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Receptor
PDB id Resolution Class Description Source Keywords
5X66 1.99 Å EC: 2.1.1.45 HUMAN THYMIDYLATE SYNTHASE IN COMPLEX WITH DUMP AND METHOTRE 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
MTX B:402;
C:402;
F:402;
A:402;
E:402;
D:402;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
submit data
454.439 C20 H22 N8 O5 CN(Cc...
UMP C:401;
F:401;
B:401;
E:401;
A:401;
D:401;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Kd = 1.19 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
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 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: 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 : 1I00; Ligand: UMP; Similar sites found with APoc: 28
This union binding pocket(no: 1) in the query (biounit: 1i00.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 6BR8 6OU 1.19048
2 2C91 TLA 1.72414
3 1LNX URI 2.46914
4 3LM9 ADP 3.10345
5 4URN NOV 3.11111
6 4P86 5GP 3.27869
7 3B6C SDN 3.84615
8 4P83 U5P 3.84615
9 1P19 IMP 4.0724
10 2E2P ADP 4.13793
11 1PZM 5GP 4.2654
12 5X3R 7Y3 4.39024
13 3OBT SLB 4.82759
14 3GD8 GOL 5.38117
15 3JQQ A2P 5.51724
16 3MYZ TFX 6
17 1ZGS XMM 6.2069
18 5JQ1 ZPF 6.2069
19 5WJ6 B4A 6.2069
20 2GNK ATP 6.25
21 3TW1 AHN 8.01688
22 2W47 UNF 8.33333
23 2CXG GLC GLC 9.31034
24 3VET TOY 10.6897
25 5B6D C5P 17.2414
26 5Z84 PEK 21.4286
27 5URY PAM 21.9178
28 1B5E DCM 32.5203
Pocket No.: 2; Query (leader) PDB : 1I00; Ligand: D16; Similar sites found with APoc: 32
This union binding pocket(no: 2) in the query (biounit: 1i00.bio1) has 47 residues
No: Leader PDB Ligand Sequence Similarity
1 6BR8 6OU 1.19048
2 2C91 TLA 1.72414
3 1YOE RIB 2.06897
4 5XHA FRU 2.06897
5 1CT9 AMP 2.41379
6 1LNX URI 2.46914
7 4GK9 MAN BMA MAN MAN MAN 2.50896
8 6FMC DUE 2.53165
9 4RW3 SHV 2.75862
10 3LM9 ADP 3.10345
11 1FX8 BOG 3.20285
12 3PUR 2HG 3.44828
13 1TUV VK3 3.50877
14 4P83 U5P 3.84615
15 3PNA CMP 3.8961
16 2E2P ADP 4.13793
17 1PZM 5GP 4.2654
18 5W0E 9U4 4.72973
19 3GD8 GOL 5.38117
20 2GGX NPJ 5.625
21 1ZGS XMM 6.2069
22 5JQ1 ZPF 6.2069
23 5WJ6 B4A 6.2069
24 2GNK ATP 6.25
25 1YRO UDP 6.50407
26 3NJQ NJQ 7.77202
27 2CXG GLC GLC 9.31034
28 5BOE PEP 9.31034
29 5FQ0 FLC 9.64912
30 6BYF CIT 10.5882
31 5B6D C5P 17.2414
32 1B5E DCM 32.5203
Pocket No.: 3; Query (leader) PDB : 1I00; Ligand: D16; Similar sites found with APoc: 18
This union binding pocket(no: 3) in the query (biounit: 1i00.bio1) has 41 residues
No: Leader PDB Ligand Sequence Similarity
1 4URN NOV 3.11111
2 4P86 5GP 3.27869
3 4WQQ MAN 3.5461
4 3B6C SDN 3.84615
5 1P19 IMP 4.0724
6 3OBT SLB 4.82759
7 5JCM ISD 5.17241
8 5JCM FAD 5.17241
9 5JCM NAD 5.17241
10 5XXH E0D 5.26316
11 1NXJ TLA 5.46448
12 2YLD CMO 5.51181
13 5N18 8HZ 6.42202
14 3TW1 AHN 8.01688
15 2W47 UNF 8.33333
16 3VET TOY 10.6897
17 5Z84 PEK 21.4286
18 5URY PAM 21.9178
Pocket No.: 4; Query (leader) PDB : 1I00; Ligand: UMP; Similar sites found with APoc: 17
This union binding pocket(no: 4) in the query (biounit: 1i00.bio1) has 60 residues
No: Leader PDB Ligand Sequence Similarity
1 1YOE RIB 2.06897
2 5XHA FRU 2.06897
3 1CT9 AMP 2.41379
4 4GK9 MAN BMA MAN MAN MAN 2.50896
5 6FMC DUE 2.53165
6 4RW3 SHV 2.75862
7 1FX8 BOG 3.20285
8 3PUR 2HG 3.44828
9 1TUV VK3 3.50877
10 3PNA CMP 3.8961
11 5W0E 9U4 4.72973
12 2GGX NPJ 5.625
13 1YRO UDP 6.50407
14 3NJQ NJQ 7.77202
15 5BOE PEP 9.31034
16 5FQ0 FLC 9.64912
17 6BYF CIT 10.5882
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