Receptor
PDB id Resolution Class Description Source Keywords
1O25 2.4 Å EC: 2.1.1.148 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROT (TM0449) FROM THERMOTOGA MARITIMA WITH DUMP AT 2.4 A RESOLU THERMOTOGA MARITIMA TM0449 THYMIDYLATE SYNTHASE COMPLEMENTING PROTEIN STRUCTURGENOMICS JCSG JOINT CENTER FOR STRUCTURAL GENOMICS PSI STRUCTURE INITIATIVE TRANSFERASE
Ref.: FUNCTIONAL ANALYSIS OF SUBSTRATE AND COFACTOR COMPL STRUCTURES OF A THYMIDYLATE SYNTHASE-COMPLEMENTING STRUCTURE V. 11 677 2003
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UMP A:603;
B:608;
C:613;
D:618;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
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
5IOR 1.95 Å EC: 2.1.1.148 FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE IN COMPLEX WITH FAD AN DEOXYURIDINE-5'-MONOSULFATE THERMOTOGA MARITIMA (STRAIN ATCC 43589DSM 3109 / JCM 10099) FAD-DEPENDENT NUCLEOTIDE BIOSYNTHESIS REDUCTIVE METHYLATIOTRANSFERASE
Ref.: DEPROTONATIONS IN THE REACTION OF FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE. BIOCHEMISTRY V. 55 3261 2016
Members (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3G4A - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 4KAT - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
3 1O2B - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4GTL - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5IOT Kd = 109 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
6 5IOQ Kd = 78 uM DUR C9 H12 N2 O5 C1[C@@H]([....
7 4GTA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 1O2A - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 4KAR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 1O29 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
11 4GTB - D16 C21 H22 N4 O6 S CC1=NC(=O)....
12 4GTF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 3N0C - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 4GTD - UMP C9 H13 N2 O8 P C1[C@@H]([....
15 5IOR Kd = 0.17 uM DUS C9 H12 N2 O8 S C1[C@@H]([....
16 1O27 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
17 4GT9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
18 4GTC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
19 3G4C - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1O26 - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 3N0B - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 5IOS Kd = 14 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 4KAS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
24 1O28 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
25 4GTE - MEF C20 H23 N7 O6 c1cc(ccc1C....
26 1O25 - UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 3G4A - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 4KAT - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
3 1O2B - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4GTL - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5IOT Kd = 109 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
6 5IOQ Kd = 78 uM DUR C9 H12 N2 O5 C1[C@@H]([....
7 4GTA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 1O2A - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 4KAR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 1O29 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
11 4GTB - D16 C21 H22 N4 O6 S CC1=NC(=O)....
12 4GTF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 3N0C - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 4GTD - UMP C9 H13 N2 O8 P C1[C@@H]([....
15 5IOR Kd = 0.17 uM DUS C9 H12 N2 O8 S C1[C@@H]([....
16 1O27 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
17 4GT9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
18 4GTC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
19 3G4C - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1O26 - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 3N0B - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 5IOS Kd = 14 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 4KAS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
24 1O28 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
25 4GTE - MEF C20 H23 N7 O6 c1cc(ccc1C....
26 1O25 - UMP C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (27)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3G4A - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 4KAT - FDA C27 H35 N9 O15 P2 Cc1cc2c(cc....
3 1O2B - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
4 4GTL - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
5 5IOT Kd = 109 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
6 5IOQ Kd = 78 uM DUR C9 H12 N2 O5 C1[C@@H]([....
7 4GTA - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
8 1O2A - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
9 4KAR - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
10 1O29 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
11 4GTB - D16 C21 H22 N4 O6 S CC1=NC(=O)....
12 4GTF - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
13 3N0C - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 4GTD - UMP C9 H13 N2 O8 P C1[C@@H]([....
15 5IOR Kd = 0.17 uM DUS C9 H12 N2 O8 S C1[C@@H]([....
16 1O27 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
17 4GT9 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
18 4GTC - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
19 3G4C - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1O26 - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 3N0B - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 5IOS Kd = 14 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 4KAS - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
24 1O28 - UFP C9 H12 F N2 O8 P C1[C@@H]([....
25 4GTE - MEF C20 H23 N7 O6 c1cc(ccc1C....
26 1O25 - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 6J61 - FAD C27 H33 N9 O15 P2 Cc1cc2c(cc....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; 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: 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 : 5IOR; Ligand: DUS; 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: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5IOR; Ligand: DUS; 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: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5IOR; Ligand: DUS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5IOR; Ligand: DUS; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5IOR; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 5IOR; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 5IOR; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 5IOR; Ligand: FAD; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 9; Query (leader) PDB : 5IOR; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 9) in the query (biounit: 5ior.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 10; Query (leader) PDB : 5IOR; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 10) in the query (biounit: 5ior.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 11; Query (leader) PDB : 5IOR; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 11) in the query (biounit: 5ior.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 12; Query (leader) PDB : 5IOR; Ligand: RBF; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 12) in the query (biounit: 5ior.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
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