Receptor
PDB id Resolution Class Description Source Keywords
5X67 2.13 Å EC: 2.1.1.45 HUMAN THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP AND NOLATREX HOMO SAPIENS METHYLTRANSFERASE TRANSFERASE
Ref.: STRUCTURAL ANALYSES OF HUMAN THYMIDYLATE SYNTHASE R SITE THAT MAY CONTROL CONFORMATIONAL SWITCHING BETW ACTIVE AND INACTIVE STATES. J. BIOL. CHEM. V. 292 13449 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UMP B:401;
A:401;
Valid;
Valid;
none;
none;
Kd = 1.19 uM
308.182 C9 H13 N2 O8 P C1[C@...
7Z9 B:402;
A:402;
Valid;
Valid;
none;
none;
submit data
284.336 C14 H12 N4 O S Cc1cc...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1I00 2.5 Å EC: 2.1.1.45 CRYSTAL STRUCTURE OF HUMAN THYMIDYLATE SYNTHASE, TERNARY COM DUMP AND TOMUDEX HOMO SAPIENS THYMIDYLATE SYNTHASE HUMAN TERNARY COMPLEX DUMP TOMUDEXCONFORMATION TRANSFERASE
Ref.: CRYSTAL STRUCTURE OF A DELETION MUTANT OF HUMAN THY SYNTHASE DELTA (7-29) AND ITS TERNARY COMPLEX WITH AND DUMP. PROTEIN SCI. V. 10 988 2001
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 5X66 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
2 1I00 Kd = 0.46 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
3 1HVY - D16 C21 H22 N4 O6 S CC1=NC(=O)....
4 5X67 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
5 5X5D Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
70% Homology Family (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 4E28 Ki = 1.3 uM 0MZ C19 H15 F3 N4 O3 S c1ccc(c(c1....
2 5X66 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
3 1I00 Kd = 0.46 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
4 1HVY - D16 C21 H22 N4 O6 S CC1=NC(=O)....
5 5X67 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
6 5X5D Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
7 5H39 - UMP C9 H13 N2 O8 P C1[C@@H]([....
8 5H3A - D16 C21 H22 N4 O6 S CC1=NC(=O)....
9 1F28 Ki = 16 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
10 2AAZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
50% Homology Family (55)
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 1LCA - UMP C9 H13 N2 O8 P C1[C@@H]([....
3 1VZC - UFP C9 H12 F N2 O8 P C1[C@@H]([....
4 1LCB - TMP C10 H15 N2 O8 P CC1=CN(C(=....
5 1BO7 - U C9 H13 N2 O9 P O=C1N(C2OC....
6 2G8A - UMP C9 H13 N2 O8 P C1[C@@H]([....
7 1JMI Kd = 0.87 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
8 1VZE - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
9 1BO8 - U C9 H13 N2 O9 P O=C1N(C2OC....
10 1BPJ - UMP C9 H13 N2 O8 P C1[C@@H]([....
11 1VZA - UMP C9 H13 N2 O8 P C1[C@@H]([....
12 1NJE Kd = 160 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
13 1JMH - UMP C9 H13 N2 O8 P C1[C@@H]([....
14 1TSL Ki = 0.7 uM A15 C24 H14 Cl2 O4 c1cc2cccc3....
15 2G86 Kd = 0.44 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
16 1VZD - UFP C9 H12 F N2 O8 P C1[C@@H]([....
17 1NJD Kd = 2.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
18 1BP6 - UMP C9 H13 N2 O8 P C1[C@@H]([....
19 1TVV - UMP C9 H13 N2 O8 P C1[C@@H]([....
20 1TVU - UMP C9 H13 N2 O8 P C1[C@@H]([....
21 1NJC Kd = 2.8 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
22 1LCE - UMP C9 H13 N2 O8 P C1[C@@H]([....
23 1TSY Kd = 11 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
24 1BP0 Kd = 4 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
25 1NJA Kd = 0.49 uM DCM C9 H14 N3 O7 P C1[C@@H]([....
26 1VZB - UMP C9 H13 N2 O8 P C1[C@@H]([....
27 2G89 - UMP C9 H13 N2 O8 P C1[C@@H]([....
28 1TSX - UMP C9 H13 N2 O8 P C1[C@@H]([....
29 1JMF Kd = 1.7 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
30 1JMG Kd = 0.85 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
31 1TVW - UMP C9 H13 N2 O8 P C1[C@@H]([....
32 2G8D - UMP C9 H13 N2 O8 P C1[C@@H]([....
33 5X66 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
34 1I00 Kd = 0.46 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
35 1HVY - D16 C21 H22 N4 O6 S CC1=NC(=O)....
36 5X67 Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
37 5X5D Kd = 1.19 uM UMP C9 H13 N2 O8 P C1[C@@H]([....
38 1BJG - TMF C20 H21 N7 O6 c1cc(ccc1C....
39 2VET - UMP C9 H13 N2 O8 P C1[C@@H]([....
40 2FTO - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 1TYS Kd = 3.27 uM DHF C19 H21 N7 O6 c1cc(ccc1C....
42 2BBQ - PFG C39 H44 N8 O15 C#CC[N@](C....
43 1BID - UMP C9 H13 N2 O8 P C1[C@@H]([....
44 4LRR Ki = 6 uM CF9 C18 H9 N O6 c1cc2c(ccc....
45 1AOB - DDU C9 H12 N2 O4 C[C@@H]1[C....
46 1F4E Ki = 1.1 mM TPR C12 H15 N O4 S Cc1ccc(cc1....
47 1BDU - DUR C9 H12 N2 O5 C1[C@@H]([....
48 1TRG - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
49 2TSC - CB3 C24 H23 N5 O6 C#CCN(Cc1c....
50 2KCE Ki = 0.67 uM D16 C21 H22 N4 O6 S CC1=NC(=O)....
51 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
52 5H39 - UMP C9 H13 N2 O8 P C1[C@@H]([....
53 5H3A - D16 C21 H22 N4 O6 S CC1=NC(=O)....
54 1F28 Ki = 16 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
55 2AAZ - UMP C9 H13 N2 O8 P C1[C@@H]([....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: UMP; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 UMP 1 1
2 DU 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 DUT MG 0.684932 0.914286
10 DUR 0.683333 0.852941
11 UMP AF3 PO4 0.675676 0.876712
12 DDN 0.632353 1
13 UFP 0.591549 0.929577
14 BRU 0.583333 0.929577
15 5HU 0.583333 0.942857
16 TMP 0.583333 0.956522
17 UM3 0.57971 0.955224
18 5IU 0.575342 0.929577
19 DCM 0.561644 0.928571
20 DC 0.561644 0.928571
21 BVP 0.531646 0.942857
22 DU DU DU DU BRU DU DU 0.53125 0.864865
23 U5P 0.527778 0.911765
24 DDU 0.523077 0.753623
25 UMC 0.520548 0.941176
26 QBT 0.493333 0.927536
27 DUA 0.487805 0.783784
28 DU3 0.487805 0.780822
29 DU4 0.47619 0.76
30 TYD 0.469136 0.942857
31 YYY 0.451219 0.915493
32 UDP 0.45 0.898551
33 TTP 0.447059 0.942857
34 8OG 0.435294 0.835443
35 UA3 0.434211 0.897059
36 U3P 0.434211 0.897059
37 U2P 0.434211 0.884058
38 UTP 0.433735 0.898551
39 44P 0.43038 0.914286
40 DCP 0.430233 0.915493
41 DUX 0.411765 0.756757
42 2KH 0.411765 0.873239
43 UMF 0.410256 0.84507
44 139 0.409091 0.8
45 UPU 0.409091 0.871429
46 U 0.408451 0.771429
47 URI 0.408451 0.771429
48 TBD 0.406977 0.90411
49 PUA 0.405172 0.833333
50 UNP 0.402299 0.873239
51 UDX 0.4 0.873239
52 UAD 0.4 0.873239
53 PUP 0.4 0.955882
Ligand no: 2; Ligand: 7Z9; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 7Z9 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1I00; Ligand: UMP; 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: 1i00.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1I00; Ligand: D16; Similar sites found: 8
This union binding pocket(no: 2) in the query (biounit: 1i00.bio1) has 47 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LNX URI 0.04055 0.40192 2.46914
2 4RW3 SHV 0.03942 0.41251 2.75862
3 3PUR 2HG 0.03645 0.40349 3.44828
4 1TUV VK3 0.01612 0.42638 3.50877
5 1PZM 5GP 0.02032 0.41167 4.2654
6 1YRO UDP 0.03064 0.40305 6.50407
7 5B6D C5P 0.000000805 0.60203 17.2414
8 1B5E DCM 0.001613 0.4193 32.5203
Pocket No.: 3; Query (leader) PDB : 1I00; Ligand: D16; 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: 1i00.bio1) has 41 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1I00; Ligand: UMP; Similar sites found: 8
This union binding pocket(no: 4) in the query (biounit: 1i00.bio1) has 60 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1LNX URI 0.04055 0.40192 2.46914
2 4RW3 SHV 0.03942 0.41251 2.75862
3 3PUR 2HG 0.03645 0.40349 3.44828
4 1TUV VK3 0.01612 0.42638 3.50877
5 1PZM 5GP 0.02032 0.41167 4.2654
6 1YRO UDP 0.03064 0.40305 6.50407
7 5B6D C5P 0.000000805 0.60203 17.2414
8 1B5E DCM 0.001613 0.4193 32.5203
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