Receptor
PDB id Resolution Class Description Source Keywords
3EWX 1.4 Å EC: 4.1.1.23 K314A MUTANT OF HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLAS COMPLEX WITH 6-AZIDO-UMP, DEGRADED TO BMP HOMO SAPIENS DECARBOXYLASE TIM BARREL UNUSUAL CATALYSIS DISEASE MUTATIGLYCOSYLTRANSFERASE LYASE MULTIFUNCTIONAL ENZYME PYRIMIDBIOSYNTHESIS TRANSFERASE
Ref.: LYS314 IS A NUCLEOPHILE IN NON-CLASSICAL REACTIONS 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
BMP A:481;
Valid;
none;
submit data
340.181 C9 H13 N2 O10 P C1=C(...
GOL A:482;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(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: BMP; Similar ligands found: 33
No: Ligand ECFP6 Tc MDL keys Tc
1 BMP 1 1
2 S5P 0.692308 0.943662
3 U6M 0.681818 0.955882
4 NUP 0.681818 0.971014
5 JW5 0.671642 0.942029
6 6AU 0.642857 0.955882
7 6CN 0.642857 0.928571
8 OMP 0.642857 0.955882
9 O7M 0.608108 0.928571
10 O7E 0.592105 0.928571
11 BMQ 0.573529 0.898551
12 FNU 0.534247 0.917808
13 UP6 0.513889 0.847222
14 U 0.513889 0.955224
15 U5P 0.513889 0.955224
16 8OP 0.5125 0.815789
17 8GM 0.4875 0.868421
18 H2U 0.479452 0.873239
19 5FU 0.466667 0.915493
20 5BU 0.454545 0.915493
21 2OM 0.448718 0.885714
22 CNU 0.4375 0.928571
23 TKW 0.417722 0.915493
24 H6Y 0.417582 0.828947
25 8OD 0.41573 0.828947
26 C5P 0.405063 0.901408
27 CAR 0.405063 0.901408
28 C 0.405063 0.901408
29 UTP 0.404762 0.970149
30 UDP 0.402439 0.970149
31 44P 0.4 0.928571
32 U5F 0.4 0.970149
33 ICR 0.4 0.821918
Similar Ligands (3D)
Ligand no: 1; Ligand: BMP; Similar ligands found: 68
No: Ligand Similarity coefficient
1 PSU 0.9699
2 UMP 0.9657
3 DUS 0.9585
4 CH 0.9564
5 16B 0.9555
6 DCM 0.9547
7 DC 0.9541
8 PFU 0.9532
9 DU 0.9504
10 UMC 0.9492
11 TMP 0.9421
12 QBT 0.9418
13 UFP 0.9416
14 5IU 0.9411
15 BRU 0.9404
16 C2R 0.9396
17 FN5 0.9382
18 AMP 0.9380
19 5CM 0.9369
20 IMP 0.9368
21 DOC 0.9368
22 DDN 0.9361
23 NIA 0.9278
24 FDM 0.9264
25 2DT 0.9256
26 AMZ 0.9256
27 IRP 0.9256
28 D4M 0.9254
29 D5M 0.9248
30 DA 0.9248
31 FMP 0.9241
32 AS 0.9235
33 U4S 0.9225
34 8BR 0.9224
35 NYM 0.9223
36 5HM 0.9204
37 AIR 0.9181
38 N5O 0.9145
39 9L3 0.9123
40 G 0.9114
41 5GP 0.9108
42 5HU 0.9098
43 XMP 0.9086
44 6MA 0.9067
45 NEC 0.9062
46 Z8B 0.9031
47 U3S 0.9012
48 T3S 0.8985
49 U1S 0.8973
50 IMU 0.8953
51 U2S 0.8943
52 DG 0.8920
53 O8M 0.8853
54 PZB 0.8842
55 ATM 0.8840
56 FAI 0.8803
57 6RE 0.8794
58 J7C 0.8794
59 IRN 0.8773
60 GAR 0.8769
61 NMN 0.8735
62 MTA 0.8727
63 NCN 0.8724
64 TXS 0.8711
65 2GE 0.8669
66 8OG 0.8659
67 URI 0.8659
68 CDP 0.8569
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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