Receptor
PDB id Resolution Class Description Source Keywords
1BJG 2.3 Å EC: 2.1.1.45 D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING ESCHERICHIA COLI TRANSFERASE ACTIVE SITE MUTANT REACTION INTERMEDIATE METHYLTRANSFERASE
Ref.: D221 IN THYMIDYLATE SYNTHASE CONTROLS CONFORMATION AND THEREBY OPENING OF THE IMIDAZOLIDINE. BIOCHEMISTRY V. 37 13893 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TMF A:267;
 Valid;
 none;
 submit data
455.424 C20 H21 N7 O6 c1cc(...
UFP A:266;
 Invalid;
 none;
 submit data
326.172 C9 H12 F N2 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2KCE 2.2 Å EC: 2.1.1.45 BINDING OF THE ANTICANCER DRUG ZD1694 TO E. COLI THYMIDYLATE ASSESSING SPECIFICITY AND AFFINITY ESCHERICHIA COLI METHYLTRANSFERASE REACTION INTERMEDIATE ANTIFOLATE DRUG D
Ref.: BINDING OF THE ANTICANCER DRUG ZD1694 TO E. COLI TH SYNTHASE: ASSESSING SPECIFICITY AND AFFINITY. STRUCTURE V. 4 1317 1996
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 33 families.
1 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
2 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
5 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
6 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
8 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
9 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
10 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
11 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
12 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
2 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
5 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
6 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
8 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
9 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
10 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
11 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
12 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
13 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
50% Homology Family (61)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4E28 Ki = 1.3 uM 0MZ C19 H15 F3 N4 O3 S c1ccc(c(c1....
2 6QXG Ki = 1.1 nM UFP C9 H12 F N2 O8 P C1[C@@H]([....
3 6QXH - UMP C9 H13 N2 O8 P C1[C@@H]([....
4 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
5 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
6 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
7 1BO7 - U C9 H13 N2 O9 P C1=CN(C(=O....
8 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
9 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
10 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
11 1BO8 - U C9 H13 N2 O9 P C1=CN(C(=O....
12 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
13 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
15 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
16 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
17 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
19 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
24 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
25 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
26 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
27 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
28 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
29 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
31 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
32 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
33 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
34 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
35 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
36 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
37 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
38 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
39 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
40 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
41 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
42 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
43 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
44 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
45 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
46 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
47 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
48 5H39 - UMP C9 H13 N2 O8 P C1[C@@H]([....
49 5H3A - D16 C21 H22 N4 O6 S CC1=NC(=O)....
50 1F28 Ki = 16 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
51 6PF6 - OEJ C22 H17 N5 O6 c1cc(ccc1C....
52 5X66 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
53 1I00 Ki = 0.46 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
54 1HVY - D16 C21 H22 N4 O6 S CC1=NC(=O)....
55 6PF3 - OE7 C21 H16 Cl N5 O4 c1cc(ccc1C....
56 6PF5 - OED C23 H21 N5 O5 COc1ccc(c(....
57 5X67 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
58 5X5D Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
59 2AAZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
60 6QYA - UMP C9 H13 N2 O8 P C1[C@@H]([....
61 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TMF; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 TMF 1 1
2 MHF 0.588785 0.96
3 MEF 0.550459 0.96
4 THF 0.518182 0.893333
5 FGD 0.445455 0.72
6 GUE 0.444444 0.92
7 FON 0.428571 0.866667
8 9L9 0.415094 0.76
9 DHF 0.412281 0.824324
10 LYA 0.410714 0.714286
11 TLL 0.408 0.8125
12 DZF 0.405172 0.723684
13 C2F 0.403361 0.833333
14 DDF 0.401709 0.779221
15 21V 0.401709 0.779221
16 FFO 0.4 0.866667
Similar Ligands (3D)
Ligand no: 1; Ligand: TMF; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2KCE; Ligand: D16; 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: 2kce.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2KCE; Ligand: D16; 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: 2kce.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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