Receptor
PDB id Resolution Class Description Source Keywords
3EX1 1.4 Å EC: 4.1.1.23 HUMAN OROTIDYL-5'-MONOPHOSPHATE DECARBOXYLASE SOAKED WITH 6- CONVERTED TO UMP 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
6CN B:481;
Valid;
none;
submit data
349.191 C10 H12 N3 O9 P C1=C(...
GOL A:482;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
U5P A:481;
Valid;
none;
submit data
324.181 C9 H13 N2 O9 P C1=CN...
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: 6CN; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 6CN 1 1
2 JW5 0.647887 0.928571
3 BMP 0.642857 0.928571
4 S5P 0.642857 0.878378
5 U6M 0.633803 0.942029
6 NUP 0.633803 0.902778
7 6AU 0.6 0.942029
8 OMP 0.6 0.942029
9 FNU 0.581081 0.855263
10 O7M 0.56962 0.915493
11 O7E 0.555556 0.915493
12 BMQ 0.534247 0.885714
13 8OP 0.5 0.828947
14 CNU 0.5 0.971014
15 U5P 0.480519 0.941176
16 UP6 0.480519 0.887324
17 8GM 0.47619 0.881579
18 5FU 0.474359 0.902778
19 H2U 0.448718 0.861111
20 5BU 0.444444 0.902778
21 2OM 0.421687 0.873239
22 8OD 0.408602 0.818182
Ligand no: 2; Ligand: U5P; Similar ligands found: 120
No: Ligand ECFP6 Tc MDL keys Tc
1 U5P 1 1
2 44P 0.790323 0.941176
3 UDP 0.78125 0.984615
4 UTP 0.746269 0.984615
5 2KH 0.735294 0.955224
6 UDP UDP 0.727273 0.953846
7 UPU 0.694444 0.954545
8 UNP 0.690141 0.955224
9 URM 0.662338 0.913043
10 660 0.662338 0.913043
11 URI 0.661017 0.848485
12 U 0.661017 0.848485
13 UFM 0.641026 0.926471
14 GDU 0.641026 0.926471
15 UPG 0.641026 0.926471
16 GUD 0.641026 0.926471
17 U2F 0.6375 0.875
18 UPF 0.6375 0.875
19 Y6W 0.632911 0.875
20 UDH 0.628205 0.851351
21 UPP 0.628205 0.926471
22 UFG 0.617284 0.875
23 CJB 0.603175 0.80597
24 UDX 0.597561 0.926471
25 UAD 0.597561 0.926471
26 UDP GAL 0.597561 0.898551
27 3UC 0.588235 0.875
28 U U 0.585366 0.969697
29 UGB 0.583333 0.940298
30 USQ 0.583333 0.807692
31 UGA 0.583333 0.940298
32 5FU 0.57971 0.927536
33 G3N 0.576471 0.9
34 U3P 0.573529 0.953846
35 UA3 0.573529 0.953846
36 C 0.571429 0.941176
37 CH 0.571429 0.926471
38 CAR 0.571429 0.941176
39 C5P 0.571429 0.941176
40 UDM 0.568182 0.9
41 5BU 0.56338 0.927536
42 U4S 0.557143 0.763889
43 UD1 0.555556 0.913043
44 UD2 0.555556 0.913043
45 CSQ 0.550562 0.863014
46 CSV 0.550562 0.863014
47 U3S 0.541667 0.763889
48 U2S 0.541667 0.777778
49 CNU 0.540541 0.941176
50 S5P 0.535211 0.901408
51 16B 0.534247 0.901408
52 U2P 0.528571 0.939394
53 DU 0.527778 0.911765
54 UMP 0.527778 0.911765
55 HP7 0.526882 0.926471
56 UD7 0.526882 0.913043
57 MJZ 0.521277 0.9
58 UP6 0.521127 0.884058
59 UD4 0.515789 0.9
60 HWU 0.515789 0.887324
61 12V 0.515789 0.887324
62 BMP 0.513889 0.955224
63 UP5 0.510204 0.84
64 DKX 0.507246 0.732394
65 U6M 0.506849 0.969697
66 NUP 0.506849 0.927536
67 IUG 0.505155 0.797468
68 EPZ 0.5 0.9
69 U1S 0.5 0.76
70 JW5 0.5 0.955224
71 4TC 0.5 0.818182
72 EPU 0.49505 0.887324
73 A U 0.49505 0.815789
74 EEB 0.49505 0.887324
75 UDZ 0.494949 0.84
76 H2U 0.486111 0.911765
77 6AU 0.480519 0.969697
78 OMP 0.480519 0.969697
79 6CN 0.480519 0.941176
80 TKW 0.48 0.927536
81 UMF 0.479452 0.869565
82 UUA 0.477612 0.757576
83 U U U U 0.476744 0.954545
84 BMQ 0.472222 0.939394
85 PUP 0.47191 0.926471
86 5HM 0.467532 0.888889
87 O7E 0.463415 0.941176
88 ICR 0.460526 0.830986
89 UMA 0.458716 0.9
90 O7M 0.45679 0.941176
91 UC5 0.455696 0.885714
92 UTP U U U 0.454545 0.909091
93 CDP 0.45 0.927536
94 2TU 0.449275 0.760563
95 FNU 0.441558 0.876712
96 2QR 0.439655 0.810127
97 N3E 0.4375 0.743243
98 DUD 0.4375 0.898551
99 2OM 0.435897 0.925373
100 U22 0.434783 0.777778
101 U21 0.434783 0.797468
102 U20 0.434783 0.797468
103 DUT 0.433735 0.898551
104 CTP 0.433735 0.927536
105 8OP 0.428571 0.849315
106 8GM 0.421687 0.853333
107 5GW 0.420455 0.927536
108 U A A U 0.418803 0.853333
109 4RA 0.414634 0.842105
110 DUP 0.411765 0.873239
111 DUN 0.409639 0.873239
112 CDP MG 0.409639 0.861111
113 UD0 0.408 0.831169
114 UVC 0.407895 0.842857
115 UM3 0.407895 0.897059
116 C5G 0.404255 0.875
117 UPA 0.401869 0.828947
118 A U C C 0.401639 0.794872
119 A G U 0.4 0.7875
120 UAG 0.4 0.851351
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
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