Receptor
PDB id Resolution Class Description Source Keywords
2QCH 1.95 Å EC: 4.1.1.23 CRYSTAL STRUCTURE OF THE OROTIDINE-5'-MONOPHOSPHATE DECARBOX DOMAIN OF HUMAN UMP SYNTHASE BOUND TO 5-IODO-UMP HOMO SAPIENS UMP SYNTHASE DECARBOXYLASE CATALYTIC PROFICIENCY LYASE
Ref.: STRUCTURES OF THE HUMAN OROTIDINE-5'-MONOPHOSPHATE DECARBOXYLASE SUPPORT A COVALENT MECHANISM AND PROV FRAMEWORK FOR DRUG DESIGN. STRUCTURE V. 16 82 2008
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5IU A:1;
B:3;
 Valid;
Valid;
 none;
none;
 submit data
434.078 C9 H12 I N2 O8 P C1[C@...
IOD A:5;
B:6;
 Invalid;
Invalid;
 none;
none;
 submit data
126.904 I [I-]
UMP A:2;
B:4;
 Valid;
Valid;
 none;
none;
 submit data
308.182 C9 H13 N2 O8 P C1[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: 5IU; Similar ligands found: 60
No: Ligand ECFP6 Tc MDL keys Tc
1 5IU 1 1
2 BRU 0.720588 0.972222
3 UFP 0.705882 0.972222
4 ID2 0.698413 0.863014
5 5HU 0.695652 0.905405
6 TMP 0.695652 0.917808
7 BVP 0.631579 0.931507
8 DU 0.575342 0.929577
9 UMP 0.575342 0.929577
10 TYD 0.564103 0.905405
11 DDN 0.561644 0.929577
12 TTP 0.536585 0.905405
13 TBD 0.493976 0.87013
14 TLO 0.483516 0.857143
15 DC 0.481013 0.866667
16 DCM 0.481013 0.866667
17 DUD 0.463415 0.916667
18 TDX 0.463158 0.857143
19 UMC 0.461538 0.876712
20 DAU 0.458333 0.846154
21 NYM 0.45679 0.893333
22 FDM 0.45679 0.932432
23 QBT 0.455696 0.864865
24 THM 0.452055 0.786667
25 LLT 0.452055 0.786667
26 THP 0.451219 0.90411
27 T46 0.44898 0.846154
28 TRH 0.447917 0.846154
29 3R2 0.447917 0.835443
30 18T 0.447917 0.846154
31 1JB 0.447917 0.846154
32 UC5 0.445783 0.90411
33 ATM 0.44186 0.835443
34 DUT 0.44186 0.916667
35 AHU 0.441558 0.813333
36 T3F 0.438776 0.825
37 T3Q 0.438776 0.825
38 3YN 0.438776 0.846154
39 DWN 0.438776 0.825
40 DUP 0.436782 0.891892
41 DUN 0.435294 0.891892
42 0N2 0.434343 0.814815
43 AKM 0.431373 0.807229
44 0FX 0.43 0.825
45 MMF 0.43 0.825
46 DT DT DT DT DT 0.428571 0.881579
47 QDM 0.421569 0.814815
48 0DN 0.421053 0.797297
49 8OG 0.420455 0.807229
50 BVD 0.417722 0.8
51 1YF 0.417476 0.835443
52 JHZ 0.417476 0.804878
53 FNF 0.417476 0.835443
54 DT DT PST 0.415842 0.822785
55 DUT MG 0.41573 0.853333
56 5BU 0.414634 0.891892
57 4TG 0.413462 0.835443
58 5FU 0.407407 0.891892
59 T3S 0.404762 0.734177
60 DU DU DU DU BRU DU DU 0.401869 0.906667
Ligand no: 2; Ligand: UMP; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUT MG 0.684932 0.914286
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
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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