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Receptor
PDB id Resolution Class Description Source Keywords
1TDU 2.1 Å EC: 2.1.1.45 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'- DEOXYURIDINE (DURD) ESCHERICHIA COLI TRANSFERASE (METHYLTRANSFERASE) SUBSTRATE MODULES
Ref.: THE ADDITIVITY OF SUBSTRATE FRAGMENTS IN ENZYME-LIGAND BINDING. STRUCTURE V. 6 839 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CB3 A:302;
B:302;
Valid;
Valid;
none;
none;
submit data
477.469 C24 H23 N5 O6 C#CCN...
DUR A:301;
B:301;
Valid;
Valid;
none;
none;
submit data
228.202 C9 H12 N2 O5 C1[C@...
PO4 A:300;
B:300;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1TDU 2.1 Å EC: 2.1.1.45 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH CB3717 AND 2'- DEOXYURIDINE (DURD) ESCHERICHIA COLI TRANSFERASE (METHYLTRANSFERASE) SUBSTRATE MODULES
Ref.: THE ADDITIVITY OF SUBSTRATE FRAGMENTS IN ENZYME-LIGAND BINDING. STRUCTURE V. 6 839 1998
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1TDU - DUR C9 H12 N2 O5 C1[C@@H]([....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 1TDU - DUR C9 H12 N2 O5 C1[C@@H]([....
50% Homology Family (24)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 1JTU - LYB C35 H42 N8 O15 c1cc(ccc1C....
2 1J3K Ki = 0.037 nM WRA C14 H18 Cl3 N5 O2 CC1(N=C(N=....
3 1J3J Ki = 9.8 nM CP6 C12 H13 Cl N4 CCc1c(c(nc....
4 1J3I Ki = 0.011 nM WRA C14 H18 Cl3 N5 O2 CC1(N=C(N=....
5 1NCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 1JTQ - LY3 C20 H21 N9 O4 c1cc(ccc1C....
7 1FWM - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
8 1JG0 ic50 = 5 uM DDT C33 H33 N3 O7 S2 CN(C)c1ccc....
9 1DNA - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
10 1F4F Ki = 24 uM TP3 C17 H20 N2 O9 S c1cc(ccc1C....
11 1SYN Kd = 0.1 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
12 1KCE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 1DDU - DDU C9 H12 N2 O4 C[C@@H]1[C....
14 4GEV - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
15 1TLC Kd = 0.076 uM DGP C10 H14 N5 O7 P c1nc2c(n1[....
16 1AIQ - UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1TDU - DUR C9 H12 N2 O5 C1[C@@H]([....
18 1AXW - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 6CDZ - UMC C9 H15 N2 O8 P C1CN(C(=O)....
20 1BQ1 - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
21 1KZI - THG C19 H23 N7 O6 c1cc(ccc1C....
22 1ZPR - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1F4G Ki = 330 nM TP4 C20 H25 N3 O10 S c1cc(ccc1C....
24 1TSD Kd = 0.04 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: CB3; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 CB3 1 1
2 PFG 0.902174 0.96875
3 DZF 0.459459 0.861538
4 NHS 0.445455 0.870968
5 3YA 0.433628 0.771429
6 3Y9 0.428571 0.782609
7 D16 0.422414 0.753425
8 9L9 0.419048 0.742857
9 83A 0.417391 0.811594
10 THF 0.40678 0.783784
11 1JY 0.406015 0.811594
12 DDF 0.405172 0.739726
13 21V 0.405172 0.739726
14 DHF 0.403509 0.785714
15 LYA 0.401786 0.794118
16 1YA 0.4 0.828571
Ligand no: 2; Ligand: DUR; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 DUR 1 1
2 UMP 0.683333 0.852941
3 DU 0.683333 0.852941
4 DUS 0.677966 0.773333
5 DUD 0.630769 0.867647
6 DDU 0.62963 0.825397
7 UM3 0.606557 0.838235
8 UC5 0.606061 0.855072
9 DUT 0.594203 0.867647
10 DUN 0.588235 0.842857
11 DUP 0.585714 0.842857
12 DU3 0.585714 0.907692
13 DU4 0.569444 0.826087
14 DUA 0.56338 0.880597
15 URI 0.508475 0.903226
16 LLT 0.508197 0.952381
17 THM 0.508197 0.952381
18 ID2 0.5 0.923077
19 DCZ 0.483871 0.921875
20 LDC 0.483871 0.921875
21 CJB 0.483871 0.857143
22 BVD 0.462687 0.9375
23 DKX 0.461538 0.80303
24 DU DU DU DU BRU DU DU 0.446809 0.808219
25 U2P 0.441176 0.797101
26 U3P 0.441176 0.782609
27 UA3 0.441176 0.782609
28 DUX 0.434211 0.771429
29 N3E 0.432432 0.865672
30 U4S 0.428571 0.835821
31 THU 0.428571 0.935484
32 UVC 0.42029 0.736111
33 BTD 0.418919 0.857143
34 U3S 0.416667 0.835821
35 3DT 0.415385 0.907692
36 UMF 0.414286 0.736111
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1TDU; Ligand: DUR; Similar sites found with APoc: 27
This union binding pocket(no: 1) in the query (biounit: 1tdu.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 5F90 GLA GAL 1.28205
2 5DQ8 FLF 2.08333
3 3TW1 AHN 2.53165
4 3ZGE ASP 2.64151
5 5X30 7XF 2.64151
6 5X2Z 3LM 2.64151
7 5O4J PJL 2.91971
8 5O4J SAH 2.91971
9 5D48 L96 3.28947
10 2IXB NAD 3.39623
11 3A5Y KAA 3.77358
12 2QV6 GTP 3.77358
13 1E5F PLP 4.15094
14 1OFD AKG 4.15094
15 5XKT GNP 4.5
16 1W5T ADP 4.5283
17 4UZI IMD 4.90566
18 2VBU CDP 5.14706
19 2GGX NPJ 6.25
20 4WQQ MAN 6.38298
21 5BRT FAD 6.79245
22 3A5Z KAA 7.32984
23 3MX2 TTP 8.30189
24 4QRH 0O2 8.57143
25 4MRP GSH 8.67924
26 5B6D C5P 28.6792
27 1B5E DCM 32.1138
Pocket No.: 2; Query (leader) PDB : 1TDU; Ligand: DUR; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 1tdu.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
1 4I5I NAD 2.64151
2 1N2A GTS 2.98507
3 2YYE APC 3.01887
4 2IXB A2G 3.39623
5 2DSA HPX 3.94089
6 2DSA GSH 3.94089
7 1RSG FAD 4.5283
8 4X7Y SAH 5.47445
9 1BZY IMU 9.67742
10 5C9P FUC 13.2075
Pocket No.: 3; Query (leader) PDB : 1TDU; Ligand: CB3; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 1tdu.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3CKJ CIT 1.88679
2 4OB6 S2T 5.28302
3 4ZY1 4U5 7.16981
4 5AOA PPI 8.30189
5 3WUR O4B 10.5263
6 5JIB OIA 10.566
Pocket No.: 4; Query (leader) PDB : 1TDU; Ligand: CB3; Similar sites found with APoc: 5
This union binding pocket(no: 4) in the query (biounit: 1tdu.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4L9Z OXL 2.94985
2 1HFU NAG NDG 3.39623
3 3CZ7 ACO 7.16981
4 2ZFN ACO 7.16981
5 5CX6 CDP 8.67924
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