Receptor
PDB id Resolution Class Description Source Keywords
1O27 2.3 Å EC: 2.1.1.148 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROT (TM0449) FROM THERMOTOGA MARITIMA WITH FAD AND BRDUMP AT 2.R ESOLUTION 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
BRU A:603;
B:608;
C:613;
D:618;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
387.078 C9 H12 Br N2 O8 P C1[C@...
FAD A:615;
B:610;
C:605;
D:600;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
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: BRU; Similar ligands found: 68
No: Ligand ECFP6 Tc MDL keys Tc
1 BRU 1 1
2 5IU 0.720588 0.972222
3 UFP 0.716418 0.972222
4 5HU 0.705882 0.905405
5 TMP 0.705882 0.917808
6 BVP 0.662162 0.958333
7 UMP 0.583333 0.929577
8 DU 0.583333 0.929577
9 5BU 0.575342 0.917808
10 TYD 0.571429 0.905405
11 DDN 0.547945 0.929577
12 TTP 0.54321 0.905405
13 DU DU DU DU BRU DU DU 0.536082 0.932432
14 DCM 0.506494 0.866667
15 DC 0.506494 0.866667
16 5CM 0.506329 0.857143
17 TBD 0.5 0.87013
18 TTP MG 0.5 0.878378
19 UMC 0.486842 0.876712
20 BUP 0.47619 0.905405
21 TLO 0.472527 0.857143
22 ID2 0.472222 0.837838
23 DUD 0.469136 0.916667
24 9RC 0.467391 0.776471
25 DAU 0.463158 0.846154
26 FDM 0.4625 0.932432
27 NYM 0.4625 0.893333
28 QBT 0.461538 0.864865
29 DUP 0.458824 0.891892
30 3YN 0.458333 0.846154
31 LLT 0.458333 0.786667
32 THM 0.458333 0.786667
33 DUN 0.457831 0.891892
34 THP 0.45679 0.90411
35 1JB 0.452632 0.846154
36 3R2 0.452632 0.835443
37 18T 0.452632 0.846154
38 TRH 0.452632 0.846154
39 TDX 0.452632 0.857143
40 UC5 0.451219 0.90411
41 DUT 0.447059 0.916667
42 ATM 0.447059 0.835443
43 0DN 0.445946 0.797297
44 T3F 0.443299 0.825
45 T3Q 0.443299 0.825
46 DWN 0.443299 0.825
47 BVD 0.441558 0.824324
48 BTD 0.439024 0.807692
49 T46 0.438776 0.846154
50 0N2 0.438776 0.814815
51 AKM 0.435644 0.807229
52 MMF 0.434343 0.825
53 0FX 0.434343 0.825
54 5FU 0.43038 0.891892
55 QDM 0.425743 0.814815
56 8OG 0.425287 0.807229
57 JHZ 0.421569 0.804878
58 FNF 0.421569 0.835443
59 1YF 0.421569 0.835443
60 GPU 0.421053 0.75
61 4TG 0.417476 0.835443
62 DU DU DU DU BRU DA DU 0.410853 0.831325
63 DUT MG 0.409091 0.888889
64 YYY 0.406977 0.855263
65 3DR DT DT DT DT DT 0.403846 0.844156
66 0KX 0.4 0.833333
67 UMP AF3 PO4 0.4 0.868421
68 T3P 0.4 0.878378
Ligand no: 2; Ligand: FAD; Similar ligands found: 147
No: Ligand ECFP6 Tc MDL keys Tc
1 FAS 1 1
2 FAD 1 1
3 FAY 0.859259 0.9875
4 RFL 0.852941 0.963855
5 UBG 0.845588 0.987654
6 6FA 0.794118 0.987654
7 FAE 0.751773 0.987654
8 SFD 0.651007 0.860215
9 FDA 0.641892 0.906977
10 FNK 0.602564 0.876405
11 JNT 0.598425 0.876543
12 FAJ 0.57485 0.97561
13 62F 0.572327 0.939024
14 F2N 0.566265 0.886364
15 FMN 0.543307 0.876543
16 FA9 0.526316 0.939759
17 6YU 0.516304 0.860215
18 CNV FAD 0.511905 0.908046
19 P6G FDA 0.511628 0.908046
20 FAD NBT 0.508876 0.83871
21 A2D 0.504065 0.875
22 DAL FAD PER 0.491429 0.836957
23 P5F 0.491329 0.941176
24 FAD CNX 0.488506 0.8125
25 APR 0.488372 0.851852
26 AR6 0.488372 0.851852
27 FAD T2C 0.485876 0.819149
28 AGS 0.484615 0.811765
29 M33 0.484375 0.864198
30 BA3 0.484127 0.875
31 ATP 0.48062 0.851852
32 HEJ 0.48062 0.851852
33 B4P 0.480315 0.875
34 ADP 0.480315 0.851852
35 AP5 0.480315 0.875
36 ANP 0.477273 0.831325
37 5FA 0.476923 0.851852
38 AQP 0.476923 0.851852
39 48N 0.469388 0.902439
40 OAD 0.467626 0.876543
41 9X8 0.467626 0.833333
42 FAD NBA 0.467033 0.793814
43 GTA 0.465753 0.892857
44 AT4 0.465116 0.821429
45 AN2 0.465116 0.841463
46 HQG 0.463235 0.841463
47 AD9 0.462121 0.831325
48 3OD 0.460993 0.876543
49 RBF 0.460938 0.790123
50 FB0 0.460606 0.835165
51 139 0.460526 0.858824
52 AP0 0.46 0.835294
53 A22 0.459854 0.864198
54 ACP 0.458015 0.853659
55 8QN 0.456522 0.864198
56 PRX 0.454545 0.831325
57 A3R 0.453237 0.86747
58 A1R 0.453237 0.86747
59 G3A 0.452055 0.902439
60 T5A 0.45098 0.872093
61 G5P 0.44898 0.902439
62 ATF 0.448529 0.821429
63 50T 0.44697 0.819277
64 OZV 0.446043 0.851852
65 6YZ 0.445255 0.853659
66 ACQ 0.444444 0.853659
67 ADQ 0.442857 0.853659
68 PAJ 0.442857 0.847059
69 KMQ 0.441379 0.843373
70 8LE 0.441176 0.855422
71 5AL 0.441176 0.864198
72 ADX 0.439394 0.775281
73 CA0 0.439394 0.853659
74 8LQ 0.438849 0.865854
75 QA7 0.438849 0.855422
76 A4P 0.437909 0.831461
77 25L 0.4375 0.864198
78 P33 FDA 0.436464 0.817204
79 KG4 0.43609 0.853659
80 5SV 0.435714 0.793103
81 8LH 0.434783 0.843373
82 OMR 0.434211 0.818182
83 TXE 0.434211 0.890244
84 45A 0.434109 0.829268
85 ABM 0.434109 0.829268
86 AMP 0.433071 0.82716
87 A 0.433071 0.82716
88 4AD 0.432624 0.855422
89 ADJ 0.432258 0.818182
90 B5M 0.431507 0.878049
91 B5Y 0.431507 0.878049
92 BIS 0.430556 0.802326
93 DJC FAD 0.43 0.827957
94 SRA 0.429688 0.788235
95 AFH 0.42953 0.825581
96 DND 0.427632 0.865854
97 TXD 0.427632 0.890244
98 UP5 0.427632 0.878049
99 6V0 0.427632 0.857143
100 DQV 0.426667 0.8875
101 SRP 0.42446 0.843373
102 PR8 0.423611 0.837209
103 TAT 0.423358 0.821429
104 T99 0.423358 0.821429
105 AMO 0.422535 0.865854
106 PTJ 0.42069 0.835294
107 TXA 0.42069 0.865854
108 FYA 0.42069 0.864198
109 CNA 0.420382 0.865854
110 AHX 0.41958 0.835294
111 00A 0.41958 0.823529
112 AMP MG 0.418605 0.814815
113 MAP 0.41844 0.811765
114 NAI 0.418301 0.845238
115 AU1 0.41791 0.831325
116 A12 0.416667 0.843373
117 AP2 0.416667 0.843373
118 9ZD 0.415493 0.845238
119 25A 0.415493 0.851852
120 9ZA 0.415493 0.845238
121 COD 0.415094 0.842697
122 4TC 0.412903 0.879518
123 APC 0.411765 0.843373
124 ME8 0.410959 0.806818
125 1ZZ 0.410959 0.806818
126 NB8 0.410959 0.835294
127 ADP BEF 0.410448 0.82716
128 ADP MG 0.410448 0.82716
129 DJ0 FAD 0.41 0.865169
130 4UW 0.409091 0.825581
131 NAX 0.409091 0.837209
132 F2R 0.408805 0.850575
133 ADV 0.408759 0.843373
134 RBY 0.408759 0.843373
135 VO4 ADP 0.407143 0.809524
136 P1H 0.405882 0.818182
137 BEF ADP 0.405797 0.807229
138 OOB 0.405594 0.864198
139 LAD 0.40411 0.825581
140 UPA 0.403846 0.86747
141 4UU 0.401316 0.833333
142 GA7 0.401316 0.865854
143 A3D 0.401235 0.876543
144 80F 0.401235 0.808989
145 DLL 0.4 0.864198
146 XAH 0.4 0.806818
147 V2G 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: BRU; Similar ligands found: 57
No: Ligand Similarity coefficient
1 DUS 0.9731
2 TKW 0.9623
3 2DT 0.9594
4 D4M 0.9594
5 CNU 0.9522
6 UP6 0.9521
7 C 0.9504
8 H2U 0.9504
9 U5P 0.9504
10 C5P 0.9482
11 CH 0.9482
12 FN5 0.9480
13 D5M 0.9453
14 DA 0.9453
15 U 0.9445
16 DI 0.9442
17 5HM 0.9439
18 DGP 0.9429
19 DG 0.9428
20 FNU 0.9405
21 BMP 0.9404
22 AMP 0.9365
23 BMQ 0.9365
24 8OP 0.9361
25 FMP 0.9352
26 NUP 0.9350
27 16B 0.9346
28 IMP 0.9338
29 G 0.9319
30 5GP 0.9319
31 XMP 0.9297
32 71V 0.9293
33 DOC 0.9275
34 U6M 0.9274
35 PSU 0.9264
36 8BR 0.9254
37 9L3 0.9214
38 8GM 0.9199
39 6MA 0.9196
40 PFU 0.9193
41 NCN 0.9125
42 C2R 0.9122
43 AMZ 0.9108
44 CAR 0.9098
45 NIA 0.9095
46 IRP 0.9059
47 NMN 0.9049
48 IMU 0.8980
49 4BH 0.8936
50 93A 0.8923
51 AIR 0.8908
52 AS 0.8811
53 5QT 0.8795
54 7D5 0.8751
55 MTE 0.8730
56 4X2 0.8665
57 Z8B 0.8575
Ligand no: 2; Ligand: FAD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 FDA T2C 0.8610
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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