Receptor
PDB id Resolution Class Description Source Keywords
1JMI 2.5 Å EC: 2.1.1.45 CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING TO CATALYS 229 MUTANTS OF THYMIDYLATE SYNTHASE LACTOBACILLUS CASEI TRANSFERASE METHYLTRANSFERASE
Ref.: CONTRIBUTIONS OF ORIENTATION AND HYDROGEN BONDING T CATALYSIS IN ASN229 MUTANTS OF THYMIDYLATE SYNTHASE J.MOL.BIOL. V. 276 113 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UMP A:317;
Valid;
none;
Kd = 0.87 uM
308.182 C9 H13 N2 O8 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2G86 2.4 Å EC: 2.1.1.45 L. CASEI THYMIDYLATE SYNTHASE Y261F IN COMPLEX WITH SUBSTRAT LACTOBACILLUS CASEI DUMP-BINDING RESIDUE DUMP COMPLEX THYMIDYLATE SYNTHASE MUTTRANSFERASE
Ref.: THE ROLE OF PROTEIN DYNAMICS IN THYMIDYLATE SYNTHAS CATALYSIS: VARIANTS OF CONSERVED 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)-BINDING TYR-261 BIOCHEMISTRY V. 45 7415 2006
Members (31)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 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]([....
70% Homology Family (32)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 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 5J7W Ki = 13 uM MTX C20 H22 N8 O5 CN(Cc1cnc2....
50% Homology Family (55)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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 C1=CN(C(=O....
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 C1=CN(C(=O....
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: 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 : 2G86; Ligand: UMP; 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: 2g86.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2G86; Ligand: UMP; 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: 2g86.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
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