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Receptor
PDB id Resolution Class Description Source Keywords
4KAT 2.14 Å EC: 2.1.1.148 CRYSTAL STRUCTURE OF FDTS FROM T. MARITIMA MUTANT (R174K) WI DUMP THERMOTOGA MARITIMA MSB8 THYX FDTS FAD DUMP NOVEL FDTS FOLD CONVERTION OF DUMP TUSING TETRAHYDROFOLATE TRANSFERASE
Ref.: FLAVIN-DEPENDENT THYMIDYLATE SYNTHASE AS A DRUG TAR DEADLY MICROBES: MUTATIONAL STUDY AND A STRATEGY FO INHIBITOR DESIGN. J BIOTERROR BIODEF V.L 12 004 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DU D:302;
C:302;
A:301;
B:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
FDA C:301;
B:302;
D:301;
A:302;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
787.566 C27 H35 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 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]([....
70% Homology Family (26)
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]([....
50% Homology Family (26)
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]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DU; Similar ligands found: 52
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 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
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 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Ligand no: 2; Ligand: FDA; Similar ligands found: 141
No: Ligand ECFP6 Tc MDL keys Tc
1 FDA 1 1
2 FNK 0.691781 0.965517
3 F2N 0.647436 0.976744
4 FAS 0.641892 0.906977
5 FAD 0.641892 0.906977
6 SFD 0.630872 0.787879
7 6FA 0.61745 0.896552
8 6YU 0.586207 0.903226
9 RFL 0.585987 0.876405
10 FAD NBT 0.584906 0.902174
11 FAY 0.579618 0.895349
12 62F 0.573248 0.895349
13 FA9 0.554217 0.918605
14 FAD CNX 0.551515 0.873684
15 P5F 0.545455 0.920455
16 FNR 0.532258 0.892857
17 FAD NBA 0.526012 0.873684
18 A2D 0.516667 0.833333
19 AR6 0.5 0.811765
20 APR 0.5 0.811765
21 M33 0.496 0.823529
22 BA3 0.495935 0.833333
23 P6G FDA 0.494186 0.827957
24 B4P 0.491935 0.833333
25 AP5 0.491935 0.833333
26 ANP 0.488372 0.813953
27 AGS 0.484375 0.795455
28 SAP 0.484375 0.795455
29 HEJ 0.480315 0.833333
30 ATP 0.480315 0.833333
31 ADP 0.48 0.833333
32 48N 0.479167 0.818182
33 FB0 0.478261 0.819149
34 AQP 0.476562 0.833333
35 5FA 0.476562 0.833333
36 AT4 0.47619 0.804598
37 AN2 0.47619 0.823529
38 GTA 0.475524 0.831461
39 AD9 0.472868 0.813953
40 3OD 0.471014 0.835294
41 FAE 0.46988 0.896552
42 ATF 0.469697 0.804598
43 AP0 0.469388 0.860465
44 ACP 0.46875 0.835294
45 OAD 0.467153 0.835294
46 9X8 0.467153 0.795455
47 PAJ 0.463235 0.808989
48 A1R 0.463235 0.827586
49 A3R 0.463235 0.827586
50 G3A 0.461538 0.83908
51 T5A 0.46 0.896552
52 A22 0.459259 0.845238
53 G5P 0.458333 0.83908
54 6YZ 0.455224 0.835294
55 DQV 0.455172 0.845238
56 ACQ 0.454545 0.835294
57 PRX 0.453846 0.793103
58 5AL 0.451128 0.823529
59 ADX 0.449612 0.741935
60 CA0 0.449612 0.813953
61 50T 0.446154 0.802326
62 8QN 0.445255 0.823529
63 ABM 0.444444 0.790698
64 A 0.443548 0.809524
65 AMP 0.443548 0.809524
66 TXE 0.442953 0.892857
67 OMR 0.442953 0.782609
68 ADQ 0.442029 0.813953
69 AMO 0.442029 0.825581
70 ADJ 0.440789 0.822222
71 139 0.440789 0.862069
72 B5M 0.440559 0.837209
73 BIS 0.439716 0.786517
74 PTJ 0.439716 0.818182
75 ME8 0.439716 0.771739
76 TXA 0.439716 0.825581
77 AFH 0.438356 0.788889
78 A4P 0.437086 0.876405
79 6V0 0.436242 0.882353
80 UP5 0.436242 0.880952
81 TXD 0.436242 0.870588
82 DND 0.436242 0.825581
83 NXX 0.436242 0.825581
84 5SV 0.434783 0.758242
85 SRP 0.433824 0.804598
86 4AD 0.431655 0.816092
87 B5Y 0.430556 0.837209
88 P1H 0.430303 0.842697
89 FYA 0.429577 0.823529
90 AHX 0.428571 0.797753
91 SRA 0.428571 0.772727
92 P33 FDA 0.427778 0.821053
93 MAP 0.427536 0.795455
94 AU1 0.427481 0.813953
95 NAI 0.426667 0.870588
96 25L 0.426573 0.845238
97 AP2 0.426357 0.825581
98 A12 0.426357 0.825581
99 CNV FAD 0.426136 0.876405
100 EAD 0.423313 0.862069
101 COD 0.423077 0.806452
102 PR8 0.422535 0.8
103 T99 0.422222 0.804598
104 TAT 0.422222 0.804598
105 APC 0.421053 0.825581
106 4TC 0.421053 0.882353
107 NB8 0.41958 0.797753
108 1ZZ 0.41958 0.771739
109 4UU 0.418919 0.837209
110 GA7 0.418919 0.825581
111 00A 0.41844 0.786517
112 ADV 0.41791 0.804598
113 RBY 0.41791 0.804598
114 A3D 0.417722 0.835294
115 NAX 0.417219 0.862069
116 OOB 0.414286 0.823529
117 25A 0.414286 0.833333
118 LAD 0.412587 0.788889
119 UPA 0.411765 0.870588
120 CNA 0.410256 0.825581
121 80F 0.408805 0.833333
122 DLL 0.408451 0.823529
123 XAH 0.408163 0.771739
124 4UW 0.407895 0.829545
125 F2R 0.407643 0.793478
126 ADP PO3 0.407407 0.788235
127 DAL AMP 0.407143 0.802326
128 3UK 0.405594 0.835294
129 4UV 0.405405 0.837209
130 TYM 0.405229 0.825581
131 NAD 0.405063 0.823529
132 9ZD 0.404255 0.827586
133 9ZA 0.404255 0.827586
134 9SN 0.40411 0.797753
135 VO4 ADP 0.402878 0.781609
136 ADP VO4 0.402878 0.781609
137 WAQ 0.402778 0.806818
138 B5V 0.402778 0.825581
139 YAP 0.401361 0.816092
140 FA5 0.401361 0.825581
141 YLP 0.401316 0.793478
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: 22
This union binding pocket(no: 1) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
1 3GD8 GOL None
2 4HN1 TDR 1.99005
3 4HN1 THM 1.99005
4 3SJK LYS PRO VAL LEU ARG THR ALA 2.63158
5 5VKM GAL SIA 3.44828
6 1R6N 434 3.79147
7 5OCQ CIT 3.87931
8 4LSJ LSJ 4.31034
9 4RW3 TDA 4.31034
10 5A04 BGC 4.31034
11 1M48 FRG 4.51128
12 5EE7 5MV 4.64602
13 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.74138
14 5W7B MYR 5.17241
15 3EYK EYK 5.81395
16 1B4P GPS 6.45161
17 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.89655
18 3O01 DXC 7.32759
19 2BVE PH5 8.40336
20 5LX9 OLB 9.48276
21 1I1E DM2 14.2241
22 1XQP 8HG 18.1034
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: 22
This union binding pocket(no: 5) in the query (biounit: 5ior.bio1) has 146 residues
No: Leader PDB Ligand Sequence Similarity
1 3GD8 GOL None
2 4HN1 TDR 1.99005
3 4HN1 THM 1.99005
4 3SJK LYS PRO VAL LEU ARG THR ALA 2.63158
5 5VKM GAL SIA 3.44828
6 1R6N 434 3.79147
7 5OCQ CIT 3.87931
8 4LSJ LSJ 4.31034
9 4RW3 TDA 4.31034
10 5A04 BGC 4.31034
11 1M48 FRG 4.51128
12 5EE7 5MV 4.64602
13 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.74138
14 5W7B MYR 5.17241
15 3EYK EYK 5.81395
16 1B4P GPS 6.45161
17 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 6.89655
18 3O01 DXC 7.32759
19 2BVE PH5 8.40336
20 5LX9 OLB 9.48276
21 1I1E DM2 14.2241
22 1XQP 8HG 18.1034
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: 21
This union binding pocket(no: 10) in the query (biounit: 5ior.bio1) has 147 residues
No: Leader PDB Ligand Sequence Similarity
1 5UGW GSH None
2 3GD8 GOL None
3 3SJK LYS PRO VAL LEU ARG THR ALA 2.63158
4 5VKM GAL SIA 3.44828
5 1R6N 434 3.79147
6 5OCQ CIT 3.87931
7 4LSJ LSJ 4.31034
8 4RW3 TDA 4.31034
9 5A04 BGC 4.31034
10 1M48 FRG 4.51128
11 5EE7 5MV 4.64602
12 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 4.74138
13 5W7B MYR 5.17241
14 3EYK EYK 5.81395
15 1B4P GPS 6.45161
16 3O01 DXC 7.32759
17 2BVE PH5 8.40336
18 5LX9 OLB 9.48276
19 4RJD TFP 10.6061
20 1I1E DM2 14.2241
21 1XQP 8HG 18.1034
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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