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: 53
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 DUS 0.692308 0.853333
9 DUT MG 0.684932 0.914286
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 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
Ligand no: 2; Ligand: FDA; Similar ligands found: 132
No: Ligand ECFP6 Tc MDL keys Tc
1 FDA 1 1
2 FNK 0.691781 0.965517
3 F2N 0.647436 0.976744
4 FAD 0.641892 0.906977
5 FAS 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 CNV FAD 0.578616 0.954023
13 62F 0.573248 0.895349
14 FA9 0.554217 0.918605
15 FAD CNX 0.551515 0.873684
16 FAD NBA 0.549708 0.882979
17 P5F 0.545455 0.920455
18 FNR 0.532258 0.892857
19 A2D 0.516667 0.833333
20 APR 0.5 0.811765
21 AR6 0.5 0.811765
22 M33 0.496 0.823529
23 BA3 0.495935 0.833333
24 P6G FDA 0.494186 0.827957
25 DAL FAD PER 0.494118 0.865169
26 B4P 0.491935 0.833333
27 AP5 0.491935 0.833333
28 ANP 0.488372 0.813953
29 SAP 0.484375 0.795455
30 AGS 0.484375 0.795455
31 ATP 0.480315 0.833333
32 ADP 0.48 0.833333
33 48N 0.479167 0.818182
34 FB0 0.478261 0.819149
35 5FA 0.476562 0.833333
36 AQP 0.476562 0.833333
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 A1R 0.463235 0.827586
47 PAJ 0.463235 0.808989
48 G3A 0.461538 0.83908
49 T5A 0.46 0.896552
50 A22 0.459259 0.845238
51 G5P 0.458333 0.83908
52 ACQ 0.454545 0.835294
53 PRX 0.453846 0.793103
54 5AL 0.451128 0.823529
55 CA0 0.449612 0.813953
56 ADX 0.449612 0.741935
57 50T 0.446154 0.802326
58 8QN 0.445255 0.823529
59 ABM 0.444444 0.790698
60 A 0.443548 0.809524
61 AMP 0.443548 0.809524
62 OMR 0.442953 0.782609
63 TXE 0.442953 0.892857
64 ADQ 0.442029 0.813953
65 AMO 0.442029 0.825581
66 139 0.440789 0.862069
67 ADJ 0.440789 0.822222
68 ME8 0.439716 0.771739
69 BIS 0.439716 0.786517
70 TXA 0.439716 0.825581
71 PTJ 0.439716 0.818182
72 AFH 0.438356 0.788889
73 A4P 0.437086 0.876405
74 TXD 0.436242 0.870588
75 UP5 0.436242 0.880952
76 NXX 0.436242 0.825581
77 6V0 0.436242 0.882353
78 DND 0.436242 0.825581
79 5SV 0.434783 0.758242
80 SRP 0.433824 0.804598
81 4AD 0.431655 0.816092
82 P1H 0.430303 0.842697
83 FYA 0.429577 0.823529
84 AHX 0.428571 0.797753
85 SRA 0.428571 0.772727
86 P33 FDA 0.427778 0.821053
87 MAP 0.427536 0.795455
88 AU1 0.427481 0.813953
89 NAI 0.426667 0.870588
90 25L 0.426573 0.845238
91 A12 0.426357 0.825581
92 AP2 0.426357 0.825581
93 AMP MG 0.425197 0.75
94 EAD 0.423313 0.862069
95 COD 0.423077 0.806452
96 PR8 0.422535 0.8
97 TAT 0.422222 0.804598
98 4TC 0.421053 0.882353
99 APC 0.421053 0.825581
100 NB8 0.41958 0.797753
101 1ZZ 0.41958 0.771739
102 4UU 0.418919 0.837209
103 00A 0.41844 0.786517
104 RBY 0.41791 0.804598
105 ADV 0.41791 0.804598
106 A3D 0.417722 0.835294
107 NAX 0.417219 0.862069
108 ADP MG 0.416667 0.761364
109 25A 0.414286 0.833333
110 OOB 0.414286 0.823529
111 ADP BEF 0.413534 0.744444
112 BEF ADP 0.413534 0.744444
113 ANP MG 0.413043 0.755556
114 LAD 0.412587 0.788889
115 UPA 0.411765 0.870588
116 CNA 0.410256 0.825581
117 DLL 0.408451 0.823529
118 XAH 0.408163 0.771739
119 4UW 0.407895 0.829545
120 ADP PO3 0.407407 0.788235
121 3UK 0.405594 0.835294
122 4UV 0.405405 0.837209
123 TYM 0.405229 0.825581
124 NAD 0.405063 0.823529
125 ATP MG 0.404412 0.761364
126 9SN 0.40411 0.797753
127 ADP VO4 0.402878 0.781609
128 VO4 ADP 0.402878 0.781609
129 WAQ 0.402778 0.806818
130 FA5 0.401361 0.825581
131 YAP 0.401361 0.816092
132 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: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5IOR; Ligand: FAD; Similar sites found: 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 P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5IOR; Ligand: RBF; Similar sites found: 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 147 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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