Receptor
PDB id Resolution Class Description Source Keywords
3TMK 2 Å EC: 2.7.4.9 CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: I MPLICATIONS FOR CATALYSIS AND AZT ACTIVATION SACCHAROMYCES CEREVISIAE KINASE PHOSPHOTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR P1-(5'-ADENOSYL) P5-(5'-THYMIDYL) PENTAPHOSPHATE (TP5A) AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION. BIOCHEMISTRY V. 37 3
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
T5A A:217;
B:217;
C:217;
D:217;
E:217;
F:217;
G:217;
H:217;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
Kd = 135 nM
891.354 C20 H30 N7 O23 P5 CC1=C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3TMK 2 Å EC: 2.7.4.9 CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: I MPLICATIONS FOR CATALYSIS AND AZT ACTIVATION SACCHAROMYCES CEREVISIAE KINASE PHOSPHOTRANSFERASE
Ref.: CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR P1-(5'-ADENOSYL) P5-(5'-THYMIDYL) PENTAPHOSPHATE (TP5A) AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION. BIOCHEMISTRY V. 37 3
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
2 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
3 1TMK - TMP C10 H15 N2 O8 P 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 2TMK - ATM C10 H14 N5 O7 P CC1=CN(C(=....
2 3TMK Kd = 135 nM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
3 1TMK - TMP C10 H15 N2 O8 P 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 = 20 uM 0DJ C14 H12 N4 O2 CN1c2cc(cn....
47 3UXM ic50 = 17 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
Ligand no: 1; Ligand: T5A; Similar ligands found: 290
No: Ligand ECFP6 Tc MDL keys Tc
1 T5A 1 1
2 4TA 0.778761 0.963415
3 B4P 0.656566 0.864198
4 AP5 0.656566 0.864198
5 BA3 0.646465 0.864198
6 AQP 0.631068 0.841463
7 5FA 0.631068 0.841463
8 HEJ 0.621359 0.841463
9 ATP 0.621359 0.841463
10 Z5A 0.615385 0.906977
11 TTP 0.61165 0.841463
12 A2D 0.61 0.864198
13 UP5 0.608333 0.91358
14 AGS 0.59434 0.802326
15 SAP 0.59434 0.802326
16 A4P 0.593496 0.842697
17 ADP 0.592233 0.841463
18 G5P 0.588235 0.825581
19 ANP 0.583333 0.821429
20 M33 0.580952 0.853659
21 G3A 0.579832 0.825581
22 AD9 0.579439 0.821429
23 TYD 0.572816 0.841463
24 AN2 0.571429 0.831325
25 AT4 0.571429 0.811765
26 139 0.571429 0.939024
27 GTA 0.570248 0.818182
28 AR6 0.570093 0.841463
29 APR 0.570093 0.841463
30 A3R 0.561404 0.879518
31 A1R 0.561404 0.879518
32 ACP 0.560748 0.843373
33 ACQ 0.554545 0.843373
34 6YZ 0.553571 0.843373
35 ADS THS THS THS 0.55303 0.863636
36 DAU 0.551724 0.855422
37 ADX 0.551402 0.766667
38 CA0 0.551402 0.843373
39 ATF 0.544643 0.811765
40 PAX 0.544118 0.939759
41 PRX 0.541284 0.821429
42 9X8 0.538462 0.823529
43 OAD 0.538462 0.865854
44 25L 0.537815 0.853659
45 5AL 0.535714 0.853659
46 4TC 0.535433 0.914634
47 ADQ 0.534483 0.843373
48 A 0.533981 0.817073
49 AMP 0.533981 0.817073
50 PR8 0.533898 0.848837
51 ABM 0.533333 0.819277
52 50T 0.53211 0.809524
53 6V0 0.531746 0.914634
54 A22 0.530435 0.853659
55 3R2 0.529915 0.845238
56 3OD 0.529412 0.865854
57 1ZZ 0.529412 0.818182
58 T99 0.526786 0.811765
59 TAT 0.526786 0.811765
60 5SV 0.525862 0.804598
61 8QN 0.525862 0.853659
62 TMP 0.524272 0.829268
63 TLO 0.521739 0.865854
64 T3F 0.521008 0.879518
65 T3Q 0.521008 0.879518
66 NAX 0.519685 0.939024
67 TRH 0.516949 0.855422
68 1JB 0.516949 0.855422
69 18T 0.516949 0.855422
70 TDX 0.516949 0.865854
71 00A 0.516949 0.813953
72 0N2 0.516667 0.869048
73 TXE 0.515625 0.902439
74 APC 0.513514 0.855422
75 SRP 0.513043 0.855422
76 OOB 0.512821 0.853659
77 0FX 0.512397 0.879518
78 AP0 0.511628 0.914634
79 AP2 0.509259 0.855422
80 A12 0.509259 0.855422
81 4AD 0.508475 0.86747
82 PAJ 0.508475 0.816092
83 DWN 0.508333 0.857143
84 3YN 0.508333 0.833333
85 TXD 0.507812 0.879518
86 NAI 0.507812 0.925926
87 DLL 0.504202 0.853659
88 T46 0.504132 0.855422
89 BIS 0.504132 0.793103
90 B5M 0.504065 0.845238
91 B5Y 0.504065 0.845238
92 OMR 0.503876 0.829545
93 MMF 0.5 0.857143
94 3UK 0.5 0.843373
95 AKM 0.5 0.83908
96 SRA 0.5 0.77907
97 UPA 0.5 0.902439
98 CNA 0.496241 0.878049
99 DND 0.496124 0.855422
100 NXX 0.496124 0.855422
101 4TG 0.496 0.86747
102 9SN 0.495935 0.804598
103 LAD 0.495868 0.837209
104 B5V 0.495868 0.833333
105 WAQ 0.495868 0.857143
106 AMO 0.495798 0.878049
107 AU1 0.495495 0.821429
108 QDM 0.491935 0.825581
109 TXA 0.491803 0.855422
110 NB8 0.491803 0.847059
111 ME8 0.491803 0.818182
112 FYA 0.491803 0.876543
113 PTJ 0.491803 0.804598
114 AHX 0.491667 0.847059
115 DAL AMP 0.491525 0.831325
116 MAP 0.491525 0.802326
117 ADJ 0.488722 0.894118
118 48N 0.488372 0.847059
119 4UU 0.488189 0.890244
120 XAH 0.488 0.818182
121 1YF 0.488 0.86747
122 FNF 0.488 0.86747
123 JHZ 0.488 0.837209
124 25A 0.487395 0.841463
125 DTP 0.486957 0.853659
126 DA DT DA DA 0.485915 0.927711
127 4UW 0.484615 0.880952
128 DQV 0.484375 0.876543
129 4UV 0.484127 0.890244
130 ADV 0.482456 0.855422
131 ADP PO3 0.482456 0.817073
132 RBY 0.482456 0.855422
133 TYM 0.480916 0.878049
134 YAP 0.48 0.86747
135 FA5 0.48 0.878049
136 ALF ADP 0.478632 0.761364
137 ADP ALF 0.478632 0.761364
138 HFD 0.478261 0.802326
139 AFH 0.476562 0.816092
140 9ZA 0.475 0.813953
141 9ZD 0.475 0.813953
142 GAP 0.474138 0.8
143 SON 0.473214 0.855422
144 80F 0.471014 0.905882
145 LAQ 0.469231 0.797753
146 7D4 0.469027 0.788235
147 ITT 0.469027 0.795181
148 EAD 0.465278 0.939024
149 GA7 0.465116 0.855422
150 5AS 0.464286 0.726316
151 MYR AMP 0.464 0.797753
152 BT5 0.463768 0.831461
153 LMS 0.462963 0.728261
154 VO4 ADP 0.462185 0.809524
155 ADP VO4 0.462185 0.809524
156 3AT 0.461538 0.841463
157 PUA 0.460993 0.926829
158 A3D 0.460432 0.865854
159 FDA 0.46 0.896552
160 QUH 0.458647 0.857143
161 FUH 0.458647 0.857143
162 6FA 0.456954 0.862069
163 PAP 0.456897 0.829268
164 NAD 0.456522 0.853659
165 YLP 0.454545 0.840909
166 P1H 0.452703 0.916667
167 DAT 0.452174 0.853659
168 ADP BMA 0.451613 0.821429
169 TBD 0.451327 0.811765
170 FAD 0.45098 0.872093
171 FAS 0.45098 0.872093
172 F2R 0.449275 0.8
173 2A5 0.448276 0.821429
174 A A 0.448 0.819277
175 COD 0.446043 0.833333
176 BTX 0.446043 0.840909
177 YLC 0.444444 0.860465
178 NAQ 0.444444 0.825581
179 ATR 0.444444 0.817073
180 YLB 0.444444 0.840909
181 SFD 0.441558 0.757576
182 AOC 0.441441 0.73494
183 FNK 0.43949 0.88764
184 AVV 0.439024 0.847059
185 TYR AMP 0.438462 0.845238
186 IOT 0.437956 0.811111
187 NAE 0.4375 0.845238
188 FAY 0.436709 0.882353
189 NAJ PZO 0.43662 0.869048
190 U A 0.43662 0.879518
191 AHZ 0.43609 0.758242
192 ATY 0.435897 0.8
193 54H 0.434426 0.734043
194 A2R 0.434426 0.831325
195 VMS 0.434426 0.734043
196 ATP A A A 0.434109 0.829268
197 RFL 0.433962 0.842697
198 7D3 0.433628 0.788235
199 9K8 0.433071 0.686869
200 DZD 0.432624 0.880952
201 7MD 0.431818 0.83908
202 AYB 0.431655 0.831461
203 ZID 0.431507 0.843373
204 N0B 0.431507 0.862069
205 LLT 0.431373 0.756098
206 THM 0.431373 0.756098
207 TSB 0.430894 0.76087
208 YLY 0.430556 0.831461
209 NA7 0.428571 0.878049
210 GP3 0.428571 0.825581
211 FB0 0.427632 0.826087
212 AMP DBH 0.427481 0.8
213 G A A A 0.425532 0.784091
214 0WD 0.425532 0.914634
215 YLA 0.42446 0.840909
216 7MC 0.423358 0.840909
217 TQP 0.422819 0.840909
218 7SG 0.422819 0.840909
219 DT DT DT 0.422764 0.819277
220 52H 0.422764 0.726316
221 JB6 0.421875 0.835294
222 F2N 0.421687 0.897727
223 6AD 0.421488 0.795455
224 PPS 0.421488 0.747253
225 ARG AMP 0.421053 0.769231
226 M24 0.42069 0.786517
227 A U 0.42029 0.86747
228 T4K 0.42 0.852273
229 T5K 0.42 0.852273
230 53H 0.419355 0.726316
231 8X1 0.419355 0.721649
232 NDC 0.418301 0.847059
233 UFP 0.418182 0.767442
234 A5A 0.418033 0.75
235 XYA 0.417476 0.731707
236 RAB 0.417476 0.731707
237 ADN 0.417476 0.731707
238 A3P 0.417391 0.817073
239 G5A 0.416667 0.744681
240 A G 0.415493 0.793103
241 NAJ PYZ 0.414966 0.829545
242 SSA 0.414634 0.763441
243 GTP 0.414634 0.802326
244 3AM 0.414414 0.783133
245 NPW 0.414286 0.927711
246 KAA 0.414062 0.739583
247 P5A 0.414062 0.75
248 DDS 0.413223 0.807229
249 MTA 0.412844 0.694118
250 U A G G 0.412587 0.793103
251 LPA AMP 0.411765 0.777778
252 NZQ 0.411348 0.926829
253 FA9 0.410714 0.883721
254 AR6 AR6 0.410448 0.819277
255 APU 0.410072 0.86747
256 5N5 0.409524 0.710843
257 0DN 0.409524 0.722892
258 ARU 0.409449 0.755556
259 NVA LMS 0.409449 0.739583
260 128 0.408759 0.741935
261 NJP 0.408451 0.845238
262 5CA 0.408 0.763441
263 EP4 0.407407 0.678161
264 TAD 0.407407 0.837209
265 LEU LMS 0.40625 0.739583
266 TPE 0.40625 0.823529
267 DT DT DT DT DT 0.40625 0.821429
268 AF3 ADP 3PG 0.405797 0.775281
269 A4D 0.40566 0.710843
270 5CD 0.40566 0.698795
271 AMP NAD 0.405594 0.831325
272 3DH 0.405405 0.694118
273 NDE 0.405229 0.833333
274 AZD 0.404959 0.793103
275 NDP 0.404255 0.914634
276 62F 0.403727 0.860465
277 M2T 0.40367 0.662921
278 GSU 0.403101 0.744681
279 5HU 0.401786 0.819277
280 DUT 0.401709 0.804878
281 D3T 0.401709 0.819277
282 NSS 0.401575 0.763441
283 LSS 0.401575 0.747368
284 DSZ 0.401575 0.763441
285 RGT 0.401515 0.811765
286 TXP 0.401408 0.869048
287 P5F 0.401198 0.865169
288 DT DT PST 0.4 0.781609
289 7DT 0.4 0.829268
290 IMO 0.4 0.783133
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio2) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio2) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio3) has 31 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio3) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio1) has 34 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio4) has 28 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 8; Query (leader) PDB : 3TMK; Ligand: T5A; 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: 3tmk.bio4) has 31 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback