Receptor
PDB id Resolution Class Description Source Keywords
1O28 2.1 Å EC: 2.1.1.148 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE COMPLEMENTING PROT (TM0449) FROM THERMOTOGA MARITIMA WITH FDUMP AT 2.1 A RESOL 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
EPE A:715;
B:710;
C:705;
D:700;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
238.305 C8 H18 N2 O4 S C1CN(...
PGE B:720;
C:725;
D:730;
D:735;
 Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
 submit data
150.173 C6 H14 O4 C(COC...
UFP A:703;
B:708;
C:713;
D:718;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
326.172 C9 H12 F 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: UFP; Similar ligands found: 71
No: Ligand ECFP6 Tc MDL keys Tc
1 UFP 1 1
2 BRU 0.716418 0.972222
3 TMP 0.716418 0.917808
4 5HU 0.716418 0.905405
5 5IU 0.705882 0.972222
6 BVP 0.648649 0.931507
7 TYD 0.6 0.905405
8 UMP 0.591549 0.929577
9 DU 0.591549 0.929577
10 TTP 0.56962 0.905405
11 5FU 0.555556 0.917808
12 DDN 0.555556 0.929577
13 TBD 0.506173 0.87013
14 TTP MG 0.506024 0.878378
15 DAU 0.5 0.846154
16 TLO 0.494382 0.857143
17 5CM 0.493671 0.857143
18 DUD 0.493671 0.916667
19 DCM 0.493506 0.866667
20 DC 0.493506 0.866667
21 TDX 0.48913 0.857143
22 TRH 0.48913 0.846154
23 18T 0.48913 0.846154
24 1JB 0.48913 0.846154
25 9RC 0.488889 0.776471
26 FDM 0.487179 0.958904
27 UMC 0.473684 0.876712
28 3R2 0.473118 0.835443
29 DUT 0.46988 0.916667
30 0FX 0.46875 0.825
31 NYM 0.468354 0.893333
32 QBT 0.467532 0.864865
33 THM 0.464789 0.786667
34 LLT 0.464789 0.786667
35 3YN 0.463158 0.846154
36 T3F 0.463158 0.825
37 T3Q 0.463158 0.825
38 DWN 0.463158 0.825
39 THP 0.4625 0.90411
40 T46 0.458333 0.846154
41 ID2 0.458333 0.837838
42 0N2 0.458333 0.814815
43 UC5 0.45679 0.90411
44 AKM 0.454545 0.807229
45 MMF 0.453608 0.825
46 ATM 0.452381 0.835443
47 0DN 0.452055 0.821918
48 4TG 0.45 0.835443
49 DUP 0.447059 0.891892
50 DUN 0.445783 0.891892
51 QDM 0.444444 0.814815
52 1YF 0.44 0.835443
53 JHZ 0.44 0.804878
54 FNF 0.44 0.835443
55 5UD 0.430556 0.786667
56 8OG 0.430233 0.807229
57 BVD 0.428571 0.8
58 UMP AF3 PO4 0.420455 0.893333
59 T5A 0.418182 0.767442
60 DUT MG 0.413793 0.888889
61 GPK 0.413333 0.75
62 YYY 0.411765 0.855263
63 3DR DT DT DT DT DT 0.407767 0.844156
64 FUH 0.407407 0.825
65 QUH 0.407407 0.825
66 5BU 0.407407 0.891892
67 T3P 0.405063 0.878378
68 F6G 0.404494 0.820513
69 DK4 0.402597 0.746667
70 6U4 0.4 0.814815
71 ATY 0.4 0.857143
Similar Ligands (3D)
Ligand no: 1; Ligand: UFP; Similar ligands found: 108
No: Ligand Similarity coefficient
1 DUS 0.9760
2 U 0.9712
3 TKW 0.9648
4 CAR 0.9564
5 U5P 0.9556
6 9L3 0.9531
7 H2U 0.9527
8 D4M 0.9526
9 2DT 0.9526
10 C 0.9516
11 UP6 0.9515
12 D5M 0.9510
13 DA 0.9510
14 DI 0.9509
15 C5P 0.9506
16 FN5 0.9506
17 CH 0.9506
18 AMP 0.9484
19 PSU 0.9474
20 IMP 0.9440
21 CNU 0.9440
22 5HM 0.9434
23 BMP 0.9416
24 FNU 0.9411
25 DOC 0.9401
26 16B 0.9379
27 T3S 0.9340
28 FMP 0.9340
29 NUP 0.9329
30 DG 0.9327
31 DGP 0.9327
32 6MA 0.9324
33 8OP 0.9314
34 5GP 0.9262
35 BMQ 0.9250
36 8BR 0.9228
37 U6M 0.9214
38 G 0.9213
39 PFU 0.9207
40 XMP 0.9195
41 71V 0.9157
42 NCN 0.9146
43 IRP 0.9134
44 S5P 0.9128
45 NIA 0.9110
46 NMN 0.9107
47 ABM 0.9095
48 7D5 0.9094
49 45A 0.9090
50 SRA 0.9087
51 AMZ 0.9084
52 6CN 0.9071
53 RVP 0.9062
54 CMP 0.9061
55 U4S 0.9056
56 C2R 0.9042
57 8GM 0.9029
58 IMU 0.9028
59 PCG 0.9000
60 RBZ 0.8996
61 TXS 0.8958
62 4BH 0.8954
63 AS 0.8944
64 Z8B 0.8938
65 SP1 0.8933
66 RP1 0.8933
67 OMP 0.8932
68 JW5 0.8932
69 93A 0.8922
70 A3N 0.8921
71 N5O 0.8920
72 35G 0.8917
73 AIR 0.8903
74 SSI 0.8893
75 MTE 0.8892
76 6AU 0.8884
77 MZP 0.8871
78 75G 0.8870
79 MTA 0.8862
80 5QT 0.8844
81 2GE 0.8842
82 NEC 0.8829
83 6OG 0.8817
84 6J7 0.8783
85 JFX 0.8762
86 MTM 0.8755
87 MTI 0.8750
88 6U5 0.8737
89 QTJ 0.8731
90 MTH 0.8729
91 3F5 0.8712
92 9X0 0.8709
93 IGP 0.8697
94 PZB 0.8694
95 6SW 0.8686
96 4X2 0.8650
97 OE2 0.8642
98 KMG 0.8626
99 IRN 0.8621
100 SNP 0.8620
101 9RK 0.8612
102 1CE 0.8608
103 43G 0.8603
104 5BT 0.8598
105 SU1 0.8588
106 FX5 0.8586
107 QNI 0.8557
108 FT1 0.8530
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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