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Receptor
PDB id Resolution Class Description Source Keywords
1F28 1.9 Å EC: 2.1.1.45 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS BOUND TO DUMP AND BW1843U89 PNEUMOCYSTIS CARINII BETA-SHEET PROTEIN-INHIBITOR COMPLEX TRANSFERASE
Ref.: APPROACHES TO SOLVING THE RIGID RECEPTOR PROBLEM BY IDENTIFYING A MINIMAL SET OF FLEXIBLE RESIDUES DURI DOCKING. CHEM.BIOL. V. 8 445 2001
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
F89 A:401;
B:402;
C:403;
D:404;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Ki = 16 nM
500.503 C27 H24 N4 O6 CC1=N...
UMP A:301;
B:302;
C:303;
D:304;
Valid;
Valid;
Valid;
Valid;
none;
none;
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
1F28 1.9 Å EC: 2.1.1.45 CRYSTAL STRUCTURE OF THYMIDYLATE SYNTHASE FROM PNEUMOCYSTIS BOUND TO DUMP AND BW1843U89 PNEUMOCYSTIS CARINII BETA-SHEET PROTEIN-INHIBITOR COMPLEX TRANSFERASE
Ref.: APPROACHES TO SOLVING THE RIGID RECEPTOR PROBLEM BY IDENTIFYING A MINIMAL SET OF FLEXIBLE RESIDUES DURI DOCKING. CHEM.BIOL. V. 8 445 2001
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 1F28 Ki = 16 nM F89 C27 H24 N4 O6 CC1=Nc2ccc....
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: F89; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 F89 1 1
2 3TU 0.465649 0.847222
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 : 1F28; Ligand: F89; Similar sites found with APoc: 12
This union binding pocket(no: 1) in the query (biounit: 1f28.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4OB6 S2T 2.6936
2 3K5I AIR 2.6936
3 5HSA FAS 3.0303
4 3WUR O4B 3.50877
5 3WLV AZA 3.7037
6 1QM5 PLP 5.05051
7 2YLD CMO 6.29921
8 4L9Z OXL 6.73401
9 3ALT MLB 7.00637
10 5Z20 NAI 9.76431
11 2CI5 HCS 12.6761
12 3P2H MTA 18.408
Pocket No.: 2; Query (leader) PDB : 1F28; Ligand: UMP; Similar sites found with APoc: 33
This union binding pocket(no: 2) in the query (biounit: 1f28.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1GAR U89 0.943396
2 4C2C ALA ALA ALA 1.0101
3 2DFV NAD 1.6835
4 4JLS 3ZE 1.97368
5 1Q0H FOM 2.6936
6 3MBI HSX 2.78746
7 3TW1 AHN 2.95359
8 5K0A FAD 3.0303
9 2WR1 NAG 3.0303
10 4P86 5GP 3.82514
11 1KNM LAT 3.84615
12 3PAK MAN 4.05405
13 1PZM 5GP 4.2654
14 5F1V 3VN 4.3771
15 2VBU CDP 4.41176
16 2CXG GLC GLC 4.7138
17 4UZI IMD 4.7138
18 4WQQ MAN 4.96454
19 1B5E DCM 5.28455
20 5E70 RCD 5.38721
21 4P83 U5P 5.49451
22 5JQ1 ZPF 5.51724
23 4XQC NAD 6.06061
24 3GFB NAD 6.06061
25 4G9N NGA 6.29371
26 3P7G MAN 6.84932
27 2ZQO NGA 6.92308
28 1RC0 KT5 7.6555
29 4OWK NGA 7.97101
30 1QHO MAL 8.41751
31 6APV 3L4 10.1852
32 5G3L SIA 15.1515
33 5B6D C5P 19.8653
Pocket No.: 3; Query (leader) PDB : 1F28; Ligand: F89; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 1f28.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5WS9 OXL 1.6835
2 4N14 WR7 3.367
3 4RJK TDL 3.367
4 4CCW VKC 3.367
5 2F7A BEZ 4.31034
6 5Z21 OXM 5.72391
7 3UVD MB3 6.45161
8 4L6T GAL NGA GAL BGC SIA 10.7143
Pocket No.: 4; Query (leader) PDB : 1F28; Ligand: UMP; Similar sites found with APoc: 12
This union binding pocket(no: 4) in the query (biounit: 1f28.bio2) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4OUJ LBT 2.3569
2 1CSI CMX 2.3569
3 1CSI OAA 2.3569
4 1TDF FAD 2.3569
5 2GGX NPJ 2.5
6 2D24 XYS XYS 3.367
7 4LOC OXM 3.367
8 1QKQ MAN 4.92958
9 2ZX2 RAM 5.12821
10 1BCJ NGA 5.84416
11 1SL6 GAL NDG FUC 8.69565
12 5G3L SIA GAL 15.1515
Pocket No.: 5; Query (leader) PDB : 1F28; 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: 5) in the query (biounit: 1f28.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1F28; Ligand: F89; Similar sites found with APoc: 7
This union binding pocket(no: 6) in the query (biounit: 1f28.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4EU7 COA 2.6936
2 2D09 FLV 3.7037
3 5JNW 6LJ 3.77358
4 6G5J EM8 4.84848
5 5LWY OLB 9.34579
6 3PE2 E1B 9.42761
7 4JX1 CAM 16.8142
Pocket No.: 7; Query (leader) PDB : 1F28; Ligand: F89; Similar sites found with APoc: 1
This union binding pocket(no: 7) in the query (biounit: 1f28.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5ICE 2H4 3.7037
Pocket No.: 8; Query (leader) PDB : 1F28; 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: 8) in the query (biounit: 1f28.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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