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 = 0.00000079 M 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 = 0.00000079 M 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 = 0.00000079 M 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 (2D)
Ligand no: 1; Ligand: 5IU; Similar ligands found: 62
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 TMP 0.695652 0.917808
6 5HU 0.695652 0.905405
7 BVP 0.631579 0.931507
8 UMP 0.575342 0.929577
9 DU 0.575342 0.929577
10 TYD 0.564103 0.905405
11 DDN 0.561644 0.929577
12 TTP 0.536585 0.905405
13 TTP MG 0.511905 0.878378
14 TBD 0.493976 0.87013
15 TLO 0.483516 0.857143
16 5CM 0.481481 0.857143
17 DC 0.481013 0.866667
18 DCM 0.481013 0.866667
19 DUD 0.463415 0.916667
20 TDX 0.463158 0.857143
21 9RC 0.462366 0.776471
22 UMC 0.461538 0.876712
23 DAU 0.458333 0.846154
24 FDM 0.45679 0.932432
25 NYM 0.45679 0.893333
26 QBT 0.455696 0.864865
27 THM 0.452055 0.786667
28 LLT 0.452055 0.786667
29 THP 0.451219 0.90411
30 T46 0.44898 0.846154
31 TRH 0.447917 0.846154
32 18T 0.447917 0.846154
33 3R2 0.447917 0.835443
34 1JB 0.447917 0.846154
35 UC5 0.445783 0.90411
36 ATM 0.44186 0.835443
37 DUT 0.44186 0.916667
38 AHU 0.441558 0.813333
39 DWN 0.438776 0.825
40 3YN 0.438776 0.846154
41 T3Q 0.438776 0.825
42 T3F 0.438776 0.825
43 DUP 0.436782 0.891892
44 DUN 0.435294 0.891892
45 0N2 0.434343 0.814815
46 AKM 0.431373 0.807229
47 0FX 0.43 0.825
48 MMF 0.43 0.825
49 QDM 0.421569 0.814815
50 0DN 0.421053 0.797297
51 DUT MG 0.420455 0.888889
52 8OG 0.420455 0.807229
53 BVD 0.417722 0.8
54 JHZ 0.417476 0.804878
55 FNF 0.417476 0.835443
56 1YF 0.417476 0.835443
57 5BU 0.414634 0.891892
58 4TG 0.413462 0.835443
59 3DR DT DT DT DT DT 0.413462 0.844156
60 5FU 0.407407 0.891892
61 T3S 0.404762 0.734177
62 DU DU DU DU BRU DU DU 0.401869 0.906667
Ligand no: 2; Ligand: UMP; Similar ligands found: 59
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 DUT MG 0.694444 0.955224
9 DUS 0.692308 0.853333
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 DC 0.561644 0.928571
20 DCM 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U 0.527778 0.911765
24 U5P 0.527778 0.911765
25 DDU 0.523077 0.753623
26 UMC 0.520548 0.941176
27 QBT 0.493333 0.927536
28 DUA 0.487805 0.783784
29 DU3 0.487805 0.780822
30 5CM 0.481013 0.890411
31 DU4 0.47619 0.76
32 TYD 0.469136 0.942857
33 YYY 0.451219 0.915493
34 UDP 0.45 0.898551
35 TTP 0.447059 0.942857
36 8OG 0.435294 0.835443
37 U2P 0.434211 0.884058
38 U3P 0.434211 0.897059
39 UA3 0.434211 0.897059
40 UTP 0.433735 0.898551
41 44P 0.43038 0.914286
42 DCP 0.430233 0.915493
43 U5F 0.428571 0.898551
44 0KX 0.425287 0.890411
45 DUX 0.411765 0.756757
46 2KH 0.411765 0.873239
47 UMF 0.410256 0.84507
48 UPU 0.409091 0.871429
49 F6G 0.409091 0.876712
50 TTP MG 0.409091 0.914286
51 139 0.409091 0.8
52 URI 0.408451 0.771429
53 TBD 0.406977 0.90411
54 DU DU DU DU BRU DA DU 0.40625 0.771084
55 PUA 0.405172 0.833333
56 UNP 0.402299 0.873239
57 UAD 0.4 0.873239
58 PUP 0.4 0.955882
59 UDX 0.4 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: 5IU; Similar ligands found: 78
No: Ligand Similarity coefficient
1 CNU 0.9679
2 TKW 0.9637
3 2DT 0.9587
4 D4M 0.9587
5 O7E 0.9587
6 U5P 0.9586
7 DUS 0.9549
8 UP6 0.9548
9 U 0.9531
10 H2U 0.9520
11 C 0.9455
12 9L3 0.9444
13 FNU 0.9442
14 DOC 0.9423
15 BMP 0.9411
16 C5P 0.9402
17 NUP 0.9394
18 5HM 0.9358
19 BMQ 0.9358
20 DA 0.9342
21 CH 0.9321
22 PSU 0.9307
23 U6M 0.9306
24 D5M 0.9294
25 CAR 0.9288
26 IMP 0.9288
27 AMP 0.9287
28 DI 0.9284
29 PFU 0.9270
30 S5P 0.9269
31 AS 0.9246
32 16B 0.9241
33 DGP 0.9217
34 DG 0.9217
35 5GP 0.9207
36 8OP 0.9192
37 FN5 0.9192
38 IRP 0.9175
39 NIA 0.9165
40 JW5 0.9095
41 8GM 0.9080
42 FMP 0.9071
43 C2R 0.9065
44 NMN 0.9061
45 AIR 0.9061
46 6CN 0.9060
47 AMZ 0.9058
48 NCN 0.9049
49 G 0.9044
50 XMP 0.9039
51 U4S 0.9024
52 71V 0.9013
53 6MA 0.8986
54 93A 0.8976
55 8BR 0.8974
56 IMU 0.8953
57 NEC 0.8943
58 TXS 0.8905
59 7D5 0.8902
60 N5O 0.8881
61 J7C 0.8861
62 U2S 0.8835
63 103 0.8834
64 2OM 0.8766
65 6AU 0.8763
66 2GE 0.8762
67 OMP 0.8721
68 K8W 0.8719
69 MTA 0.8689
70 MTH 0.8675
71 PZB 0.8673
72 4HG 0.8650
73 IRN 0.8646
74 5BT 0.8626
75 MTE 0.8613
76 MTM 0.8606
77 KU1 0.8591
78 GAR 0.8542
Ligand no: 2; Ligand: UMP; Similar ligands found: 228
No: Ligand Similarity coefficient
1 O7E 0.9818
2 UP6 0.9811
3 CAR 0.9786
4 C5P 0.9776
5 H2U 0.9734
6 DOC 0.9731
7 FN5 0.9709
8 CH 0.9709
9 C 0.9709
10 BMP 0.9657
11 5FU 0.9654
12 PSU 0.9649
13 NUP 0.9639
14 FDM 0.9637
15 NYM 0.9607
16 9L3 0.9600
17 DI 0.9588
18 16B 0.9581
19 DA 0.9576
20 D5M 0.9575
21 5BU 0.9565
22 AS 0.9552
23 BMQ 0.9550
24 TKW 0.9540
25 D4M 0.9520
26 2DT 0.9518
27 U6M 0.9472
28 FNU 0.9456
29 PFU 0.9436
30 S5P 0.9389
31 AMP 0.9373
32 6MA 0.9373
33 NIA 0.9372
34 AMZ 0.9352
35 C2R 0.9339
36 U4S 0.9318
37 IMP 0.9317
38 JW5 0.9289
39 IRP 0.9280
40 AIR 0.9272
41 T3S 0.9262
42 6CN 0.9250
43 FMP 0.9226
44 CNU 0.9218
45 8BR 0.9207
46 8OP 0.9197
47 CDP 0.9193
48 6SY 0.9172
49 ATM 0.9158
50 U2S 0.9156
51 VIB 0.9154
52 NMN 0.9150
53 DGP 0.9149
54 DG 0.9149
55 5HM 0.9140
56 NCN 0.9130
57 7D5 0.9123
58 U1S 0.9118
59 U3S 0.9118
60 CC7 0.9117
61 GAR 0.9071
62 0RA 0.9063
63 103 0.9062
64 TXS 0.9056
65 2GE 0.9052
66 27M 0.9047
67 5QT 0.9046
68 MTE 0.9036
69 ZAS 0.9035
70 M2T 0.9033
71 5GP 0.9002
72 G 0.9002
73 71V 0.8999
74 AOC 0.8989
75 FT1 0.8985
76 XMP 0.8981
77 6AU 0.8980
78 6OG 0.8979
79 AZU 0.8977
80 N5O 0.8973
81 OMP 0.8973
82 IRN 0.8969
83 IGP 0.8969
84 3RC 0.8965
85 CMP 0.8957
86 T7O 0.8956
87 QTJ 0.8953
88 HDI 0.8952
89 IMU 0.8944
90 FX5 0.8942
91 UN3 0.8936
92 K4T 0.8926
93 VKE 0.8917
94 NEC 0.8912
95 A3N 0.8912
96 S0J 0.8894
97 8GM 0.8889
98 FT2 0.8886
99 2JP 0.8880
100 M8Q 0.8875
101 FAI 0.8859
102 43J 0.8854
103 2T4 0.8854
104 K8W 0.8849
105 90J 0.8849
106 PZB 0.8844
107 6PG 0.8843
108 GA6 0.8843
109 2OM 0.8826
110 9RK 0.8826
111 RP1 0.8826
112 DRM 0.8822
113 43F 0.8816
114 90G 0.8810
115 G3P IDM 0.8805
116 JVD 0.8804
117 6JD 0.8804
118 GG5 0.8801
119 0SX 0.8797
120 T3P 0.8797
121 43G 0.8796
122 QTK 0.8794
123 MTA 0.8790
124 MTI 0.8789
125 U55 0.8784
126 MTH 0.8783
127 SP1 0.8783
128 ML2 0.8775
129 34L 0.8773
130 PB2 0.8764
131 20P 0.8761
132 IWH 0.8750
133 TWB 0.8748
134 1CE 0.8747
135 IPJ 0.8746
136 QTV 0.8744
137 OAQ 0.8742
138 42M 0.8740
139 TDH 0.8738
140 S1D 0.8737
141 101 0.8735
142 JSX 0.8733
143 SNJ 0.8731
144 MTM 0.8731
145 22T 0.8728
146 HDU 0.8728
147 WDW 0.8726
148 KU1 0.8726
149 15I 0.8725
150 TCL 0.8725
151 L02 0.8724
152 QTD 0.8722
153 SIJ 0.8716
154 HMK 0.8715
155 N8M 0.8713
156 PCG 0.8712
157 S45 0.8711
158 O7M 0.8709
159 9W8 0.8706
160 BHF 0.8706
161 JON 0.8698
162 0QX 0.8693
163 9XZ 0.8689
164 VBC 0.8686
165 4BH 0.8682
166 UUL 0.8671
167 69W 0.8664
168 F91 0.8662
169 O8M 0.8659
170 1Q2 0.8654
171 6JJ 0.8652
172 DZJ 0.8650
173 97K 0.8649
174 AZZ 0.8647
175 W1G 0.8645
176 C5Q 0.8642
177 4X2 0.8639
178 9HK 0.8639
179 49K 0.8637
180 I5A 0.8635
181 BL6 0.8634
182 583 0.8634
183 5KN 0.8629
184 8RK 0.8629
185 IPL 0.8629
186 SYD 0.8628
187 EUB 0.8623
188 3N4 0.8621
189 SJR 0.8619
190 BIT 0.8618
191 Q7U 0.8616
192 FBP 0.8616
193 613 0.8615
194 GO1 0.8615
195 H3W 0.8613
196 122 0.8606
197 35G 0.8606
198 CTN 0.8605
199 58L 0.8604
200 I22 0.8603
201 F5A 0.8602
202 JHY 0.8601
203 0QR 0.8600
204 RF2 0.8599
205 HVE 0.8596
206 1ER 0.8589
207 62D 0.8584
208 DCZ 0.8582
209 UN9 0.8570
210 THP 0.8570
211 MBY 0.8569
212 D25 0.8567
213 CAP 0.8564
214 121 0.8559
215 WLL 0.8551
216 WDT 0.8550
217 Z3R 0.8548
218 35K 0.8546
219 5WS 0.8542
220 CLM 0.8535
221 AFP 0.8535
222 JP5 0.8535
223 H48 0.8533
224 13F 0.8532
225 RGK 0.8530
226 EFX 0.8518
227 TVC 0.8518
228 6QT 0.8507
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3MI2; Ligand: PFU; 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: 3mi2.bio1) has 48 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3MI2; Ligand: PFU; 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: 3mi2.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
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