Receptor
PDB id Resolution Class Description Source Keywords
5J7W 2.5 Å EC: 2.1.1.45 ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE COMPLEX WITH METH ENTEROCOCCUS FAECALIS ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE METHOTREXATE CTRANSFERASE
Ref.: X-RAY CRYSTAL STRUCTURES OF ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE WITH FOLATE BINDING SITE INHIB EUR.J.MED.CHEM. V. 123 649 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:401;
B:401;
C:401;
D:401;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
MTX C:402;
D:402;
Valid;
Valid;
none;
none;
Ki = 13 uM
454.439 C20 H22 N8 O5 CN(Cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5J7W 2.5 Å EC: 2.1.1.45 ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE COMPLEX WITH METH ENTEROCOCCUS FAECALIS ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE METHOTREXATE CTRANSFERASE
Ref.: X-RAY CRYSTAL STRUCTURES OF ENTEROCOCCUS FAECALIS THYMIDYLATE SYNTHASE WITH FOLATE BINDING SITE INHIB EUR.J.MED.CHEM. V. 123 649 2016
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 33 families.
1 6QYA - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
70% Homology Family (33)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
3 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 1BO7 - U C9 H13 N2 O9 P C1=CN(C(=O....
5 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
6 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
7 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
8 1BO8 - U C9 H13 N2 O9 P C1=CN(C(=O....
9 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
10 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
11 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
12 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
13 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
14 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
15 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
16 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
17 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
21 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
22 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
24 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
25 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
26 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
28 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
29 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
31 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
32 6QYA - UMP C9 H13 N2 O8 P C1[C@@H]([....
33 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
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: MTX; Similar ligands found: 8
No: Ligand ECFP6 Tc MDL keys Tc
1 MTX 1 1
2 3BI 0.783505 0.884058
3 2MX 0.778947 0.924242
4 04J 0.663043 0.870968
5 MT1 0.632653 0.968254
6 MOT 0.534653 0.923077
7 COP 0.453782 0.815385
8 FOL 0.410714 0.779412
Similar Ligands (3D)
Ligand no: 1; Ligand: MTX; Similar ligands found: 10
No: Ligand Similarity coefficient
1 THG 0.9330
2 DHF 0.9249
3 LYA 0.9222
4 CB3 0.9108
5 DZF 0.9044
6 FFO 0.8934
7 GPB 0.8911
8 LY3 0.8744
9 D16 0.8666
10 GHW 0.8601
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5J7W; Ligand: MTX; 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: 5j7w.bio2) has 26 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5J7W; Ligand: MTX; 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: 5j7w.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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