23 C 0.423077 0.853333
24 C5P 0.423077 0.853333
25 CAR 0.423077 0.853333
26 UDP 0.419753 0.915493
27 TKW 0.417722 0.866667
28 44P 0.417722 0.878378
29 8OD 0.41573 0.7875
30 16B 0.4125 0.820513
31 UTP 0.404762 0.915493
32 H6Y 0.402174 0.7875
33 U5F 0.4 0.915493
34 2KH 0.4 0.890411
Similar Ligands (3D)
Ligand no: 1; Ligand: S5P; Similar ligands found: 57
No: Ligand Similarity coefficient
1 PSU 0.9631
2 UMP 0.9389
3 DUS 0.9364
4 DOC 0.9351
5 C2R 0.9342
6 UMC 0.9340
7 PFU 0.9319
8 DU 0.9295
9 TMP 0.9291
10 QBT 0.9291
11 FN5 0.9279
12 5IU 0.9269
13 DCM 0.9235
14 DC 0.9235
15 IMP 0.9221
16 D4M 0.9202
17 2DT 0.9201
18 CH 0.9198
19 U4S 0.9187
20 AMP 0.9167
21 5CM 0.9135
22 9L3 0.9134
23 UFP 0.9128
24 AIR 0.9116
25 6MZ 0.9111
26 NIA 0.9108
27 IRP 0.9108
28 DDN 0.9102
29 FMP 0.9098
30 ICR 0.9088
31 AMZ 0.9081
32 8BR 0.9077
33 D5M 0.9071
34 DA 0.9071
35 U1S 0.9046
36 5HM 0.9043
37 6MA 0.8938
38 AS 0.8936
39 N5O 0.8922
40 5GP 0.8919
41 NEC 0.8911
42 NYM 0.8907
43 Z8B 0.8903
44 U3S 0.8899
45 FDM 0.8895
46 U2S 0.8895
47 T3S 0.8859
48 G 0.8854
49 O8M 0.8834
50 XMP 0.8793
51 IMU 0.8783
52 GAR 0.8747
53 8OG 0.8707
54 6RE 0.8693
55 J7C 0.8693
56 ATM 0.8690
57 NMN 0.8568
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MI2; Ligand: PFU; 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: 3mi2.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3MI2; Ligand: PFU; 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: 3mi2.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
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