Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DUS A:302;
Valid;
none;
Kd = 0.17 uM
308.265 C9 H12 N2 O8 S C1[C@...
FAD A:301;
Valid;
none;
submit data
785.55 C27 H33 N9 O15 P2 Cc1cc...
RBF A:303;
Valid;
none;
submit data
376.364 C17 H20 N4 O6 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: DUS; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 DUS 1 1
2 UMP 0.692308 0.853333
3 DU 0.692308 0.853333
4 DUR 0.677966 0.773333
5 UC5 0.642857 0.831169
6 DUD 0.642857 0.842105
7 DUN 0.625 0.820513
8 DUT 0.608108 0.842105
9 DUP 0.6 0.820513
10 DUT MG 0.6 0.84
11 UMP AF3 PO4 0.584416 0.777778
12 DDU 0.539683 0.684211
13 UM3 0.507042 0.815789
14 DU3 0.5 0.7125
15 DUA 0.5 0.716049
16 DU4 0.487805 0.695122
17 DU DU DU DU BRU DU DU 0.45 0.768293
18 DUX 0.421687 0.691358
19 DDN 0.415584 0.853333
20 TMP 0.4 0.820513
21 URI 0.4 0.701299
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
Ligand no: 3; Ligand: RBF; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 RBF 1 1
2 FMN 0.75641 0.876712
3 RS3 0.74026 0.942029
4 DLZ 0.546667 0.885714
5 1VY 0.525641 0.871429
6 C3F 0.523256 0.816901
7 LFN 0.513889 0.712121
8 CF4 0.511364 0.805556
9 FAS 0.460938 0.790123
10 FAD 0.460938 0.790123
11 FAE 0.457364 0.780488
12 UBG 0.443609 0.780488
13 RLP 0.438202 0.833333
14 HDF 0.423913 0.871429
15 FO1 0.423913 0.871429
16 9O9 0.40404 0.818182
Similar Ligands (3D)
Ligand no: 1; Ligand: DUS; Similar ligands found: 74
No: Ligand Similarity coefficient
1 UFP 0.9760
2 UP6 0.9754
3 BRU 0.9731
4 U5P 0.9718
5 H2U 0.9718
6 C5P 0.9706
7 C 0.9706
8 FN5 0.9706
9 CH 0.9706
10 U 0.9618
11 TKW 0.9589
12 5FU 0.9588
13 BMP 0.9585
14 FDM 0.9561
15 NUP 0.9558
16 5IU 0.9549
17 BMQ 0.9538
18 5BU 0.9536
19 16B 0.9518
20 DCM 0.9516
21 D4M 0.9494
22 2DT 0.9494
23 DC 0.9471
24 UMC 0.9432
25 U6M 0.9379
26 PSU 0.9377
27 9L3 0.9373
28 QBT 0.9370
29 S5P 0.9364
30 5CM 0.9350
31 CAR 0.9346
32 NYM 0.9312
33 DOC 0.9310
34 FNU 0.9285
35 DI 0.9255
36 PFU 0.9253
37 5HU 0.9247
38 DA 0.9220
39 D5M 0.9219
40 C2R 0.9195
41 AMP 0.9192
42 AIR 0.9185
43 IMP 0.9179
44 FMP 0.9132
45 AMZ 0.9125
46 NIA 0.9125
47 5HM 0.9082
48 CNU 0.9038
49 ATM 0.9035
50 MZP 0.9007
51 NMN 0.8994
52 NCN 0.8991
53 8BR 0.8983
54 MTE 0.8982
55 6MA 0.8975
56 8OP 0.8968
57 IRP 0.8948
58 DG 0.8931
59 DGP 0.8931
60 2OM 0.8868
61 AS 0.8848
62 5GP 0.8828
63 IRN 0.8822
64 G 0.8821
65 GAR 0.8804
66 XMP 0.8779
67 2T4 0.8758
68 5QT 0.8756
69 8OG 0.8753
70 71V 0.8734
71 IMU 0.8702
72 MTA 0.8681
73 MTH 0.8604
74 8GM 0.8601
Ligand no: 2; Ligand: FAD; Similar ligands found: 1
No: Ligand Similarity coefficient
1 FDA T2C 0.8610
Ligand no: 3; Ligand: RBF; Similar ligands found: 36
No: Ligand Similarity coefficient
1 FNR 0.9203
2 E2X 0.9078
3 5UU 0.9037
4 E2L 0.9035
5 E2F 0.9010
6 5DD 0.8959
7 5UV 0.8939
8 RDL 0.8932
9 GDW 0.8928
10 5UX 0.8928
11 1WK 0.8924
12 NE8 0.8911
13 C1L 0.8901
14 E2R 0.8854
15 9HJ 0.8814
16 AFQ 0.8785
17 2Q8 0.8780
18 3NG 0.8743
19 CQO 0.8734
20 NEZ 0.8714
21 FEF 0.8713
22 6FV 0.8707
23 O74 0.8690
24 7L6 0.8676
25 AEK 0.8642
26 74U 0.8634
27 FQW 0.8628
28 CRM 0.8617
29 AAQ 0.8607
30 8OW 0.8606
31 7AA 0.8603
32 Z80 0.8598
33 6FQ 0.8585
34 4X4 0.8569
35 7CK 0.8560
36 CRZ 0.8544
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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