Receptor
PDB id Resolution Class Description Source Keywords
4E1B 1.8 Å NON-ENZYME: OTHER RE-REFINEMENT OF PDB ENTRY 2EQA - SUA5 PROTEIN FROM SULFOLOB TOKODAII WITH BOUND THREONYLCARBAMOYLADENYLATE SULFOLOBUS TOKODAII YRDC/RIBB FOLD YRDC DOMAIN SUA5 DOMAIN TRNA MODIFICATION BINDING PROTEIN
Ref.: THE O-CARBAMOYLTRANSFERASE TOBZ CATALYZES AN ANCIEN ENZYMATIC REACTION. ANGEW.CHEM.INT.ED.ENGL. V. 51 4046 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:2001;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
TXA A:2002;
Valid;
none;
submit data
492.335 C15 H21 N6 O11 P C[C@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2EQA 1.8 Å NON-ENZYME: OTHER CRYSTAL STRUCTURE OF THE HYPOTHETICAL SUA5 PROTEIN FROM SULFOLOBUS TOKODAII SULFOLOBUS TOKODAII YRDC/RIBB FOLD YRDC DOMAIN SUA5 DOMAIN STRUCTURAL GENOMICS NPPSFA NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE RSGI RNA BINDING PROTEIN
Ref.: X-RAY CRYSTAL STRUCTURE OF A HYPOTHETICAL SUA5 PROTEIN FROM SULFOLOBUS TOKODAII STRAIN 7 PROTEINS V. 70 1108 2008
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 2EQA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 4E1B - TXA C15 H21 N6 O11 P C[C@H]([C@....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 2EQA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 4E1B - TXA C15 H21 N6 O11 P C[C@H]([C@....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 2EQA - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 4E1B - TXA C15 H21 N6 O11 P C[C@H]([C@....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TXA; Similar ligands found: 361
No: Ligand ECFP6 Tc MDL keys Tc
1 TXA 1 1
2 QA7 0.72043 0.934211
3 KG4 0.715909 0.959459
4 5AL 0.714286 0.972603
5 8QN 0.712766 0.972603
6 CA0 0.704545 0.986301
7 8LQ 0.702128 0.946667
8 8LH 0.698925 0.946667
9 8LE 0.677419 0.934211
10 PAJ 0.670103 0.923077
11 A2D 0.666667 0.932432
12 SRP 0.663158 0.921053
13 PTJ 0.66 0.910256
14 AMO 0.653061 0.946667
15 BA3 0.651685 0.932432
16 M33 0.648352 0.945946
17 AP5 0.644444 0.932432
18 B4P 0.644444 0.932432
19 ADP 0.644444 0.932432
20 OOB 0.642857 0.945946
21 9ZD 0.642857 0.922078
22 9ZA 0.642857 0.922078
23 V2G 0.642105 0.886076
24 ACP 0.641304 0.907895
25 AT4 0.637363 0.896104
26 AN2 0.637363 0.92
27 4AD 0.636364 0.934211
28 PRX 0.634409 0.883117
29 LAD 0.633663 0.875
30 WAQ 0.633663 0.897436
31 A 0.632184 0.905405
32 AMP 0.632184 0.905405
33 ADX 0.630435 0.841463
34 DLL 0.63 0.945946
35 00A 0.63 0.897436
36 45A 0.629214 0.906667
37 ABM 0.629214 0.906667
38 ME8 0.627451 0.876543
39 1ZZ 0.627451 0.876543
40 NB8 0.627451 0.910256
41 ATP 0.623656 0.932432
42 50T 0.623656 0.894737
43 HEJ 0.623656 0.932432
44 5FA 0.617021 0.932432
45 APR 0.617021 0.958904
46 AQP 0.617021 0.932432
47 AR6 0.617021 0.958904
48 48N 0.614679 0.935065
49 ANP 0.614583 0.907895
50 AHX 0.613861 0.886076
51 AU1 0.612903 0.907895
52 AD9 0.610526 0.907895
53 AGS 0.610526 0.884615
54 B5Y 0.609524 0.934211
55 3UK 0.607843 0.933333
56 AMP MG 0.606742 0.891892
57 LAQ 0.605505 0.853659
58 B5V 0.601942 0.921053
59 PR8 0.601942 0.864198
60 DAL AMP 0.6 0.945946
61 ACQ 0.597938 0.907895
62 A12 0.597826 0.896104
63 AP2 0.597826 0.896104
64 B5M 0.59434 0.934211
65 FA5 0.59434 0.921053
66 OAD 0.592233 0.986301
67 HQG 0.59 0.945946
68 SRA 0.588889 0.858974
69 XAH 0.588785 0.831325
70 IOT 0.587719 0.823529
71 ATF 0.585859 0.896104
72 YLP 0.585586 0.855422
73 9SN 0.584906 0.886076
74 TSB 0.584158 0.833333
75 JNT 0.582524 0.907895
76 GAP 0.581633 0.907895
77 3OD 0.580952 0.986301
78 6YZ 0.58 0.907895
79 5SV 0.578431 0.839506
80 9X8 0.576923 0.934211
81 A3R 0.572816 0.873418
82 4UU 0.572727 0.909091
83 YLB 0.570175 0.855422
84 YLC 0.570175 0.876543
85 YLA 0.568965 0.855422
86 4UV 0.568807 0.909091
87 A22 0.568627 0.92
88 ADP MG 0.568421 0.905405
89 SON 0.568421 0.921053
90 ADP BEF 0.568421 0.905405
91 APC 0.56701 0.896104
92 4UW 0.566372 0.898734
93 TAT 0.565657 0.896104
94 T99 0.565657 0.896104
95 AYB 0.564103 0.86747
96 25A 0.563107 0.906667
97 OZV 0.563107 0.932432
98 ADV 0.561224 0.921053
99 RBY 0.561224 0.921053
100 F2R 0.559322 0.855422
101 GA7 0.558559 0.896104
102 A1R 0.557692 0.873418
103 ADQ 0.557692 0.933333
104 A5A 0.554455 0.821429
105 DQV 0.553571 0.945946
106 BIS 0.551402 0.873418
107 FYA 0.551402 0.87013
108 BT5 0.55 0.823529
109 TYM 0.547826 0.921053
110 OMR 0.547826 0.888889
111 MYR AMP 0.546296 0.853659
112 ATP MG 0.545455 0.905405
113 APC MG 0.545455 0.881579
114 ADP PO3 0.545455 0.905405
115 52H 0.543689 0.793103
116 VMS 0.543689 0.802326
117 54H 0.543689 0.802326
118 LMS 0.543478 0.797619
119 5AS 0.541667 0.772727
120 BEF ADP 0.54 0.881579
121 G5A 0.54 0.772727
122 ANP MG 0.539216 0.894737
123 ALF ADP 0.539216 0.8375
124 53H 0.538462 0.793103
125 MAP 0.538462 0.884615
126 KMQ 0.536364 0.946667
127 TXE 0.534483 0.897436
128 YLY 0.532258 0.845238
129 25L 0.53211 0.92
130 7MD 0.530973 0.876543
131 AFH 0.530973 0.875
132 ARG AMP 0.530973 0.821429
133 LPA AMP 0.530435 0.831325
134 L3W 0.529915 0.921053
135 AP0 0.529915 0.886076
136 7MC 0.529915 0.878049
137 COD 0.528926 0.825581
138 LSS 0.528302 0.775281
139 TXD 0.525862 0.897436
140 DND 0.525862 0.946667
141 NAX 0.525862 0.864198
142 VO4 ADP 0.524272 0.883117
143 JB6 0.522936 0.85
144 G3A 0.522124 0.886076
145 SSA 0.519231 0.793103
146 LEU LMS 0.518519 0.764045
147 G5P 0.517544 0.886076
148 DSZ 0.514019 0.813953
149 GTA 0.513043 0.876543
150 NAI 0.512821 0.897436
151 6V0 0.512821 0.886076
152 5CA 0.509434 0.793103
153 NVA LMS 0.509259 0.766667
154 80F 0.508065 0.855422
155 N0B 0.507812 0.855422
156 ADP BMA 0.504587 0.907895
157 ADJ 0.504132 0.843373
158 D4F 0.503937 0.853659
159 GSU 0.5 0.793103
160 NAQ 0.5 0.886076
161 A4P 0.5 0.813953
162 CNA 0.5 0.921053
163 5N5 0.5 0.786667
164 FB0 0.5 0.797753
165 NSS 0.5 0.793103
166 TAD 0.5 0.875
167 KAA 0.5 0.747253
168 AMP DBH 0.5 0.883117
169 AOC 0.5 0.789474
170 A3D 0.496 0.933333
171 ALF ADP 3PG 0.495798 0.851852
172 AF3 ADP 3PG 0.495798 0.851852
173 AHZ 0.495726 0.853659
174 8X1 0.495327 0.747253
175 5X8 0.49505 0.779221
176 5CD 0.494382 0.773333
177 RAB 0.494253 0.810811
178 ADN 0.494253 0.810811
179 XYA 0.494253 0.810811
180 BTX 0.491935 0.811765
181 T5A 0.491803 0.855422
182 6RE 0.489583 0.710843
183 3DH 0.489362 0.766234
184 UP5 0.487395 0.909091
185 P5A 0.486486 0.73913
186 SA8 0.485437 0.743902
187 M24 0.484375 0.864198
188 SXZ 0.482143 0.746988
189 A3T 0.480392 0.837838
190 SFG 0.480392 0.766234
191 NAD 0.48 0.92
192 UPA 0.479339 0.897436
193 4TC 0.479339 0.886076
194 7D5 0.478723 0.820513
195 YSA 0.478261 0.772727
196 EP4 0.478261 0.746835
197 A4D 0.477778 0.786667
198 S7M 0.476636 0.72619
199 DZD 0.47619 0.875
200 2A5 0.475728 0.858974
201 7D3 0.474747 0.846154
202 M2T 0.473118 0.728395
203 DTA 0.473118 0.75641
204 EEM 0.471698 0.72619
205 ATR 0.471154 0.905405
206 PAP 0.471154 0.918919
207 7D4 0.470588 0.846154
208 A3P 0.47 0.905405
209 ATP A A A 0.469565 0.893333
210 ATP A 0.469565 0.893333
211 8PZ 0.469565 0.793103
212 NAE 0.469231 0.909091
213 9K8 0.469027 0.747253
214 MTA 0.468085 0.766234
215 139 0.467742 0.864198
216 2SA 0.46729 0.921053
217 SAH 0.466667 0.759494
218 SAI 0.466667 0.75
219 EAD 0.466165 0.8875
220 AR6 AR6 0.466102 0.906667
221 H1Q 0.466019 0.868421
222 J7C 0.464646 0.719512
223 NDE 0.463235 0.896104
224 SMM 0.462963 0.72093
225 SAM 0.462264 0.72619
226 4YB 0.462185 0.775281
227 ZID 0.462121 0.907895
228 J4G 0.460177 0.909091
229 6MZ 0.46 0.893333
230 GJV 0.46 0.702381
231 S4M 0.46 0.662921
232 0UM 0.459459 0.73494
233 A2R 0.458716 0.945946
234 6AD 0.457944 0.875
235 PPS 0.457944 0.819277
236 ITT 0.456311 0.88
237 A2P 0.455446 0.891892
238 62X 0.455357 0.701149
239 NAD TDB 0.455285 0.906667
240 NAD IBO 0.455285 0.906667
241 A3G 0.454545 0.792208
242 3AM 0.453608 0.866667
243 B1U 0.452991 0.731183
244 JSQ 0.45283 0.884615
245 HFD 0.45283 0.884615
246 P1H 0.452555 0.865854
247 A3N 0.45 0.75641
248 V3L 0.448598 0.932432
249 6IA 0.448598 0.807229
250 WSA 0.447154 0.781609
251 NWW 0.445652 0.753425
252 AMP NAD 0.445312 0.92
253 ARU 0.442478 0.829268
254 MAO 0.441176 0.752941
255 DSH 0.44 0.698795
256 NEC 0.44 0.763158
257 FDA 0.439716 0.825581
258 O02 0.439252 0.8625
259 NA7 0.438596 0.896104
260 K15 0.438596 0.717647
261 FNK 0.438356 0.797753
262 CUU 0.438095 0.906667
263 AVV 0.4375 0.8625
264 K3E 0.436975 0.7625
265 6FA 0.43662 0.855422
266 IMO 0.435644 0.866667
267 649 0.435484 0.73913
268 3AT 0.435185 0.906667
269 NAJ PZO 0.435115 0.839506
270 ZAS 0.434343 0.7375
271 7C5 0.433333 0.810127
272 A7D 0.432692 0.746835
273 A3S 0.432692 0.802632
274 NO7 0.432432 0.871795
275 K3K 0.432203 0.772152
276 8Q2 0.432 0.766667
277 KOY 0.430894 0.818182
278 SFD 0.430556 0.747368
279 NWQ 0.428571 0.756757
280 2AM 0.428571 0.88
281 MHZ 0.428571 0.693182
282 QXG 0.426087 0.75
283 NDC 0.425532 0.8625
284 QXP 0.424779 0.758621
285 GEK 0.424779 0.753086
286 2VA 0.424528 0.815789
287 V47 0.423423 0.8
288 4TA 0.423077 0.821429
289 NAJ PYZ 0.422222 0.8
290 5AD 0.422222 0.739726
291 MCD 0.421429 0.818182
292 ETB 0.421053 0.825581
293 DCA 0.421053 0.816092
294 FAD 0.42069 0.865854
295 FAS 0.42069 0.865854
296 FCX 0.42029 0.808989
297 38V 0.419118 0.853659
298 CMC 0.41844 0.818182
299 C2R 0.418367 0.893333
300 AAT 0.418182 0.682353
301 FME ARG THR GLY ASN ALA ASP ND7 0.418182 0.782609
302 N5A 0.417476 0.730769
303 NVA 2AD 0.416667 0.775
304 KYE 0.416667 0.709302
305 LQJ 0.416667 0.881579
306 A5D 0.416667 0.75641
307 K2W 0.416667 0.714286
308 GGZ 0.415929 0.795181
309 OVE 0.415842 0.846154
310 P5F 0.415584 0.837209
311 NJP 0.415385 0.909091
312 ODP 0.415385 0.875
313 KB1 0.415254 0.714286
314 COA 0.414815 0.816092
315 0T1 0.414815 0.816092
316 KH3 0.414634 0.709302
317 KXW 0.414634 0.722892
318 AV2 0.414414 0.857143
319 SCO 0.413043 0.837209
320 CMX 0.413043 0.837209
321 6C6 0.412844 0.825
322 SO8 0.412844 0.805195
323 0WD 0.412214 0.886076
324 Q2P 0.412214 0.689655
325 N5O 0.411765 0.75641
326 SOP 0.411348 0.797753
327 OXK 0.411348 0.818182
328 DAT 0.411215 0.846154
329 NPW 0.410853 0.853659
330 R2V 0.410256 0.758621
331 FAM 0.410072 0.797753
332 MCA 0.409722 0.808989
333 Q34 0.409449 0.689655
334 62F 0.409396 0.853659
335 DTP 0.409091 0.846154
336 U4Y 0.408 0.753086
337 OZP 0.408 0.743902
338 TXP 0.407692 0.886076
339 2CP 0.406897 0.808989
340 K2R 0.40678 0.87013
341 FAY 0.406667 0.876543
342 COS 0.405797 0.797753
343 CAO 0.405797 0.788889
344 AMX 0.405797 0.825581
345 30N 0.405797 0.747368
346 2MC 0.405594 0.763441
347 Y3J 0.404255 0.697368
348 AMZ 0.40404 0.88
349 RFL 0.403974 0.835294
350 KY2 0.403509 0.686047
351 PGS 0.401869 0.82716
352 OK8 0.401786 0.87013
353 YZS 0.401408 0.72449
354 KGP 0.401408 0.72449
355 F2N 0.401274 0.806818
356 VRT 0.4 0.78481
357 K38 0.4 0.75
358 71V 0.4 0.85
359 NDP 0.4 0.886076
360 HZ2 0.4 0.746988
361 ACO 0.4 0.788889
Similar Ligands (3D)
Ligand no: 1; Ligand: TXA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2EQA; Ligand: AMP; 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: 2eqa.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
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