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 = 0.0000251 mM 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 = 0.0000251 mM 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 = 0.0000251 mM 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
Ligand no: 1; Ligand: BMP; Similar ligands found: 31
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 U5P 0.513889 0.955224
15 8OP 0.5125 0.815789
16 8GM 0.4875 0.868421
17 H2U 0.479452 0.873239
18 5FU 0.466667 0.915493
19 5BU 0.454545 0.915493
20 2OM 0.448718 0.885714
21 CNU 0.4375 0.928571
22 TKW 0.417722 0.915493
23 H6Y 0.417582 0.828947
24 8OD 0.41573 0.828947
25 CAR 0.405063 0.901408
26 C 0.405063 0.901408
27 C5P 0.405063 0.901408
28 UTP 0.404762 0.970149
29 UDP 0.402439 0.970149
30 44P 0.4 0.928571
31 ICR 0.4 0.821918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MI2; Ligand: PFU; Similar sites found: 71
This union binding pocket(no: 1) in the query (biounit: 3mi2.bio1) has 48 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2BTM PGA 0.01238 0.44359 1.5873
2 1LBF 137 0.007622 0.41141 2.02429
3 2Q3R FMN 0.01416 0.41562 2.15054
4 1PCA VAL 0.04615 0.41348 2.15054
5 2DUR MAN MAN 0.04042 0.40705 2.15054
6 4XP7 FNR 0.02998 0.40294 2.50896
7 3GAY P6T 0.027 0.40238 2.50896
8 4IXH IMP 0.01663 0.40424 2.86738
9 1QPR PPC 0.02472 0.40153 2.86738
10 2B4B B33 0.0469 0.41398 2.92398
11 4UTU LRY 0.001113 0.4847 3.05677
12 4UTW RFW 0.001399 0.47512 3.05677
13 3GLC R5P 0.01626 0.42918 3.22581
14 4ETZ C2E 0.04913 0.40293 3.367
15 2F6U CIT 0.001159 0.50537 3.4188
16 3OVR 5SP 0.001661 0.45208 3.50877
17 4QNW FMN 0.0105 0.41875 3.58423
18 3VKC FPQ 0.002855 0.44479 3.84615
19 1JCM 137 0.004421 0.44648 3.861
20 4V15 PLP 0.01482 0.43128 3.94265
21 2OEM 1AE 0.02367 0.42065 3.94265
22 3WJO IPE 0.04112 0.41998 3.94265
23 1UZH CAP 0.0124 0.41542 3.94265
24 4HN1 TYD 0.01403 0.43645 3.9801
25 1VKF CIT 0.02276 0.42826 4.25532
26 2VDH CAP 0.007613 0.42519 4.28571
27 2V63 CAP 0.008284 0.4235 4.28571
28 2V68 CAP 0.0105 0.42175 4.28571
29 2V67 CAP 0.01188 0.41628 4.28571
30 3P3Z P3Z 0.04604 0.41144 4.30108
31 4YMZ 13P 0.01769 0.43513 4.38247
32 4NAE 1GP 0.0006846 0.5212 4.44444
33 3B0P FMN 0.004898 0.44809 4.6595
34 1Z44 FMN 0.006914 0.44446 4.6595
35 1Z41 FMN 0.009138 0.4346 4.6595
36 1Z42 FMN 0.02876 0.41622 4.6595
37 1RBL CAP 0.006157 0.42639 5.01792
38 5T9C G3P 0.04103 0.41667 5.22388
39 2YPI PGA 0.007938 0.44961 5.26316
40 1M5W DXP 0.01262 0.44767 5.34979
41 3W9Z FMN 0.006228 0.43573 5.37634
42 1UZD CAP 0.009391 0.42099 5.37634
43 1TRD PGH 0.008877 0.44287 5.6
44 5KJW 53C 0.042 0.41731 5.73477
45 5CSS G3P 0.03523 0.41871 5.75221
46 1W8S FBP 0.03221 0.41033 6.08365
47 5VSM 5AD 0.0243 0.40456 6.09319
48 2FKA BEF 0.02389 0.41618 6.20155
49 3EXS 5RP 0.0001372 0.54299 6.33484
50 5EYW PGA 0.01335 0.4418 6.4257
51 3CTL S6P 0.00605 0.43298 6.49351
52 4TO8 FLC 0.01937 0.40915 6.81004
53 2VD9 IN5 0.03436 0.40579 6.81004
54 1SW0 PGA 0.01012 0.4399 6.85484
55 1Q6O LG6 0.00002988 0.55801 6.94444
56 2OMN IPH 0.02649 0.41929 7.52688
57 2FLI DX5 0.001856 0.45339 7.72727
58 4RW3 IPD 0.02798 0.42421 7.8853
59 5TCI MLI 0.01438 0.44536 8.33333
60 4IP7 FLC 0.01272 0.44747 8.60215
61 3TAO PGH 0.01304 0.43815 8.61423
62 3QH2 3NM 0.003583 0.47813 9.04977
63 4EWN 0VR 0.01568 0.4229 9.48617
64 1UJP CIT 0.002197 0.46127 9.5941
65 1IR2 CAP 0.01196 0.41614 10
66 2OO0 PLP 0.01154 0.42955 10.3943
67 1B57 PGH 0.04623 0.40865 10.3943
68 1L5Y BEF 0.0063 0.4546 12.2581
69 5GJO PLP 0.004221 0.45535 12.5448
70 3HRD NIO 0.03531 0.40592 14.375
71 1WDD CAP 0.01136 0.42013 25.7812
Pocket No.: 2; Query (leader) PDB : 3MI2; Ligand: PFU; 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: 3mi2.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Feedback