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 = 20 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 10 families.
1 3UWK ic50 = 58 uM 0DF C13 H11 N3 O CN1c2cc(cn....
2 3UWO ic50 = 0.44 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
3 3UXM ic50 = 20 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 10 families.
1 3UWK ic50 = 58 uM 0DF C13 H11 N3 O CN1c2cc(cn....
2 3UWO ic50 = 0.44 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
3 3UXM ic50 = 20 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
50% Homology Family (54)
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 2CCJ - TMP C10 H15 N2 O8 P CC1=CN(C(=....
11 2CCG - TMP C10 H15 N2 O8 P CC1=CN(C(=....
12 4HDC ic50 = 1.2 nM 13Y C28 H32 Cl N3 O5 CC1=CN(C(=....
13 4HEJ ic50 = 24000 nM 14D C24 H24 F3 N3 O3 CC1=CN(C(=....
14 4GSY ic50 = 120 nM 0Y5 C25 H24 F3 N3 O5 CC1=CN(C(=....
15 4HLC ic50 = 174 nM T05 C24 H25 N3 O7 S Cc1cccc(c1....
16 4TMK Kd = 20 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
17 1E2Q - TMP C10 H15 N2 O8 P CC1=CN(C(=....
18 1E9C - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
19 1NN0 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 1E2G - TMP C10 H15 N2 O8 P CC1=CN(C(=....
21 1NN1 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
22 1NMX - FDM C10 H14 F N2 O7 P CC1=CN(C(=....
23 1E2E - AF3 Al F3 F[Al](F)F
24 1NN5 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
25 1E9B - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
26 1E2D - TMP C10 H15 N2 O8 P CC1=CN(C(=....
27 1E99 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
28 1NMY - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
29 2XX3 - TAE C9 H14 N2 O8 P2 CC1=CN(C(=....
30 1NMZ - NYM C10 H16 N3 O7 P CC1=CN(C(=....
31 1E9D - ATM C10 H14 N5 O7 P CC1=CN(C(=....
32 1NN3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
33 1E9A - Z5A C20 H24 N10 O22 P5 CC1=CN(C(=....
34 1E9F - TMP C10 H15 N2 O8 P CC1=CN(C(=....
35 1E9E - TMP C10 H15 N2 O8 P CC1=CN(C(=....
36 1E98 - ATM C10 H14 N5 O7 P CC1=CN(C(=....
37 1E2F - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
38 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
39 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
40 1TMK - TMP C10 H15 N2 O8 P CC1=CN(C(=....
41 5X8C - ACP C11 H18 N5 O12 P3 c1nc(c2c(n....
42 5ZB4 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
43 5ZAX - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
44 5X86 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
45 5X8B - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
46 3UWO ic50 = 0.44 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
47 3UXM ic50 = 20 uM 0DN C10 H13 F N2 O4 CC1=CN(C(=....
48 5UIV - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
49 5XB2 - TMP C10 H15 N2 O8 P CC1=CN(C(=....
50 5XB3 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
51 5XAI - TMP C10 H15 N2 O8 P CC1=CN(C(=....
52 5H56 - TYD C10 H16 N2 O11 P2 CC1=CN(C(=....
53 5H5B - FLC C6 H5 O7 C(C(=O)[O-....
54 5H5K - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
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 TTP MG 0.56 0.857143
12 AZZ 0.544118 0.816901
13 FDM 0.521127 0.835616
14 WMJ 0.512195 0.75
15 TLO 0.506024 0.810811
16 TDX 0.5 0.810811
17 1JB 0.5 0.8
18 NYM 0.5 0.821918
19 TRH 0.5 0.8
20 18T 0.5 0.8
21 9RC 0.5 0.731707
22 3R2 0.5 0.789474
23 DAU 0.494253 0.8
24 THP 0.493151 0.830986
25 ID2 0.492308 0.867647
26 T3Q 0.488636 0.779221
27 T3F 0.488636 0.779221
28 DWN 0.488636 0.779221
29 0N2 0.483146 0.769231
30 T46 0.483146 0.8
31 ATM 0.480519 0.766234
32 BVD 0.478261 0.909091
33 0FX 0.477778 0.779221
34 74X 0.477778 0.78481
35 74W 0.477778 0.78481
36 MMF 0.477778 0.779221
37 ATY 0.475 0.786667
38 4TG 0.473118 0.789474
39 3YN 0.47191 0.8
40 QDM 0.467391 0.769231
41 FNF 0.462366 0.789474
42 1YF 0.462366 0.789474
43 BTD 0.453333 0.833333
44 UFP 0.452055 0.821918
45 AKM 0.446809 0.740741
46 JHZ 0.446809 0.759494
47 BRU 0.445946 0.797297
48 AZD 0.445783 0.75641
49 3DR DT DT DT DT DT 0.442105 0.821918
50 2DT 0.430556 0.819444
51 5HU 0.426667 0.808219
52 FUH 0.425743 0.779221
53 QUH 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 Ligands (3D)
Ligand no: 1; Ligand: 0DN; Similar ligands found: 350
No: Ligand Similarity coefficient
1 B86 0.9978
2 MCY 0.9955
3 5MD 0.9950
4 5BT 0.9910
5 DCZ 0.9766
6 DUR 0.9749
7 3D1 0.9728
8 SCT 0.9725
9 TMC 0.9711
10 AHU 0.9700
11 F01 0.9640
12 THU 0.9636
13 CTN 0.9621
14 5UD 0.9613
15 MDR 0.9597
16 URI 0.9535
17 URD 0.9491
18 ADN 0.9486
19 5AE 0.9474
20 DDU 0.9472
21 GNG 0.9455
22 2FD 0.9448
23 CTD 0.9445
24 RAB 0.9435
25 AR3 0.9430
26 IMH 0.9411
27 TBN 0.9410
28 5AD 0.9408
29 1DA 0.9408
30 UA2 0.9403
31 2TU 0.9402
32 A 0.9397
33 CL9 0.9389
34 NOS 0.9387
35 FMB 0.9378
36 DNB 0.9375
37 FMC 0.9374
38 TYU 0.9355
39 9DI 0.9354
40 PIR 0.9336
41 3BH 0.9325
42 7D7 0.9305
43 GEO 0.9303
44 UUA 0.9298
45 5NB 0.9291
46 DHZ 0.9285
47 H7S 0.9285
48 PRH 0.9280
49 HPR 0.9280
50 TRP 0.9279
51 PUR 0.9270
52 ZEB 0.9268
53 ZYV 0.9264
54 I5A 0.9264
55 AD3 0.9262
56 NWW 0.9258
57 GMP 0.9257
58 6CR 0.9248
59 2FA 0.9241
60 CDY 0.9239
61 IMG 0.9207
62 5JT 0.9203
63 ZYW 0.9180
64 FTU 0.9170
65 EXR 0.9165
66 NNR 0.9159
67 TIZ 0.9155
68 DCF 0.9155
69 6MD 0.9151
70 CTE 0.9150
71 8HG 0.9147
72 YOF 0.9146
73 EKH 0.9144
74 DAH 0.9137
75 5ID 0.9133
76 MTP 0.9122
77 JY4 0.9121
78 RFZ 0.9121
79 CFE 0.9116
80 FM1 0.9111
81 A4D 0.9110
82 3AD 0.9110
83 W29 0.9104
84 LL1 0.9101
85 9UL 0.9094
86 5CD 0.9077
87 TIA 0.9063
88 TR7 0.9056
89 BRD 0.9049
90 FM2 0.9048
91 MTA 0.9048
92 KYN 0.9045
93 4UO 0.9039
94 MTM 0.9018
95 6J9 0.9017
96 MMS 0.9006
97 OCZ 0.9005
98 5V7 0.9003
99 DBM 0.9000
100 LDC 0.8998
101 XYA 0.8993
102 LTT 0.8992
103 ZIQ 0.8989
104 EXL 0.8982
105 8OX 0.8972
106 MG7 0.8971
107 KF5 0.8971
108 DTR 0.8967
109 CC5 0.8966
110 XFE 0.8963
111 NIY 0.8963
112 MTH 0.8960
113 JMQ 0.8958
114 II4 0.8957
115 X11 0.8957
116 1QP 0.8950
117 MBY 0.8946
118 CCV 0.8945
119 PF1 0.8944
120 78U 0.8943
121 3L1 0.8943
122 6ZW 0.8942
123 9B3 0.8941
124 DBS 0.8941
125 DTE 0.8936
126 TAL 0.8932
127 JGB 0.8931
128 ALN 0.8931
129 89J 0.8930
130 IOS 0.8928
131 MIL 0.8927
132 5I5 0.8926
133 AMR 0.8920
134 GL6 0.8913
135 ETV 0.8909
136 8DA 0.8904
137 M5H 0.8903
138 MPK 0.8903
139 KP2 0.8897
140 OA1 0.8892
141 GA2 0.8886
142 26A 0.8878
143 4OG 0.8876
144 QMS 0.8872
145 K80 0.8871
146 N8M 0.8867
147 WOE 0.8864
148 88R 0.8862
149 X48 0.8862
150 NEU 0.8861
151 M02 0.8860
152 8U3 0.8853
153 30G 0.8852
154 CK2 0.8845
155 IOP 0.8839
156 Q4G 0.8834
157 4I5 0.8825
158 IQQ 0.8823
159 DXK 0.8821
160 EN1 0.8821
161 790 0.8816
162 MPU 0.8815
163 FTV 0.8814
164 TYR 0.8813
165 M2T 0.8812
166 YF3 0.8812
167 M3Q 0.8811
168 0A1 0.8809
169 4Z9 0.8806
170 FWD 0.8806
171 51Y 0.8805
172 MCF 0.8804
173 L5D 0.8804
174 E0O 0.8802
175 22L 0.8800
176 3VW 0.8799
177 7AP 0.8798
178 61M 0.8795
179 XTS 0.8791
180 54X 0.8789
181 ITW 0.8789
182 W8G 0.8787
183 5E5 0.8787
184 4GU 0.8784
185 RVE 0.8784
186 DBQ 0.8784
187 B5A 0.8783
188 AOJ 0.8781
189 HVE 0.8780
190 B41 0.8778
191 HBI 0.8777
192 A4G 0.8775
193 MXD 0.8773
194 6DP 0.8772
195 NCV 0.8772
196 H2B 0.8771
197 1VK 0.8770
198 AVA 0.8770
199 S0G 0.8768
200 0GA 0.8768
201 3RP 0.8765
202 H4B 0.8765
203 HO4 0.8764
204 ENG 0.8764
205 AUV 0.8764
206 BZE 0.8761
207 C0H 0.8759
208 FHC 0.8756
209 EZN 0.8756
210 I2E 0.8753
211 CWD 0.8752
212 5F8 0.8751
213 LTN 0.8748
214 BP7 0.8744
215 SBI 0.8740
216 PE2 0.8738
217 1KN 0.8737
218 C2Y 0.8736
219 WCU 0.8736
220 BG6 0.8736
221 7CI 0.8736
222 MUK 0.8735
223 2O6 0.8734
224 WVV 0.8734
225 X6P 0.8733
226 BIO 0.8732
227 78P 0.8731
228 WSD 0.8730
229 SYE 0.8727
230 3Y7 0.8725
231 5F5 0.8725
232 VM1 0.8724
233 TQU 0.8722
234 2B4 0.8720
235 Q5M 0.8720
236 4KL 0.8719
237 2GQ 0.8717
238 5FL 0.8715
239 1A7 0.8713
240 EXD 0.8710
241 XDK 0.8710
242 4R1 0.8707
243 9FH 0.8703
244 TI7 0.8701
245 G6P 0.8700
246 LIP 0.8697
247 MJ5 0.8697
248 BWD 0.8692
249 7L4 0.8688
250 657 0.8687
251 N1E 0.8684
252 IWD 0.8683
253 XYS XYP 0.8683
254 KCH 0.8681
255 GZ2 0.8679
256 BBY 0.8676
257 C9E 0.8673
258 0F9 0.8672
259 MAJ 0.8671
260 EXG 0.8671
261 LJ3 0.8670
262 5WN 0.8669
263 VYM 0.8668
264 MP5 0.8667
265 0FR 0.8666
266 Y4L 0.8664
267 B4O 0.8664
268 68A 0.8663
269 HA5 0.8661
270 CFA 0.8661
271 BPY 0.8659
272 363 0.8658
273 ACE TRP 0.8656
274 6HO 0.8653
275 5P3 0.8652
276 ISA 0.8652
277 AWE 0.8650
278 2UZ 0.8649
279 YO5 0.8649
280 3TC 0.8649
281 1Z6 0.8648
282 2GD 0.8647
283 4FF 0.8647
284 V2Z 0.8646
285 MEX 0.8645
286 SGV 0.8644
287 6HX 0.8642
288 JA3 0.8640
289 3B4 0.8635
290 92G 0.8635
291 CH9 0.8633
292 F2W 0.8632
293 EAT 0.8631
294 EV2 0.8627
295 SG2 0.8626
296 ZSP 0.8625
297 FPL 0.8621
298 EYA 0.8621
299 69K 0.8620
300 RVD 0.8618
301 SKF 0.8617
302 DIH 0.8615
303 ONR 0.8614
304 6HP 0.8614
305 92P 0.8609
306 4G2 0.8607
307 CH8 0.8607
308 4I8 0.8604
309 JR2 0.8603
310 HNK 0.8602
311 ENO 0.8600
312 TT4 0.8600
313 B2Y 0.8600
314 ID8 0.8600
315 EUE 0.8596
316 AJD 0.8595
317 S0E 0.8595
318 MOK 0.8595
319 BZQ 0.8592
320 9FG 0.8591
321 I4D 0.8590
322 A1Y 0.8588
323 1WC 0.8580
324 M01 0.8578
325 BB4 0.8577
326 BQ2 0.8575
327 SGP 0.8573
328 GRX 0.8572
329 N2M 0.8572
330 KTJ 0.8571
331 0OL 0.8570
332 JRB 0.8565
333 96U 0.8563
334 IMQ 0.8561
335 AVX 0.8559
336 54E 0.8555
337 9ZE 0.8554
338 PH3 0.8553
339 50C 0.8551
340 ABF 0.8550
341 S3C 0.8549
342 LJ4 0.8544
343 JZA 0.8544
344 IA2 0.8544
345 X04 0.8542
346 1SF 0.8537
347 K48 0.8536
348 92O 0.8534
349 M5E 0.8520
350 BGP 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3uxm.bio3) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3uxm.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3uxm.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3UXM; Ligand: 0DN; 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: 3uxm.bio5) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 3uxm.bio6) has 14 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3UXM; Ligand: 0DN; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3UXM; Ligand: 0DN; 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: 3uxm.bio4) has 14 residues
No: Leader PDB Ligand Sequence Similarity
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