Receptor
PDB id Resolution Class Description Source Keywords
2YOG 1.5 Å EC: 2.7.4.9 PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A (THIO)UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR PLASMODIUM FALCIPARUM TRANSFERASE MALARIA INHIBITOR
Ref.: SYNTHESIS AND EVALUATION OF ALPHA-THYMIDINE ANALOGU NOVEL ANTIMALARIALS. J.MED.CHEM. V. 55 10948 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
74X B:211;
A:211;
Valid;
Valid;
none;
none;
Ki = 31 uM
478.873 C18 H18 Cl F3 N4 O4 S CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YOH 1.6 Å EC: 2.7.4.9 PLASMODIUM FALCIPARUM THYMIDYLATE KINASE IN COMPLEX WITH A UREA-ALPHA-DEOXYTHYMIDINE INHIBITOR PLASMODIUM FALCIPARUM TRANSFERASE MALARIA INHIBITOR
Ref.: SYNTHESIS AND EVALUATION OF ALPHA-THYMIDINE ANALOGU NOVEL ANTIMALARIALS. J.MED.CHEM. V. 55 10948 2012
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2YOH Ki = 11 uM WMJ C17 H19 N5 O7 CC1=CN(C(=....
2 2YOF Ki = 25 uM 74W C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
3 2WWF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2YOG Ki = 31 uM 74X C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 2YOH Ki = 11 uM WMJ C17 H19 N5 O7 CC1=CN(C(=....
2 2YOF Ki = 25 uM 74W C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
3 2WWF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2YOG Ki = 31 uM 74X C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
50% Homology Family (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2YOH Ki = 11 uM WMJ C17 H19 N5 O7 CC1=CN(C(=....
2 2YOF Ki = 25 uM 74W C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
3 2WWF - TMP C10 H15 N2 O8 P CC1=CN(C(=....
4 2YOG Ki = 31 uM 74X C18 H18 Cl F3 N4 O4 S CC1=CN(C(=....
5 2V54 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
6 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
7 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
8 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
9 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
10 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
11 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
12 4TMK Kd = 20 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
13 1E2Q - TMP C10 H15 N2 O8 P CC1=CN(C(=....
14 1E9C - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
15 1NN0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
16 1E2G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
17 1NN1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
18 1NMX - FDM C10 H14 F N2 O7 P CC1=CN(C(=....
19 1E2E - AF3 Al F3 F[Al](F)F
20 1NN5 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
21 1E9B - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
22 1E2D - TMP C10 H15 N2 O8 P CC1=CN(C(=....
23 1E99 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
24 1NMY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 2XX3 - TAE C9 H14 N2 O8 P2 CC1=CN(C(=....
26 1NMZ - NYM C10 H16 N3 O7 P CC1=CN(C(=....
27 1E9D - ATM C10 H14 N5 O7 P CC1=CN(C(=....
28 1NN3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
29 1E9A - Z5A C20 H24 N10 O22 P5 CC1=CN(C(=....
30 1E9F - TMP C10 H15 N2 O8 P CC1=CN(C(=....
31 1E9E - TMP C10 H15 N2 O8 P CC1=CN(C(=....
32 1E98 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
33 1E2F - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
34 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
35 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
36 1TMK - TMP C10 H15 N2 O8 P CC1=CN(C(=....
37 3UWO ic50 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
38 3UXM ic50 = 17 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
39 5UIV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
40 5XB2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 5XB3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
42 5XAI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
43 5H56 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
44 5H5B - FLC C6 H5 O7 C(C(=O)[O-....
45 5H5K - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 74X; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 74X 1 1
2 74W 1 1
3 WMJ 0.5 0.764045
4 THM 0.488636 0.775
5 LLT 0.488636 0.775
6 0DN 0.477778 0.78481
7 TXS 0.424242 0.746988
8 TMP 0.42 0.72093
9 T3S 0.415842 0.768293
10 TYD 0.4 0.732558
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YOH; Ligand: WMJ; Similar sites found: 61
This union binding pocket(no: 1) in the query (biounit: 2yoh.bio1) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1ZUI SKM 0.0001344 0.45247 None
2 1UKZ ADP 0.00004092 0.46852 2.46305
3 1Z83 AP5 0.0001504 0.44773 2.55102
4 2DPY ADP 0.003829 0.46094 2.85714
5 2FNA ADP 0.005655 0.41592 3.33333
6 3A9B BGC 0.02423 0.41379 3.33333
7 1P72 ADP 0.0004005 0.42907 3.80952
8 4TTQ ATP 0.000002359 0.41827 3.80952
9 1HE1 GDP 0.01374 0.40185 3.97727
10 1QF9 C5P 0.00002331 0.48224 4.12371
11 1QF9 ADP 0.00002331 0.48224 4.12371
12 1QF9 ALF 0.00002331 0.48224 4.12371
13 1Z2A GDP 0.006277 0.41088 4.16667
14 2JAQ DCP 0.0002711 0.40748 4.39024
15 2NCD ADP 0.0001063 0.54763 4.7619
16 1YTM ATP 0.0002329 0.40134 4.7619
17 2WJG GDP 0.000559 0.49329 4.78723
18 4BQS K2Q 0.00005303 0.46746 5.68182
19 4BQS ADP 0.00005303 0.4546 5.68182
20 4BFW ZVW 0.001969 0.41387 5.71429
21 2RGX AP5 0.00001001 0.50327 5.82524
22 1O3Y GTP 0.0002274 0.4084 6.0241
23 1W4R TTP 0.0006463 0.40644 6.15385
24 3N5C GDP 0.0001035 0.53049 6.17284
25 1S3G AP5 0.0000101 0.5003 6.19048
26 4X8O AP5 0.00001586 0.49957 6.19048
27 1ZIN AP5 0.00001242 0.49691 6.19048
28 4NU0 AP5 0.00006201 0.46782 6.19048
29 1AKY AP5 0.00003726 0.44958 6.19048
30 1OS1 PYR 0.0004752 0.41936 6.19048
31 1OS1 ATP 0.0004105 0.41808 6.19048
32 1XKV ATP 0.00003892 0.40407 6.19048
33 1M7B GTP 0.007416 0.41387 6.52174
34 5G41 AP5 0.000005856 0.5162 6.66667
35 4MKG AP5 0.00001577 0.49299 6.66667
36 3FB4 AP5 0.00001805 0.49078 6.66667
37 2C04 GCP 0.005202 0.42773 6.66667
38 1NHX FTB 0.00268 0.41296 6.66667
39 1NHX PEP 0.002523 0.41296 6.66667
40 2GMV PEP 0.001001 0.40801 6.66667
41 3LXR GDP 0.003727 0.44248 7.02703
42 2VOH CIT 0.0376 0.41826 8.9172
43 2CBZ ATP 0.00002135 0.60025 9.04762
44 1E2K TMC 0.0001432 0.45683 9.04762
45 1GOJ ADP 0.0001307 0.54721 9.52381
46 3GJ8 GDP 0.0005508 0.48804 10
47 2ZFI ADP 0.003134 0.45525 10
48 1X6V ADP 0.0001029 0.43922 10
49 2OFW ADX 0.0001513 0.45464 10.0962
50 1KO8 6PG 0.000002314 0.44582 10.2857
51 4Q1A 2XZ 0.00169 0.46757 10.9524
52 4Q1A UDP 0.00169 0.46757 10.9524
53 2QG6 NMN 0.00004202 0.44824 11.0553
54 2PEZ DAT 0.0001543 0.44414 11.7318
55 2PEZ GGZ 0.0001543 0.44414 11.7318
56 4MKF AP5 0.000006165 0.50985 12.8571
57 3H86 AP5 0.0002762 0.43946 13.0208
58 1OE0 TTP 0.00008259 0.43266 16.1905
59 1TQ4 GDP 0.0007051 0.45952 17.619
60 1M7G ADX 0.0001703 0.43951 35.2381
61 1M7G ADP 0.0002563 0.42529 35.2381
Pocket No.: 2; Query (leader) PDB : 2YOH; Ligand: WMJ; Similar sites found: 39
This union binding pocket(no: 2) in the query (biounit: 2yoh.bio2) has 35 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WIC GNP 0.00001832 0.40194 1.90476
2 4LPS GDP 0.00002035 0.40442 2.38095
3 4P4T GDP 0.0001023 0.40676 2.85714
4 2WKQ GTP 0.005617 0.41042 3.33333
5 1SKQ GDP 0.00002639 0.40101 3.80952
6 1VHT BA3 0.00008732 0.4005 3.80952
7 1LVG ADP 0.0000009507 0.41185 4.0404
8 3IIJ ADP 0.0000139 0.4076 4.44444
9 1CLU DBG 0.005433 0.40379 4.81928
10 1HTW ADP 0.00002095 0.40437 5.06329
11 3DOE GTP 0.0002577 0.4101 5.20833
12 1ZJ6 G3D 0.00002028 0.40024 5.34759
13 1ZCB GDP 0.0003801 0.41419 5.71429
14 2J59 GTP 0.0002228 0.41224 6.0241
15 1R4A GNP 0.0004064 0.40872 6.06061
16 1J2J GTP 0.0002114 0.41312 6.66667
17 2HF9 GSP 0.00005804 0.41149 6.66667
18 1DAK DPU 0.004737 0.40613 6.66667
19 2QQ0 TMP 0.00242 0.407 7.06522
20 2QQ0 THM 0.001922 0.40569 7.06522
21 2QQ0 ANP 0.002621 0.40569 7.06522
22 1SVK ALF GDP 0.001758 0.40693 7.61905
23 1Y3A GDP 0.000343 0.40554 7.61905
24 2OM2 GDP 0.0003083 0.40216 7.61905
25 4BAS GNP 0.0003204 0.4023 8.54271
26 1UJ2 C5P 0.0006037 0.41083 8.57143
27 1UJ2 ADP 0.0006378 0.41031 8.57143
28 2A5F GTP 0.0002098 0.41895 8.80829
29 1R2Q GNP 0.003103 0.40547 8.82353
30 4V0K GDP 0.0005947 0.40359 8.87574
31 2W83 GTP 0.0001913 0.41416 9.09091
32 1GP2 GDP 0.000564 0.40055 9.52381
33 3QBT GNP 0.006725 0.4014 9.77011
34 1UPT GTP 0.0002483 0.40598 10
35 4WZA ADP 0.01002 0.40624 10.4762
36 4WZA ACP 0.01002 0.40624 10.4762
37 4NE2 ADP 0.00254 0.40879 11.4286
38 4NE2 SH2 0.002938 0.40879 11.4286
39 1M7G AV2 0.000004196 0.41458 35.2381
Feedback