Receptor
PDB id Resolution Class Description Source Keywords
3UXM 1.95 Å EC: 2.7.4.9 STRUCTURE GUIDED DEVELOPMENT OF NOVEL THYMIDINE MIMETICS TAR PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE: FROM HIT TO LEADG ENERATION PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE THYMIDINE TRIPHOSPHATE TRANSFERASE-TRANINHIBITOR COMPLEX
Ref.: STRUCTURE GUIDED DEVELOPMENT OF NOVEL THYMIDINE MIM TARGETING PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE HIT TO LEAD GENERATION. J.MED.CHEM. V. 55 852 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
0DN A:800;
B:801;
C:802;
D:803;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
ic50 = 17 uM
244.22 C10 H13 F N2 O4 CC1=C...
MG A:1;
A:213;
C:213;
C:214;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3UXM 1.95 Å EC: 2.7.4.9 STRUCTURE GUIDED DEVELOPMENT OF NOVEL THYMIDINE MIMETICS TAR PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE: FROM HIT TO LEADG ENERATION PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE THYMIDINE TRIPHOSPHATE TRANSFERASE-TRANINHIBITOR COMPLEX
Ref.: STRUCTURE GUIDED DEVELOPMENT OF NOVEL THYMIDINE MIM TARGETING PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE HIT TO LEAD GENERATION. J.MED.CHEM. V. 55 852 2012
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3UWK ic50 = 58 uM 0DF C13 H11 N3 O CN1c2cc(cn....
2 3UWO ic50 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
3 3UXM ic50 = 17 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3UWK ic50 = 58 uM 0DF C13 H11 N3 O CN1c2cc(cn....
2 3UWO ic50 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
3 3UXM ic50 = 17 uM 0DN C10 H13 F N2 O4 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: 0DN; Similar ligands found: 61
No: Ligand ECFP6 Tc MDL keys Tc
1 0DN 1 1
2 LLT 0.777778 0.923077
3 THM 0.777778 0.923077
4 TXS 0.65625 0.882353
5 TMP 0.646154 0.84507
6 T3S 0.636364 0.882353
7 TYD 0.6 0.833333
8 TBD 0.583333 0.8
9 TTP 0.567568 0.833333
10 T3P 0.560606 0.805556
11 AZZ 0.544118 0.816901
12 FDM 0.521127 0.835616
13 WMJ 0.512195 0.75
14 TLO 0.506024 0.810811
15 TRH 0.5 0.8
16 NYM 0.5 0.821918
17 18T 0.5 0.8
18 3R2 0.5 0.789474
19 1JB 0.5 0.8
20 TDX 0.5 0.810811
21 DAU 0.494253 0.8
22 THP 0.493151 0.830986
23 ID2 0.492308 0.867647
24 DWN 0.488636 0.779221
25 T3Q 0.488636 0.779221
26 T3F 0.488636 0.779221
27 0N2 0.483146 0.769231
28 T46 0.483146 0.8
29 ATM 0.480519 0.766234
30 BVD 0.478261 0.909091
31 MMF 0.477778 0.779221
32 74X 0.477778 0.78481
33 74W 0.477778 0.78481
34 0FX 0.477778 0.779221
35 DT DT DT DT DT 0.477273 0.810811
36 ATY 0.475 0.786667
37 4TG 0.473118 0.789474
38 3YN 0.47191 0.8
39 QDM 0.467391 0.769231
40 FNF 0.462366 0.789474
41 1YF 0.462366 0.789474
42 DT DT PST 0.461538 0.8
43 BTD 0.453333 0.833333
44 UFP 0.452055 0.821918
45 DT DT DT 0.451219 0.794521
46 JHZ 0.446809 0.759494
47 AKM 0.446809 0.740741
48 BRU 0.445946 0.797297
49 AZD 0.445783 0.75641
50 2DT 0.430556 0.819444
51 5HU 0.426667 0.808219
52 QUH 0.425743 0.779221
53 FUH 0.425743 0.779221
54 5IU 0.421053 0.797297
55 TPE 0.413043 0.766234
56 3DT 0.411765 0.880597
57 T5A 0.409524 0.722892
58 DT ME6 DT 0.407767 0.789474
59 BVP 0.407407 0.833333
60 0TT 0.404762 0.857143
61 ABT 0.4 0.7375
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: 7
This union binding pocket(no: 1) in the query (biounit: 3uxm.bio3) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4JGT PYR 0.008849 0.41066 3.31754
2 4C1W SLT 0.01769 0.41412 4.25532
3 1PZ1 NAP 0.03717 0.40198 5.21327
4 1JXZ BCA 0.01909 0.41867 9.95261
5 4MZU TDR 0.00744 0.4081 11.8483
6 1NZY BCA 0.01844 0.41948 12.7962
7 1J78 OLA 0.005984 0.42572 18.9573
Pocket No.: 2; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: 4
This union binding pocket(no: 2) in the query (biounit: 3uxm.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4I90 CHT 0.02789 0.40351 4.73934
2 5MGJ 7MX 0.007417 0.41667 5.71429
3 1KI6 AHU 0.009491 0.40905 6.16114
4 1P72 THM 0.00473 0.42878 7.109
Pocket No.: 3; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: 2
This union binding pocket(no: 3) in the query (biounit: 3uxm.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1H9G COA MYR 0.0244 0.40005 2.36967
2 5JO1 6LM 0.01067 0.40825 6.48649
Pocket No.: 4; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3uxm.bio5) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 3uxm.bio5) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: 2
This union binding pocket(no: 6) in the query (biounit: 3uxm.bio6) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3AGC RCC 0.03338 0.40447 2.89855
2 4G28 0W8 0.004012 0.42714 12.7451
Pocket No.: 7; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 7) in the query (biounit: 3uxm.bio6) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 3uxm.bio4) has 14 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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