Receptor
PDB id Resolution Class Description Source Keywords
3WJY 1.72 Å EC: 4.1.1.23 OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE K72A MUTANT FROM M. THERMOAUTOTROPHICUS COMPLEXED WITH 6-AMINO-UMP METHANOTHERMOBACTER THERMAUTOTROPHICUSORGANISM_TAXID: 187420 PROTEIN-LIGAND COMPLEX TIM BARREL DECARBOXYLASE PYRIMIDINBIOSYNTHESIS LYASE
Ref.: SUBSTRATE DISTORTION CONTRIBUTES TO THE CATALYSIS O OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE. J.AM.CHEM.SOC. V. 135 17432 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:302;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
NUP A:301;
 Valid;
 none;
 submit data
339.196 C9 H14 N3 O9 P C1=C(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1LOR 1.6 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE COMPLEXED WI METHANOTHERMOBACTER THERMAUTOTROPHICUSORGANISM_TAXID: 145262 TIM BARREL LYASE
Ref.: CRYSTAL STRUCTURES OF INHIBITOR COMPLEXES REVEAL AN ALTERNATE BINDING MODE IN OROTIDINE-5'-MONOPHOSPHAT DECARBOXYLASE. J.BIOL.CHEM. V. 277 28080 2002
Members (64)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3V1P - BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3G24 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 1LOS Ki = 64 nM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
4 3NQG - BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 3NQD - BMP C9 H13 N2 O10 P C1=C(N(C(=....
6 3LHY - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
7 3LTS - BMP C9 H13 N2 O10 P C1=C(N(C(=....
8 3G1X - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1KM0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
10 3WJX Ki = 840 nM NUP C9 H14 N3 O9 P C1=C(N(C(=....
11 1LP6 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
12 3LLF - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
13 3G1D - U C9 H13 N2 O9 P C1=CN(C(=O....
14 3LHT - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
15 3NQE - BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3WK1 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
17 1KM3 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 3LV5 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
19 3LHW - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
20 1KM1 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
21 3LV6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
22 3G1F Ki = 100 uM 2OM C10 H15 N2 O11 P C1[C@@H](N....
23 3M1Z - BMP C9 H13 N2 O10 P C1=C(N(C(=....
24 3W07 Kd = 0.00042 M U5P C9 H13 N2 O9 P C1=CN(C(=O....
25 3PBU - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
26 1LOR Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
27 3NQC - BMP C9 H13 N2 O10 P C1=C(N(C(=....
28 3LHZ - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
29 1KM2 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
30 3PC0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
31 3WK2 - O7M C11 H15 N2 O11 P COC(=O)C1=....
32 3PBY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
33 3LI0 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
34 1KM4 - U C9 H13 N2 O9 P C1=CN(C(=O....
35 3LHU - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
36 3G22 - U C9 H13 N2 O9 P C1=CN(C(=O....
37 2ZZ1 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
38 4GC4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
39 4FX8 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
40 3LI1 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
41 1KLY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
42 3G1V - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
43 1DVJ Ki = 0.51 mM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
44 3LTY - BMP C9 H13 N2 O10 P C1=C(N(C(=....
45 3WJY - NUP C9 H14 N3 O9 P C1=C(N(C(=....
46 1KM5 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
47 3PBW - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
48 3WK0 - O7M C11 H15 N2 O11 P COC(=O)C1=....
49 2ZZ7 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
50 3NQM - BMP C9 H13 N2 O10 P C1=C(N(C(=....
51 4FX6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
52 3G1H - H2U C9 H15 N2 O9 P C1CN(C(=O)....
53 4FXR - BMP C9 H13 N2 O10 P C1=C(N(C(=....
54 1KM6 - OMP C10 H13 N2 O11 P C1=C(N(C(=....
55 3LTP - BMP C9 H13 N2 O10 P C1=C(N(C(=....
56 3WJW Ki = 134 uM U6M C10 H15 N2 O9 P CC1=CC(=O)....
57 3LLD - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
58 3NQF - BMP C9 H13 N2 O10 P C1=C(N(C(=....
59 1LOQ Ki = 0.2 mM U C9 H13 N2 O9 P C1=CN(C(=O....
60 3G1A - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
61 3PBV - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
62 3WK3 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
63 3LHV - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
64 1LOL Ki = 0.41 uM XMP C10 H14 N4 O9 P c1[nH+]c2c....
70% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3V1P - BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3G24 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 1LOS Ki = 64 nM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
4 3NQG - BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 3NQD - BMP C9 H13 N2 O10 P C1=C(N(C(=....
6 3LHY - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
7 3LTS - BMP C9 H13 N2 O10 P C1=C(N(C(=....
8 3G1X - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1KM0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
10 3WJX Ki = 840 nM NUP C9 H14 N3 O9 P C1=C(N(C(=....
11 1LP6 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
12 3LLF - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
13 3G1D - U C9 H13 N2 O9 P C1=CN(C(=O....
14 3LHT - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
15 3NQE - BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3WK1 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
17 1KM3 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 3LV5 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
19 3LHW - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
20 1KM1 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
21 3LV6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
22 3G1F Ki = 100 uM 2OM C10 H15 N2 O11 P C1[C@@H](N....
23 3M1Z - BMP C9 H13 N2 O10 P C1=C(N(C(=....
24 3W07 Kd = 0.00042 M U5P C9 H13 N2 O9 P C1=CN(C(=O....
25 3PBU - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
26 1LOR Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
27 3NQC - BMP C9 H13 N2 O10 P C1=C(N(C(=....
28 3LHZ - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
29 1KM2 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
30 3PC0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
31 3WK2 - O7M C11 H15 N2 O11 P COC(=O)C1=....
32 3PBY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
33 3LI0 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
34 1KM4 - U C9 H13 N2 O9 P C1=CN(C(=O....
35 3LHU - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
36 3G22 - U C9 H13 N2 O9 P C1=CN(C(=O....
37 2ZZ1 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
38 4GC4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
39 4FX8 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
40 3LI1 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
41 1KLY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
42 3G1V - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
43 1DVJ Ki = 0.51 mM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
44 3LTY - BMP C9 H13 N2 O10 P C1=C(N(C(=....
45 3WJY - NUP C9 H14 N3 O9 P C1=C(N(C(=....
46 1KM5 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
47 3PBW - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
48 3WK0 - O7M C11 H15 N2 O11 P COC(=O)C1=....
49 2ZZ7 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
50 3NQM - BMP C9 H13 N2 O10 P C1=C(N(C(=....
51 4FX6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
52 3G1H - H2U C9 H15 N2 O9 P C1CN(C(=O)....
53 4FXR - BMP C9 H13 N2 O10 P C1=C(N(C(=....
54 1KM6 - OMP C10 H13 N2 O11 P C1=C(N(C(=....
55 3LTP - BMP C9 H13 N2 O10 P C1=C(N(C(=....
56 3WJW Ki = 134 uM U6M C10 H15 N2 O9 P CC1=CC(=O)....
57 3LLD - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
58 3NQF - BMP C9 H13 N2 O10 P C1=C(N(C(=....
59 1LOQ Ki = 0.2 mM U C9 H13 N2 O9 P C1=CN(C(=O....
60 3G1A - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
61 3PBV - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
62 3WK3 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
63 3LHV - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
64 1LOL Ki = 0.41 uM XMP C10 H14 N4 O9 P c1[nH+]c2c....
65 2ZZ5 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
66 1KLZ - U C9 H13 N2 O9 P C1=CN(C(=O....
67 3WJZ - NUP C9 H14 N3 O9 P C1=C(N(C(=....
68 1X1Z Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
69 2ZZ2 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
50% Homology Family (69)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 3V1P - BMP C9 H13 N2 O10 P C1=C(N(C(=....
2 3G24 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
3 1LOS Ki = 64 nM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
4 3NQG - BMP C9 H13 N2 O10 P C1=C(N(C(=....
5 3NQD - BMP C9 H13 N2 O10 P C1=C(N(C(=....
6 3LHY - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
7 3LTS - BMP C9 H13 N2 O10 P C1=C(N(C(=....
8 3G1X - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1KM0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
10 3WJX Ki = 840 nM NUP C9 H14 N3 O9 P C1=C(N(C(=....
11 1LP6 - C5P C9 H14 N3 O8 P C1=CN(C(=O....
12 3LLF - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
13 3G1D - U C9 H13 N2 O9 P C1=CN(C(=O....
14 3LHT - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
15 3NQE - BMP C9 H13 N2 O10 P C1=C(N(C(=....
16 3WK1 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
17 1KM3 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
18 3LV5 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
19 3LHW - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
20 1KM1 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
21 3LV6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
22 3G1F Ki = 100 uM 2OM C10 H15 N2 O11 P C1[C@@H](N....
23 3M1Z - BMP C9 H13 N2 O10 P C1=C(N(C(=....
24 3W07 Kd = 0.00042 M U5P C9 H13 N2 O9 P C1=CN(C(=O....
25 3PBU - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
26 1LOR Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
27 3NQC - BMP C9 H13 N2 O10 P C1=C(N(C(=....
28 3LHZ - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
29 1KM2 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
30 3PC0 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
31 3WK2 - O7M C11 H15 N2 O11 P COC(=O)C1=....
32 3PBY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
33 3LI0 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
34 1KM4 - U C9 H13 N2 O9 P C1=CN(C(=O....
35 3LHU - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
36 3G22 - U C9 H13 N2 O9 P C1=CN(C(=O....
37 2ZZ1 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
38 4GC4 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
39 4FX8 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
40 3LI1 - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
41 1KLY - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
42 3G1V - 5FU C9 H12 F N2 O9 P C1=C(C(=O)....
43 1DVJ Ki = 0.51 mM UP6 C8 H12 N3 O9 P C1=NN(C(=O....
44 3LTY - BMP C9 H13 N2 O10 P C1=C(N(C(=....
45 3WJY - NUP C9 H14 N3 O9 P C1=C(N(C(=....
46 1KM5 - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
47 3PBW - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
48 3WK0 - O7M C11 H15 N2 O11 P COC(=O)C1=....
49 2ZZ7 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
50 3NQM - BMP C9 H13 N2 O10 P C1=C(N(C(=....
51 4FX6 - BMP C9 H13 N2 O10 P C1=C(N(C(=....
52 3G1H - H2U C9 H15 N2 O9 P C1CN(C(=O)....
53 4FXR - BMP C9 H13 N2 O10 P C1=C(N(C(=....
54 1KM6 - OMP C10 H13 N2 O11 P C1=C(N(C(=....
55 3LTP - BMP C9 H13 N2 O10 P C1=C(N(C(=....
56 3WJW Ki = 134 uM U6M C10 H15 N2 O9 P CC1=CC(=O)....
57 3LLD - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
58 3NQF - BMP C9 H13 N2 O10 P C1=C(N(C(=....
59 1LOQ Ki = 0.2 mM U C9 H13 N2 O9 P C1=CN(C(=O....
60 3G1A - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
61 3PBV - UP6 C8 H12 N3 O9 P C1=NN(C(=O....
62 3WK3 - O7E C12 H17 N2 O11 P CCOC(=O)C1....
63 3LHV - BMQ C9 H13 N2 O10 P C1C(=O)NC(....
64 1LOL Ki = 0.41 uM XMP C10 H14 N4 O9 P c1[nH+]c2c....
65 2ZZ5 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
66 1KLZ - U C9 H13 N2 O9 P C1=CN(C(=O....
67 3WJZ - NUP C9 H14 N3 O9 P C1=C(N(C(=....
68 1X1Z Ki = 8.8 pM BMP C9 H13 N2 O10 P C1=C(N(C(=....
69 2ZZ2 - 6CN C10 H12 N3 O9 P C1=C(N(C(=....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NUP; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 NUP 1 1
2 S5P 0.681818 0.917808
3 BMP 0.681818 0.971014
4 U6M 0.671642 0.928571
5 JW5 0.661765 0.915493
6 6AU 0.633803 0.928571
7 6CN 0.633803 0.902778
8 OMP 0.633803 0.928571
9 O7M 0.6 0.902778
10 O7E 0.584416 0.902778
11 FNU 0.569444 0.945205
12 BMQ 0.565217 0.873239
13 8OP 0.544304 0.842105
14 8GM 0.518987 0.894737
15 UP6 0.506849 0.824324
16 U 0.506849 0.927536
17 U5P 0.506849 0.927536
18 H2U 0.493151 0.849315
19 5FU 0.460526 0.890411
20 5BU 0.448718 0.890411
21 8OD 0.443182 0.855263
22 2OM 0.443038 0.861111
23 CAR 0.435897 0.929577
24 C 0.435897 0.929577
25 C5P 0.435897 0.929577
26 CNU 0.432099 0.902778
27 TKW 0.43038 0.943662
28 H6Y 0.428571 0.855263
29 5HM 0.419753 0.931507
30 G8D 0.41573 0.907895
31 8GT 0.406593 0.907895
Similar Ligands (3D)
Ligand no: 1; Ligand: NUP; Similar ligands found: 68
No: Ligand Similarity coefficient
1 UMP 0.9639
2 PSU 0.9585
3 CH 0.9571
4 DUS 0.9558
5 PFU 0.9467
6 UMC 0.9419
7 DC 0.9406
8 DCM 0.9406
9 DU 0.9400
10 5IU 0.9394
11 16B 0.9392
12 TMP 0.9391
13 QBT 0.9391
14 C2R 0.9377
15 BRU 0.9350
16 UFP 0.9329
17 5CM 0.9319
18 FN5 0.9303
19 DOC 0.9301
20 FDM 0.9278
21 DDN 0.9275
22 IMP 0.9272
23 NIA 0.9250
24 AMP 0.9238
25 U4S 0.9214
26 AMZ 0.9205
27 AIR 0.9165
28 D4M 0.9165
29 2DT 0.9165
30 IRP 0.9153
31 9L3 0.9135
32 NYM 0.9134
33 FMP 0.9118
34 DA 0.9107
35 D5M 0.9107
36 AS 0.9096
37 6MZ 0.9082
38 8BR 0.9078
39 N5O 0.9042
40 G 0.9005
41 T3S 0.8997
42 NEC 0.8979
43 U1S 0.8974
44 U3S 0.8957
45 6MA 0.8953
46 5GP 0.8946
47 Z8B 0.8929
48 U2S 0.8923
49 A3N 0.8919
50 XMP 0.8857
51 O8M 0.8854
52 IRN 0.8836
53 IMU 0.8832
54 ATM 0.8810
55 FAI 0.8804
56 PZB 0.8775
57 7D5 0.8768
58 J7C 0.8750
59 6RE 0.8750
60 8OG 0.8736
61 GAR 0.8695
62 MTE 0.8692
63 MTA 0.8686
64 NCN 0.8672
65 UDP 0.8671
66 TXS 0.8645
67 NMN 0.8628
68 2GE 0.8610
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1LOR; Ligand: BMP; 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: 1lor.bio1) has 58 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1LOR; Ligand: BMP; 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: 1lor.bio1) has 58 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback