Receptor
PDB id Resolution Class Description Source Keywords
2QCM 1.67 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE DOMAIN (ASP312ASN MUTANT) OF HUMAN UMP S YNTHASE BOUND TO 6-HYDROXYMETHYL-UMP HOMO SAPIENS UMP SYNTHASE DECARBOXYLASE CATALYTIC PROFICIENCY LYASE
Ref.: STRUCTURES OF THE HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE SUPPORT A COVALENT MECHANISM AND PROVIDE A FRAMEWORK FOR DRUG DESIGN. STRUCTURE V. 16 82 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
JW5 A:482;
 Valid;
 none;
 submit data
354.207 C10 H15 N2 O10 P C1=C(...
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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: JW5; Similar ligands found: 30
No: Ligand ECFP6 Tc MDL keys Tc
1 JW5 1 1
2 S5P 0.671642 0.890411
3 BMP 0.671642 0.942029
4 U6M 0.661765 0.955882
5 NUP 0.661765 0.915493
6 6CN 0.647887 0.928571
7 6AU 0.625 0.955882
8 OMP 0.625 0.955882
9 O7M 0.613333 0.928571
10 O7E 0.597403 0.928571
11 BMQ 0.557143 0.926471
12 FNU 0.52 0.866667
13 8OP 0.518519 0.815789
14 UP6 0.5 0.847222
15 U5P 0.5 0.955224
16 U 0.5 0.955224
17 H2U 0.486486 0.9
18 8GM 0.47561 0.844156
19 2OM 0.455696 0.913043
20 5FU 0.454545 0.915493
21 5BU 0.443038 0.915493
22 5HM 0.432099 0.90411
23 CNU 0.426829 0.928571
24 8OD 0.422222 0.805195
25 C5P 0.4125 0.901408
26 CAR 0.4125 0.901408
27 C 0.4125 0.901408
28 H6Y 0.408602 0.805195
29 TKW 0.407407 0.915493
30 16B 0.402439 0.864865
Similar Ligands (3D)
Ligand no: 1; Ligand: JW5; Similar ligands found: 34
No: Ligand Similarity coefficient
1 UMP 0.9289
2 IMP 0.9157
3 PFU 0.9151
4 PSU 0.9137
5 5IU 0.9095
6 TMP 0.9074
7 CH 0.9034
8 NYM 0.8991
9 QBT 0.8975
10 2DT 0.8969
11 8BR 0.8966
12 UFP 0.8932
13 AMP 0.8914
14 O8M 0.8898
15 UMC 0.8889
16 DU 0.8877
17 DDN 0.8857
18 FN5 0.8834
19 C2R 0.8828
20 DOC 0.8811
21 5GP 0.8806
22 NIA 0.8803
23 G 0.8800
24 XMP 0.8757
25 FAI 0.8744
26 DCM 0.8738
27 FDM 0.8734
28 AMZ 0.8659
29 AIR 0.8650
30 D5M 0.8629
31 IRP 0.8627
32 DC 0.8624
33 6MZ 0.8581
34 ATM 0.8532
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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