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Receptor
PDB id Resolution Class Description Source Keywords
2UZ3 2.5 Å EC: 2.7.1.21 CRYSTAL STRUCTURE OF THYMIDINE KINASE WITH DTTP FROM U. UREALYTICUM UREAPLASMA UREALYTICUM DEOXYRIBONUCLEOSIDE KINASE ZINC-BINDING DOMAIN FEED-BACK INHIBITOR TK1 DTTP UU-TK KINASE TRANSFERASE ATP- BINDING LASSO-DOMAIN DNA SYNTHESIS NUCLEOTIDE-BINDING
Ref.: STRUCTURES OF THYMIDINE KINASE 1 OF HUMAN AND MYCOPLASMIC ORIGIN PROC.NATL.ACAD.SCI.USA V. 101 17970 2004
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:2219;
D:4219;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
TTP A:1220;
B:2220;
C:3220;
D:4220;
 Valid;
Valid;
Valid;
Valid;
 none;
none;
none;
none;
 submit data
482.168 C10 H17 N2 O14 P3 CC1=C...
ZN A:1218;
B:2218;
C:3218;
D:4218;
 Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2B8T 2 Å EC: 2.7.1.21 CRYSTAL STRUCTURE OF THYMIDINE KINASE FROM U.UREALYTICUM IN WITH THYMIDINE UREAPLASMA PARVUM DEOXYRIBONUCLEOSIDE KINASE ZINC-BINDING DOMAIN TK1 UU-TKTHYMIDINE TRANSFERASE
Ref.: STRUCTURE OF THE SUBSTRATE COMPLEX OF THYMIDINE KIN UREAPLASMA UREALYTICUM AND INVESTIGATIONS OF POSSIB TARGETS FOR THE ENZYME FEBS LETT. V. 272 6365 2005
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 2B8T - THM C10 H14 N2 O5 CC1=CN(C(=....
2 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 2B8T - THM C10 H14 N2 O5 CC1=CN(C(=....
2 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1XBT - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
2 1W4R - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
3 2WVJ - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
4 4UXH ic50 = 1.1 uM T5A C20 H30 N7 O23 P5 CC1=CN(C(=....
5 2ORV Kd = 29 nM 4TA C20 H25 N7 O20 P4 CC1=CN(C(=....
6 2UZ3 - TTP C10 H17 N2 O14 P3 CC1=CN(C(=....
7 1XX6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
8 5FUV - THM C10 H14 N2 O5 CC1=CN(C(=....
9 5FUW - QBT C10 H17 N2 O8 P C[C@H]1CN(....
10 5FUX - QBT C10 H17 N2 O8 P C[C@H]1CN(....
11 2ORW - 4TA C20 H25 N7 O20 P4 CC1=CN(C(=....
12 2QQ0 - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
13 2QQE - THM C10 H14 N2 O5 CC1=CN(C(=....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TTP; Similar ligands found: 79
No: Ligand ECFP6 Tc MDL keys Tc
1 TTP 1 1
2 TYD 0.884058 1
3 TMP 0.760563 0.985714
4 TLO 0.722892 0.945205
5 DAU 0.701149 0.932432
6 TDX 0.689655 0.945205
7 18T 0.689655 0.932432
8 TRH 0.689655 0.932432
9 3R2 0.689655 0.92
10 1JB 0.689655 0.932432
11 3YN 0.674157 0.932432
12 T3Q 0.674157 0.907895
13 DWN 0.674157 0.907895
14 T3F 0.674157 0.907895
15 0N2 0.666667 0.896104
16 T46 0.666667 0.932432
17 0FX 0.659341 0.907895
18 MMF 0.659341 0.907895
19 QDM 0.645161 0.896104
20 AKM 0.638298 0.886076
21 1YF 0.638298 0.92
22 JHZ 0.638298 0.884615
23 FNF 0.638298 0.92
24 4TG 0.631579 0.92
25 TBD 0.62963 0.958904
26 DUT 0.62963 0.957143
27 D3T 0.62963 0.971831
28 T5A 0.61165 0.841463
29 THM 0.605634 0.873239
30 LLT 0.605634 0.873239
31 ATY 0.6 0.945205
32 FUH 0.588235 0.907895
33 QUH 0.588235 0.907895
34 AZD 0.586207 0.907895
35 DT DT DT 0.571429 0.917808
36 UFP 0.56962 0.905405
37 0DN 0.567568 0.833333
38 DCP 0.55814 0.891892
39 5HU 0.54321 0.971831
40 BRU 0.54321 0.905405
41 DUD 0.542169 0.957143
42 DT DT DT DT DT 0.541667 0.945205
43 NYM 0.536585 0.958333
44 FDM 0.536585 0.918919
45 5IU 0.536585 0.905405
46 ABT 0.531915 0.884615
47 T3P 0.531646 0.943662
48 DT DT PST 0.530612 0.87013
49 THP 0.53012 0.971429
50 D4T 0.528736 0.928571
51 6U4 0.521277 0.848101
52 ATM 0.517241 0.894737
53 7SG 0.512605 0.864198
54 TQP 0.512605 0.864198
55 TXS 0.512195 0.789474
56 TPE 0.510204 0.894737
57 T5K 0.508333 0.853659
58 T4K 0.508333 0.853659
59 BVP 0.5 0.944444
60 T3S 0.5 0.789474
61 8DG 0.489583 0.829268
62 YYY 0.477273 0.891892
63 2DT 0.47561 0.957747
64 4TA 0.469565 0.807229
65 DT ME6 DT 0.468468 0.87013
66 D4D 0.449438 0.928571
67 AZZ 0.447059 0.779221
68 DU 0.447059 0.942857
69 UMP 0.447059 0.942857
70 DUP 0.430108 0.930556
71 ADS THS THS THS 0.429752 0.758621
72 UTP 0.428571 0.875
73 8DD 0.424242 0.8125
74 WMJ 0.42 0.761905
75 DDN 0.418605 0.942857
76 8GD 0.418367 0.829268
77 DGT 0.415842 0.759036
78 UC5 0.406593 0.943662
79 ID2 0.402439 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found with APoc: 358
This union binding pocket(no: 1) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1B0U ATP None
2 1FZQ GDP None
3 3AQ4 GDP None
4 2CJW GDP None
5 1NN5 2DT None
6 1NN5 ANP None
7 2X2T GAL NGA None
8 4USI AKG None
9 4YLG GDP None
10 4E03 ADP None
11 3B7G ANP 0.896861
12 2HT6 GDP 1.14943
13 2CBZ ATP 1.34529
14 3EWA ANP 1.34529
15 4R98 GNH 1.34529
16 3JQG AX6 1.34529
17 3BMO AX4 1.34529
18 4WOP CTP 1.34529
19 3BMQ AX5 1.34529
20 6BSX GDP 1.68539
21 3CNL GNP 1.79372
22 4YDS ATP 1.79372
23 3T5G GDP 1.97368
24 2AWN ADP 2.24215
25 3U6B GDP 2.24215
26 1D8T GDP 2.24215
27 2RCN GDP 2.24215
28 5JBQ GDP 2.24215
29 4IEE AGS 2.24215
30 4G5G GDP 2.24215
31 3U6K GDP 2.24215
32 1US2 XYP XYP XYP XYP 2.24215
33 2BVN GNP 2.24215
34 1NE7 16G 2.24215
35 3DEF GDP 2.24215
36 4NU0 AP5 2.30415
37 4MKG AP5 2.30415
38 3Q72 GNP 2.40964
39 4WEI GLC GAL 2.52708
40 5GVR LMR 2.69058
41 3LRE ADP 2.69058
42 2VVG ADP 2.69058
43 3COB ADP 2.69058
44 4FRZ ADP 2.69058
45 3TK1 GDP 2.69058
46 5Y6N ADP 2.69058
47 2HCJ GDP 2.69058
48 5W76 GDP 2.69058
49 2EFE GNH 2.69058
50 4KBF AMP 2.69058
51 4U8P UDP 2.69058
52 4U8P FDA 2.69058
53 1OE0 TTP 2.69058
54 5VGR GDP 2.69058
55 5FHD ADP ALF 2.69058
56 3URB DPF 2.69058
57 3TMK T5A 2.77778
58 4BQS ADP 2.84091
59 4BQS K2Q 2.84091
60 1RYH GNP 2.95567
61 5U32 GDP 3.13901
62 4B47 GDP 3.13901
63 2NCD ADP 3.13901
64 1U0J ADP 3.13901
65 5HCN GCP 3.13901
66 1MKY GDP 3.13901
67 5W75 GDP 3.13901
68 2ZFI ADP 3.13901
69 4R43 GDP 3.13901
70 4Q1A UDP 3.13901
71 4Q1A 2XZ 3.13901
72 4N2R AHR 3.13901
73 3GXO MQA 3.13901
74 1A4R GNH 3.14136
75 1A4R GDP 3.14136
76 2WMO GTP 3.15789
77 4K79 GAL A2G 3.18182
78 1ZJ6 G3D 3.20856
79 1ZIN AP5 3.22581
80 4MKF AP5 3.22581
81 1VG1 GDP 3.24324
82 4DID GDP 3.28947
83 1MR3 G3D 3.31492
84 1YZG GDP 3.35196
85 1Z0F GDP 3.35196
86 2RGX AP5 3.39806
87 1T5C ADP 3.58744
88 1XP8 AGS 3.58744
89 1I4D GDP 3.58744
90 1SQ5 ADP 3.58744
91 5C9P FUC 3.58744
92 4XGU ADP 3.58744
93 4U60 SIA 3.58744
94 3BFV ADP 3.58744
95 4U60 SIA GAL NGA 3.58744
96 5A9A UTP 3.58744
97 1UJ2 ADP 3.58744
98 1UJ2 C5P 3.58744
99 3OBT SLB 3.58744
100 5WXU FLC 3.58744
101 4RDN 6MD 3.59281
102 3N5C GDP 3.7037
103 2X77 GDP 3.7037
104 4TTQ ATP 3.72093
105 1TLG GAL 4
106 1KO8 6PG 4
107 1G6H ADP 4.03587
108 2PZE ATP 4.03587
109 4WZ6 ATP 4.03587
110 5CK5 GDP 4.03587
111 3DKP ADP 4.03587
112 4NE2 ADP 4.03587
113 4NE2 SH2 4.03587
114 1SKQ GDP 4.03587
115 3BOS CDP 4.03587
116 4NON GDP 4.03587
117 4LYA ATP 4.03587
118 6B8B ADP 4.03587
119 1NHX FTB 4.03587
120 1NHX PEP 4.03587
121 5X40 ACP 4.03587
122 2GMV PEP 4.03587
123 3QTP 2PG 4.03587
124 2QES ADE 4.03587
125 3Q85 GNP 4.14201
126 2J0V GDP 4.24528
127 5O74 GDP 4.44444
128 1F9V ADP 4.4843
129 1XMV ADP 4.4843
130 4PX9 ADP 4.4843
131 1ZUI SKM 4.4843
132 1VHT BA3 4.4843
133 5H7K GDP 4.4843
134 5H4S RAM 4.4843
135 1HFU NAG NDG 4.4843
136 5H7J GCP 4.4843
137 3K4Z CBI 4.4843
138 1RE0 GDP 4.52489
139 4X8O AP5 4.6729
140 2NGR GDP 4.70085
141 5BQ5 ADP BEF 4.7619
142 2WJG GDP 4.78723
143 2WJH GDP 4.81928
144 2WJH FLC 4.81928
145 5TB5 GDP 4.86486
146 5TAR GDP 4.86486
147 2WHX ADP 4.93274
148 1BG2 ADP 4.93274
149 2Y65 ADP 4.93274
150 6A20 ADP 4.93274
151 5LB3 ADP 4.93274
152 5UIV ADP 4.93274
153 1LVK MNT BEF 4.93274
154 1KK1 GNP 4.93274
155 5BN3 ADP 4.93274
156 2IYL GDP 4.93274
157 3EC1 GDP 4.93274
158 1SVM ATP 4.93274
159 2JLR ANP 4.93274
160 2QS8 MET 4.93274
161 2I6U CP 4.93274
162 5ZBR ANP 4.93274
163 3UIE ANP 5
164 1DS6 GDP 5
165 5KSP GDP 5.26316
166 4AG5 ADP 5.38117
167 2XT3 ADP 5.38117
168 1JJV ATP 5.38117
169 3DC4 ADP 5.38117
170 6C90 ADP 5.38117
171 2BIF SIN 5.38117
172 4LC1 GDP 5.38117
173 1VG9 GDP 5.38117
174 2WIC GNP 5.38117
175 2BIF ANP 5.38117
176 3RC3 ANP 5.38117
177 1G7S GDP 5.38117
178 1VG0 GDP 5.38117
179 5D63 FUC GLA GLA 5.38117
180 2CXG GLC GLC 5.38117
181 6FAA ADP 5.38117
182 4ITR GDP 5.38117
183 1S9D GDP 5.41872
184 1UKZ ADP 5.41872
185 1Y63 ADP 5.43478
186 4FGC PQ0 5.45455
187 2QG6 NMN 5.52764
188 1F6B GDP 5.55556
189 3M3E GAL A2G NPO 5.59006
190 1S8F GDP 5.64972
191 1NRJ GTP 5.6962
192 3P4X ADP 5.8296
193 5L3V GDP 5.8296
194 4OJP MAL 5.8296
195 5N69 ADP 5.8296
196 3VSV XYP 5.8296
197 4QM7 GTP 5.84795
198 3W5J GDP 5.88235
199 1AKY AP5 5.90909
200 2OBM ADP 6.05187
201 1M7G AV2 6.16114
202 1M7G ADP 6.16114
203 1M7G ADX 6.16114
204 2OG2 MLI 6.27803
205 1GOJ ADP 6.27803
206 3B9Q MLI 6.27803
207 2GKS ADP 6.27803
208 4BFW ZVW 6.27803
209 2CE7 ADP 6.27803
210 1HTW ADP 6.27803
211 5AK0 8V1 6.27803
212 1G6O ADP 6.27803
213 3HU3 AGS 6.27803
214 2G77 AF3 6.27803
215 2G77 GDP 6.27803
216 5IFS ADP 6.27803
217 1UPT GTP 6.43275
218 5TPV TYD 6.53595
219 1LVG ADP 6.56566
220 4TMK T5A 6.57277
221 5TSH ADP 6.72646
222 5TSH ANP 6.72646
223 1D2E GDP 6.72646
224 5W7Q GDP 6.72646
225 4DCT GDP 6.72646
226 5MZN ADP 6.72646
227 3A1S GDP 6.72646
228 1XKV ATP 6.72646
229 4PC3 GDP 6.72646
230 1R0X ATP 6.72646
231 3H86 AP5 6.77083
232 2W58 ADP 6.93069
233 1KSH GDP 6.98925
234 4OIT MAN 7.07965
235 5OEC GDP 7.10383
236 3NHB ADP 7.17489
237 5M04 GDP 7.17489
238 2FSH ANP 7.17489
239 1R6B ADP 7.17489
240 5GOE GDP 7.17489
241 3CPJ GDP 7.17489
242 3PQC GDP 7.17949
243 3GJ0 GDP 7.23982
244 3GJ7 GDP 7.23982
245 3GJ3 GDP 7.23982
246 3GJ4 GDP 7.23982
247 3GJ8 GDP 7.23982
248 3GJ5 GDP 7.23982
249 1KJ1 MAN 7.33945
250 5BXQ GDP 7.40741
251 3CH5 GDP 7.40741
252 5Z69 AGS 7.52688
253 5ZXD ATP 7.62332
254 5YT0 GDP 7.62332
255 3B5J 12D 7.62332
256 5FG3 GDP 7.62332
257 5VHC BEF ADP 7.62332
258 6G14 G4P 7.62332
259 5XDR ADP 7.68116
260 4P3Y GDP 7.69231
261 3IIJ ADP 7.77778
262 2KIN ADP 8
263 3QF7 ANP 8
264 5IRC GDP 8.06452
265 2PL3 ADP 8.07175
266 2V7Q ADP 8.07175
267 2V7Q ATP 8.07175
268 2D7D ADP 8.07175
269 2CK3 ANP 8.07175
270 5WC2 ADP 8.07175
271 1W0J ADP 8.07175
272 6C0B MLI 8.07175
273 4JLV ADP 8.07175
274 6F1J EDG 8.07175
275 2YOH WMJ 8.09524
276 4R2I ANP 8.09524
277 4D0N GDP 8.10811
278 3LXR GDP 8.10811
279 1JJ7 ADP 8.52018
280 4J0Q GDP 8.52018
281 5KUT GDP 8.52018
282 3QVV A3P 8.52018
283 2QN6 GDP 8.60215
284 2JAQ DCP 8.78049
285 3A4M ADP 8.84615
286 1PUJ GNP 8.86525
287 2A5J GDP 8.90052
288 5LTJ BEF 8.96861
289 3MD0 GDP 8.96861
290 1YRB GDP 8.96861
291 3WY9 GDP 8.96861
292 3WYA GDP 8.96861
293 4HSE ADP 8.96861
294 5LLB 6YZ 8.96861
295 5LTJ ADP 8.96861
296 2XAU ADP 8.96861
297 2O0J ADP 8.96861
298 4ZNL BEF ADP 8.96861
299 4QOS ADP 9.41704
300 4UYW H1S 9.41704
301 2IS6 ADP 9.41704
302 5KSZ GCP 9.41704
303 3DZD ADP 9.41704
304 4CVN ADP 9.42408
305 1Z0A GDP 9.77011
306 2ZE7 AMP 9.86547
307 2ZE7 DST 9.86547
308 5WJ6 B4A 9.86547
309 1X6V ADP 9.86547
310 3VOZ 04A 9.86547
311 4KFU ACP 10.3774
312 1KY3 GDP 10.4396
313 2OFW ADX 10.5769
314 2WCU FUC 10.7383
315 3ZIA ATP 10.7623
316 4IHQ ADP 10.7623
317 3E70 GDP 10.7623
318 3ZIA ADP 10.7623
319 5MVR ADP 11.1111
320 4V0K GDP 11.2426
321 2IXE ATP 11.6592
322 4A4Z ANP 12.1076
323 2PEZ DAT 12.2905
324 2PEZ GGZ 12.2905
325 1SVI GDP 12.5561
326 3FB4 AP5 12.5561
327 4U00 ADP 13.0045
328 1V8K ANP 13.0045
329 5G41 AP5 13.0045
330 3ZFD ANP 13.0045
331 1DUV PSQ 13.0045
332 3KTA AP5 13.2948
333 3H4S ADP 13.3333
334 3EF0 ALF 13.4529
335 3LN9 FLC 13.4529
336 4PPF FLC 13.9013
337 1OXV ANP 13.9013
338 1G16 GDP 14.1176
339 1GXU 2HP 14.2857
340 1RRC ADP 14.3498
341 2ZR9 DTP 14.3498
342 1DAR GDP 14.3498
343 1S3G AP5 14.3498
344 5L3W GDP 14.3498
345 5L3S G 14.3498
346 3TBK ANP 14.7982
347 6B4K ANP 14.7982
348 4YMU ATP 15
349 1JI0 ATP 15.2466
350 5YV5 ADP 15.2466
351 1YQT ADP 15.2466
352 2GDJ ANP 15.6951
353 2PFZ PCA 16.5919
354 4DKX GDP 17.1296
355 2DPY ADP 17.4888
356 3WVC FEG 21.7647
357 2CDN ADP 21.8905
358 5WLB GNP 23.5294
Pocket No.: 2; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found with APoc: 13
This union binding pocket(no: 2) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 2RDK MAN MAN None
2 2V57 PRL 1.57895
3 3IUY AMP 1.75439
4 3R7F CP 2.69058
5 1CT9 GLN 3.13901
6 2EUG URA 3.58744
7 3TII ANP 3.58744
8 5YB7 ORN 4.93274
9 3BP1 GUN 4.93274
10 3BY8 MLT 5.6338
11 1UCD U5P 5.78947
12 3BER AMP 9.63855
13 2GGH NLQ 14.3498
Pocket No.: 3; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found with APoc: 18
This union binding pocket(no: 3) in the query (biounit: 2b8t.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5HGZ MLA 1.79372
2 3B8I OXL 1.79372
3 5K21 6QF 2.12766
4 4IV9 TSR 3.58744
5 1R6T TYM 3.58744
6 5OSW DIU 4.03587
7 5OQW A4E 4.03587
8 2D3Y DU 4.10959
9 1GVF PGH 4.4843
10 1ML4 PAL 4.87013
11 2ZTS ADP 4.93274
12 5WZN A2G 4.93274
13 5YSQ INS 6.27803
14 2QZ4 ADP 6.72646
15 5NC1 NAG 7.62332
16 4KTP BGC 8.96861
17 5HR5 ADP 10.7623
18 1MFI FHC 32.4561
Pocket No.: 4; Query (leader) PDB : 2B8T; Ligand: THM; Similar sites found with APoc: 3
This union binding pocket(no: 4) in the query (biounit: 2b8t.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 5Z21 OXM 3.58744
2 2D2F ADP 6.27803
3 3F9W SAH 11.4458
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