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Receptor
PDB id Resolution Class Description Source Keywords
1AXW 1.7 Å EC: 2.1.1.45 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) ESCHERICHIA COLI METHYLTRANSFERASE TRANSFERASE INHIBITOR
Ref.: DISCOVERY OF THYMIDYLATE SYNTHASE INHIBITORS USING FLEXIBLE DOCKING AND AN EMPIRICALLY TUNED SCORING FUNCTION TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTX A:732;
B:733;
Valid;
Valid;
none;
none;
submit data
454.439 C20 H22 N8 O5 CN(Cc...
UMP A:603;
B:604;
Valid;
Valid;
none;
none;
submit data
308.182 C9 H13 N2 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1AXW 1.7 Å EC: 2.1.1.45 E. COLI THYMIDYLATE SYNTHASE IN COMPLEX WITH METHOTREXATE (MTX) AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP) ESCHERICHIA COLI METHYLTRANSFERASE TRANSFERASE INHIBITOR
Ref.: DISCOVERY OF THYMIDYLATE SYNTHASE INHIBITORS USING FLEXIBLE DOCKING AND AN EMPIRICALLY TUNED SCORING FUNCTION TO BE PUBLISHED
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1AXW - UMP C9 H13 N2 O8 P 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 1AXW - UMP C9 H13 N2 O8 P 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: 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
Ligand no: 2; Ligand: UMP; Similar ligands found: 52
No: Ligand ECFP6 Tc MDL keys Tc
1 DU 1 1
2 UMP 1 1
3 DUD 0.8 0.985075
4 UC5 0.772727 0.970588
5 DUT 0.753623 0.985075
6 DUN 0.75 0.956522
7 DUP 0.742857 0.956522
8 DUS 0.692308 0.853333
9 DUR 0.683333 0.852941
10 DDN 0.632353 1
11 UFP 0.591549 0.929577
12 TMP 0.583333 0.956522
13 BRU 0.583333 0.929577
14 5HU 0.583333 0.942857
15 UM3 0.57971 0.955224
16 5IU 0.575342 0.929577
17 DC 0.561644 0.928571
18 DCM 0.561644 0.928571
19 BVP 0.531646 0.942857
20 DU DU DU DU BRU DU DU 0.53125 0.864865
21 U 0.527778 0.911765
22 U5P 0.527778 0.911765
23 DDU 0.523077 0.753623
24 UMC 0.520548 0.941176
25 QBT 0.493333 0.927536
26 DUA 0.487805 0.783784
27 DU3 0.487805 0.780822
28 DU4 0.47619 0.76
29 TYD 0.469136 0.942857
30 YYY 0.451219 0.915493
31 UDP 0.45 0.898551
32 TTP 0.447059 0.942857
33 8OG 0.435294 0.835443
34 U3P 0.434211 0.897059
35 UA3 0.434211 0.897059
36 U2P 0.434211 0.884058
37 UTP 0.433735 0.898551
38 44P 0.43038 0.914286
39 DCP 0.430233 0.915493
40 2KH 0.411765 0.873239
41 DUX 0.411765 0.756757
42 UMF 0.410256 0.84507
43 139 0.409091 0.8
44 UPU 0.409091 0.871429
45 URI 0.408451 0.771429
46 TBD 0.406977 0.90411
47 DU DU DU DU BRU DA DU 0.40625 0.771084
48 PUA 0.405172 0.833333
49 UNP 0.402299 0.873239
50 UDX 0.4 0.873239
51 PUP 0.4 0.955882
52 UAD 0.4 0.873239
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1AXW; Ligand: UMP; Similar sites found with APoc: 26
This union binding pocket(no: 1) in the query (biounit: 1axw.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1PZM 5GP 0.947867
2 2O3Z AI7 1.88679
3 3TW1 AHN 2.53165
4 4OPC PGT 2.64151
5 6FLZ MMA 2.77778
6 4P86 5GP 3.27869
7 2CXG GLC GLC 3.77358
8 4C2C ALA ALA ALA 3.77358
9 1QHO MAL 4.5283
10 5F1V 3VN 4.5283
11 2VBU CDP 5.14706
12 1Q0H NDP 5.28302
13 1Q0H FOM 5.28302
14 5Y6Q FAD 5.28302
15 5JQ1 ZPF 6.2069
16 4WQQ MAN 6.38298
17 2ZQO NGA 6.92308
18 4OWK NGA 7.97101
19 4P83 U5P 8.24176
20 4XQC NAD 9.0566
21 1GAR U89 9.90566
22 2CDC NAP 10.566
23 2CDC XYP 10.566
24 1KNM LAT 10.7692
25 5B6D C5P 28.6792
26 1B5E DCM 32.1138
Pocket No.: 2; Query (leader) PDB : 1AXW; Ligand: UMP; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 1axw.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 3MBI HSX 1.88679
2 2FXV 5GP 2.57732
3 1N2A GTS 2.98507
4 6APV 3L4 3.24074
5 5LRT ADP 3.77358
6 3GFB NAD 4.5283
7 5WHT SIA GAL 5.07246
8 3WLE NAD 5.66038
9 2DFV NAD 6.03774
10 2GGX NPJ 6.25
11 1V8B NAD 6.41509
12 3MX2 TTP 8.30189
13 1RC0 KT5 10.5263
14 3KLL MAL 14.3396
Pocket No.: 3; Query (leader) PDB : 1AXW; Ligand: MTX; Similar sites found with APoc: 3
This union binding pocket(no: 3) in the query (biounit: 1axw.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJK TPP 4.15094
2 4RJK TDL 4.15094
3 4ZY1 4U5 7.16981
Pocket No.: 4; Query (leader) PDB : 1AXW; Ligand: MTX; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 1axw.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 5URY PAM 1.36986
2 4OB6 S2T 5.28302
3 4PYA 2X3 6.21118
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