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
Ligand no: 1; Ligand: UMP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 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 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 BRU 0.583333 0.929577
13 5HU 0.583333 0.942857
14 TMP 0.583333 0.956522
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 U5F 0.428571 0.898551
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 F6G 0.409091 0.876712
45 UPU 0.409091 0.871429
46 139 0.409091 0.8
47 TTP MG 0.409091 0.914286
48 URI 0.408451 0.771429
49 TBD 0.406977 0.90411
50 DU DU DU DU BRU DA DU 0.40625 0.771084
51 PUA 0.405172 0.833333
52 UNP 0.402299 0.873239
53 PUP 0.4 0.955882
54 UDX 0.4 0.873239
55 UAD 0.4 0.873239
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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