Receptor
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0YB A:301;
B:301;
Valid;
Valid;
none;
none;
Ki = 330 pM
584.501 C29 H34 Br N3 O5 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4GFD 1.8 Å EC: 2.7.4.9 THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-6 STAPHYLOCOCCUS AUREUS SUBSP. AUREUS KINASE THYMIDINE MONPHOSPHATE SOLUBLE TRANSFERASE-TRANSFEINHIBITOR COMPLEX
Ref.: IN VIVO VALIDATION OF THYMIDYLATE KINASE (TMK) WITH RATIONALLY DESIGNED, SELECTIVE ANTIBACTERIAL COMPOU ACS CHEM.BIOL. V. 7 1866 2012
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 4QGA ic50 = 12 nM 31Z C24 H23 Cl F N3 O5 CC1=CN(C(=....
2 4HLD ic50 = 0.5 nM 16T C22 H22 Cl N3 O6 S CC1=CN(C(=....
3 4QGG ic50 = 1 nM 32C C28 H31 Cl F N3 O5 CC1=CN(C(=....
4 4QGF ic50 = 69 nM 32B C27 H30 Cl N3 O6 CC[C@H](c1....
5 4QG7 ic50 = 10 nM 32K C25 H26 Cl N3 O6 CC1=CN(C(=....
6 4QGH ic50 = 1 nM 32E C28 H31 Cl F N3 O5 CC1=CN(C(=....
7 4GFD Ki = 330 pM 0YB C29 H34 Br N3 O5 CC1=CN(C(=....
8 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
9 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
10 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
11 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
12 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
13 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
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: 0YB; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 0YB 1 1
2 13Y 0.666667 0.934211
3 32B 0.531746 0.8625
4 32E 0.519685 0.922078
5 32C 0.519685 0.922078
6 0Y5 0.484127 0.894737
7 T05 0.468254 0.725275
8 31Z 0.427481 0.883117
9 32K 0.427481 0.873418
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4GFD; Ligand: 0YB; Similar sites found: 47
This union binding pocket(no: 1) in the query (biounit: 4gfd.bio1) has 25 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 5MWE TCE 0.001799 0.46639 None
2 5UGW GSH 0.008453 0.46596 None
3 3NFD COA 0.01964 0.40818 None
4 4LWU 20U 0.01144 0.40798 None
5 5LWY OLA 0.002737 0.42509 2.43902
6 5W3Y IHP 0.01718 0.41115 2.43902
7 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 0.02543 0.40246 2.43902
8 5VRH OLB 0.008694 0.43382 2.92683
9 4WGF HX2 0.02304 0.40064 2.92683
10 1RL4 BL5 0.01607 0.41053 3.19149
11 1NF8 BOG 0.002057 0.47654 3.41463
12 4RW3 SHV 0.008781 0.43966 3.41463
13 4RW3 PLM 0.02357 0.42811 3.41463
14 1P72 THM 0.02399 0.4079 3.41463
15 5IKR ID8 0.01996 0.40009 3.41463
16 4G8R 96P 0.008122 0.43414 3.90244
17 2JFZ 003 0.01902 0.40809 3.90244
18 2JFZ DGL 0.02102 0.4061 3.90244
19 5MES 7LT 0.01305 0.40903 3.91304
20 4HBM 0Y7 0.01422 0.40353 4.16667
21 1M2Z BOG 0.008468 0.43882 4.39024
22 1V6A TRE 0.03303 0.40199 4.87805
23 2XN5 FUN 0.01236 0.41415 5.36585
24 1TV5 N8E 0.02074 0.41122 5.36585
25 3R9V DXC 0.03403 0.40035 5.36585
26 5V4R MGT 0.01312 0.43544 5.55556
27 3TDC 0EU 0.002532 0.47308 5.85366
28 4UCC ZKW 0.006122 0.44976 6.34146
29 4YSX E23 0.01701 0.41571 6.38298
30 4URN NOV 0.01611 0.41695 7.31707
31 5LX9 OLA 0.0099 0.40728 7.31707
32 3VM7 GLC 0.032 0.4098 7.80488
33 3FUR Z12 0.01652 0.40192 7.80488
34 4TUZ 36J 0.01557 0.40531 8.29268
35 4TV1 36M 0.03084 0.40218 8.29268
36 2Q8H TF4 0.03813 0.40937 9.7561
37 3I7V ATP 0.02392 0.4017 10.4478
38 3KO0 TFP 0.01749 0.42324 10.8911
39 5CHR 4NC 0.02078 0.41079 10.9489
40 5A0U CHT 0.009249 0.4295 11.2195
41 3SQP 3J8 0.02003 0.41882 11.7073
42 2VWA PTY 0.03392 0.40642 12.8713
43 3OGN 3OG 0.01136 0.40112 13.7097
44 3B6C SDN 0.01384 0.42038 17.0732
45 5OCA 9QZ 0.01709 0.40832 17.561
46 5BVT PAM 0.003382 0.41748 23.8806
47 2JAQ DCP 0.004564 0.40541 37.561
Pocket No.: 2; Query (leader) PDB : 4GFD; Ligand: 0YB; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4gfd.bio1) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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