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 12 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 4KNZ - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
10 1DNA - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
11 1F4F Ki = 24 uM TP3 C17 H20 N2 O9 S c1cc(ccc1C....
12 1SYN Kd = 0.1 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
13 1KCE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
14 1DDU - DDU C9 H12 N2 O4 C[C@@H]1[C....
15 4GEV - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
16 1TLC Kd = 0.076 uM DGP C10 H14 N5 O7 P c1nc2c(n1[....
17 1AIQ - UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1TDU - DUR C9 H12 N2 O5 C1[C@@H]([....
19 1AXW - UMP C9 H13 N2 O8 P C1[C@@H]([....
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 21V 0.405172 0.739726
13 DDF 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: 39
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 DUT MG 0.555556 0.828571
16 UMP AF3 PO4 0.547945 0.794521
17 U 0.508475 0.903226
18 URI 0.508475 0.903226
19 THM 0.508197 0.952381
20 LLT 0.508197 0.952381
21 ID2 0.5 0.923077
22 LDC 0.483871 0.921875
23 CJB 0.483871 0.857143
24 DCZ 0.483871 0.921875
25 BVD 0.462687 0.9375
26 DKX 0.461538 0.80303
27 DU DU DU DU BRU DU DU 0.446809 0.808219
28 U2P 0.441176 0.797101
29 U3P 0.441176 0.782609
30 UA3 0.441176 0.782609
31 DUX 0.434211 0.771429
32 N3E 0.432432 0.865672
33 THU 0.428571 0.935484
34 U4S 0.428571 0.835821
35 UVC 0.42029 0.736111
36 BTD 0.418919 0.857143
37 U3S 0.416667 0.835821
38 3DT 0.415385 0.907692
39 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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 1tdu.bio1) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1TDU; Ligand: DUR; Similar sites found: 9
This union binding pocket(no: 2) in the query (biounit: 1tdu.bio1) has 15 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5DQ8 FLF 0.03523 0.40296 2.08333
2 4I5I NAD 0.02519 0.40815 2.64151
3 1N2A GTS 0.009398 0.41151 2.98507
4 1W5T ADP 0.01868 0.4009 4.5283
5 2VBU CDP 0.0147 0.4252 5.14706
6 3MX2 TTP 0.007921 0.41932 8.30189
7 4QRH 0O2 0.01391 0.4109 8.57143
8 1CSI OAA 0.04297 0.40747 10.9434
9 5B6D C5P 0.0000003819 0.55076 28.6792
Pocket No.: 3; Query (leader) PDB : 1TDU; Ligand: CB3; 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: 1tdu.bio1) has 16 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1TDU; Ligand: CB3; Similar sites found: 2
This union binding pocket(no: 4) in the query (biounit: 1tdu.bio1) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3CZ7 ACO 0.0183 0.40125 7.16981
2 2ZFN ACO 0.01794 0.40023 7.16981
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