Receptor
PDB id Resolution Class Description Source Keywords
3G1F 2.5 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM C OMPLEXED WITH 5,6-DIHYDROOROTIDINE 5'-MONOPHOSPHATE METHANOTHERMOBACTER THERMAUTOTROPHICUSSTR. DELTA H OROTIDINE 5-prime -MONOPHOSPHATE DECARBOXYLASE H2-OMP CRYSTAL STRUCTURE DECARBOXYLASE PYRIMIDINE BIOSYNTHESIS LYASE
Ref.: MECHANISM OF THE OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE-CATALYZED REACTION: EVIDENCE FOR SUBSTRATE DESTABILIZATION. BIOCHEMISTRY V. 48 5518 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
2OM A:229;
B:229;
C:229;
D:229;
E:229;
F:229;
G:229;
H:229;
I:229;
J:229;
K:229;
L:229;
M:229;
 Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 Ki = 100 uM
370.207 C10 H15 N2 O11 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: 2OM; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 2OM 1 1
2 BMQ 0.506849 0.984615
3 H2U 0.5 0.955224
4 OMP 0.475 0.926471
5 U6M 0.461538 0.898551
6 6AU 0.45679 0.898551
7 JW5 0.455696 0.913043
8 UP6 0.454545 0.871429
9 S5P 0.448718 0.837838
10 BMP 0.448718 0.885714
11 NUP 0.443038 0.861111
12 O7E 0.44186 0.9
13 FNU 0.4375 0.815789
14 U5P 0.435897 0.925373
15 U 0.435897 0.925373
16 O7M 0.435294 0.9
17 5FU 0.43038 0.861111
18 6CN 0.421687 0.873239
19 ICR 0.419753 0.84507
20 5BU 0.419753 0.861111
21 8GM 0.418605 0.794872
22 CNU 0.404762 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: 2OM; Similar ligands found: 24
No: Ligand Similarity coefficient
1 C 0.9062
2 C5P 0.9033
3 PSU 0.8880
4 DUS 0.8868
5 TMP 0.8831
6 FN5 0.8827
7 UMP 0.8826
8 16B 0.8805
9 AMP 0.8774
10 5IU 0.8766
11 CAR 0.8751
12 FAI 0.8734
13 IMP 0.8730
14 TKW 0.8721
15 JLN 0.8721
16 UMC 0.8703
17 G 0.8678
18 5GP 0.8656
19 DOC 0.8653
20 PFU 0.8649
21 DC 0.8615
22 DCM 0.8593
23 XMP 0.8585
24 8BR 0.8556
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
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