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 1256 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 1068 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 922 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
Ligand no: 1; Ligand: TXA; Similar ligands found: 298
No: Ligand ECFP6 Tc MDL keys Tc
1 TXA 1 1
2 5AL 0.714286 0.972603
3 8QN 0.712766 0.972603
4 CA0 0.704545 0.986301
5 PAJ 0.670103 0.923077
6 A2D 0.666667 0.932432
7 SRP 0.663158 0.921053
8 PTJ 0.66 0.910256
9 AMO 0.653061 0.946667
10 BA3 0.651685 0.932432
11 M33 0.648352 0.945946
12 ADP 0.644444 0.932432
13 B4P 0.644444 0.932432
14 AP5 0.644444 0.932432
15 OOB 0.642857 0.945946
16 ACP 0.641304 0.907895
17 AN2 0.637363 0.92
18 4AD 0.636364 0.934211
19 PRX 0.634409 0.883117
20 WAQ 0.633663 0.897436
21 LAD 0.633663 0.875
22 A 0.632184 0.905405
23 AMP 0.632184 0.905405
24 ADX 0.630435 0.841463
25 00A 0.63 0.897436
26 DLL 0.63 0.945946
27 ABM 0.629214 0.906667
28 ME8 0.627451 0.876543
29 NB8 0.627451 0.910256
30 1ZZ 0.627451 0.876543
31 ATP 0.623656 0.932432
32 50T 0.623656 0.894737
33 AQP 0.617021 0.932432
34 AR6 0.617021 0.958904
35 APR 0.617021 0.958904
36 5FA 0.617021 0.932432
37 48N 0.614679 0.935065
38 ANP 0.614583 0.907895
39 AHX 0.613861 0.886076
40 AU1 0.612903 0.907895
41 SAP 0.610526 0.884615
42 AD9 0.610526 0.907895
43 AGS 0.610526 0.884615
44 3UK 0.607843 0.933333
45 LAQ 0.605505 0.853659
46 PR8 0.601942 0.864198
47 AMP MG 0.6 0.857143
48 DAL AMP 0.6 0.945946
49 ACQ 0.597938 0.907895
50 A12 0.597826 0.896104
51 AP2 0.597826 0.896104
52 YAP 0.59434 0.909091
53 FA5 0.59434 0.921053
54 OAD 0.592233 0.986301
55 SRA 0.588889 0.858974
56 XAH 0.588785 0.831325
57 IOT 0.587719 0.823529
58 ATF 0.585859 0.896104
59 YLP 0.585586 0.855422
60 9SN 0.584906 0.886076
61 TSB 0.584158 0.833333
62 GAP 0.581633 0.907895
63 3OD 0.580952 0.986301
64 5SV 0.578431 0.839506
65 4UU 0.572727 0.909091
66 YLC 0.570175 0.876543
67 YLB 0.570175 0.855422
68 YLA 0.568965 0.855422
69 4UV 0.568807 0.909091
70 A22 0.568627 0.92
71 SON 0.568421 0.921053
72 APC 0.56701 0.896104
73 4UW 0.566372 0.898734
74 TAT 0.565657 0.896104
75 AYB 0.564103 0.86747
76 25A 0.563107 0.906667
77 ADP MG 0.5625 0.87013
78 RBY 0.561224 0.921053
79 ADV 0.561224 0.921053
80 A1R 0.557692 0.873418
81 ADQ 0.557692 0.933333
82 ADP BEF 0.556701 0.848101
83 BEF ADP 0.556701 0.848101
84 A5A 0.554455 0.821429
85 BIS 0.551402 0.873418
86 FYA 0.551402 0.87013
87 BT5 0.55 0.823529
88 OMR 0.547826 0.888889
89 TYM 0.547826 0.921053
90 MYR AMP 0.546296 0.853659
91 ADP PO3 0.545455 0.905405
92 52H 0.543689 0.793103
93 VMS 0.543689 0.802326
94 54H 0.543689 0.802326
95 5AS 0.541667 0.772727
96 ATP MG 0.54 0.87013
97 G5A 0.54 0.772727
98 ADP ALF 0.539216 0.8375
99 ALF ADP 0.539216 0.8375
100 MAP 0.538462 0.884615
101 53H 0.538462 0.793103
102 TXE 0.534483 0.897436
103 ANP MG 0.533981 0.860759
104 YLY 0.532258 0.845238
105 25L 0.53211 0.92
106 AFH 0.530973 0.875
107 7MD 0.530973 0.876543
108 LPA AMP 0.530435 0.831325
109 7MC 0.529915 0.878049
110 AP0 0.529915 0.886076
111 COD 0.528926 0.825581
112 LSS 0.528302 0.775281
113 NAX 0.525862 0.864198
114 TXD 0.525862 0.897436
115 NXX 0.525862 0.946667
116 DND 0.525862 0.946667
117 JB6 0.522936 0.85
118 G3A 0.522124 0.886076
119 VO4 ADP 0.519231 0.894737
120 ADP VO4 0.519231 0.894737
121 SSA 0.519231 0.793103
122 LEU LMS 0.518519 0.775281
123 TYR AMP 0.517857 0.896104
124 G5P 0.517544 0.886076
125 DSZ 0.514019 0.813953
126 GTA 0.513043 0.876543
127 6V0 0.512821 0.886076
128 NAI 0.512821 0.897436
129 5CA 0.509434 0.793103
130 NVA LMS 0.509259 0.775281
131 ARG AMP 0.508621 0.821429
132 N0B 0.507812 0.855422
133 ADP BMA 0.504587 0.907895
134 ADJ 0.504132 0.843373
135 A A 0.5 0.881579
136 CNA 0.5 0.921053
137 KAA 0.5 0.747253
138 AOC 0.5 0.789474
139 TAD 0.5 0.875
140 AMP DBH 0.5 0.883117
141 FB0 0.5 0.797753
142 NSS 0.5 0.793103
143 5N5 0.5 0.786667
144 GSU 0.5 0.793103
145 A4P 0.5 0.813953
146 NAQ 0.5 0.886076
147 A3D 0.496 0.933333
148 AF3 ADP 3PG 0.495798 0.851852
149 ALF ADP 3PG 0.495798 0.851852
150 LA8 ALF 3PG 0.495798 0.851852
151 AHZ 0.495726 0.853659
152 5X8 0.49505 0.779221
153 5CD 0.494382 0.773333
154 XYA 0.494253 0.810811
155 RAB 0.494253 0.810811
156 ADN 0.494253 0.810811
157 BTX 0.491935 0.811765
158 T5A 0.491803 0.855422
159 6RE 0.489583 0.710843
160 3DH 0.489362 0.766234
161 UP5 0.487395 0.909091
162 P5A 0.486486 0.73913
163 SA8 0.485437 0.743902
164 M24 0.484375 0.864198
165 SXZ 0.482143 0.746988
166 A3T 0.480392 0.837838
167 SFG 0.480392 0.766234
168 NAD 0.48 0.92
169 4TC 0.479339 0.886076
170 UPA 0.479339 0.897436
171 7D5 0.478723 0.820513
172 YSA 0.478261 0.772727
173 EP4 0.478261 0.746835
174 A4D 0.477778 0.786667
175 S7M 0.476636 0.72619
176 DZD 0.47619 0.875
177 2A5 0.475728 0.858974
178 7D3 0.474747 0.846154
179 DTA 0.473118 0.75641
180 M2T 0.473118 0.728395
181 NAD IBO 0.472 0.884615
182 EEM 0.471698 0.72619
183 PAP 0.471154 0.918919
184 ATR 0.471154 0.905405
185 7D4 0.470588 0.846154
186 A3P 0.47 0.905405
187 ATP A A A 0.469565 0.893333
188 NAE 0.469231 0.909091
189 MTA 0.468085 0.766234
190 139 0.467742 0.864198
191 2SA 0.46729 0.921053
192 SAH 0.466667 0.759494
193 SAI 0.466667 0.75
194 EAD 0.466165 0.8875
195 AR6 AR6 0.466102 0.906667
196 J7C 0.464646 0.719512
197 NDE 0.463235 0.896104
198 SMM 0.462963 0.72093
199 SAM 0.462264 0.72619
200 4YB 0.462185 0.775281
201 ZID 0.462121 0.907895
202 GJV 0.46 0.702381
203 S4M 0.46 0.662921
204 0UM 0.459459 0.73494
205 A2R 0.458716 0.945946
206 PPS 0.457944 0.819277
207 6AD 0.457944 0.875
208 ITT 0.456311 0.88
209 A2P 0.455446 0.891892
210 62X 0.455357 0.701149
211 A3G 0.454545 0.792208
212 3AM 0.453608 0.866667
213 P1H 0.452555 0.865854
214 A3N 0.45 0.75641
215 6IA 0.448598 0.807229
216 V3L 0.448598 0.932432
217 WSA 0.447154 0.781609
218 ARU 0.442478 0.829268
219 MAO 0.441176 0.752941
220 DSH 0.44 0.698795
221 NEC 0.44 0.763158
222 FDA 0.439716 0.825581
223 NA7 0.438596 0.896104
224 K15 0.438596 0.717647
225 FNK 0.438356 0.797753
226 AVV 0.4375 0.8625
227 6FA 0.43662 0.855422
228 IMO 0.435644 0.866667
229 649 0.435484 0.73913
230 3AT 0.435185 0.906667
231 NAJ PZO 0.435115 0.839506
232 ZAS 0.434343 0.7375
233 7C5 0.433333 0.810127
234 NAJ PYZ 0.432836 0.841463
235 A7D 0.432692 0.746835
236 A3S 0.432692 0.802632
237 SFD 0.430556 0.747368
238 AMP NAD 0.42963 0.921053
239 2AM 0.428571 0.88
240 MHZ 0.428571 0.693182
241 NDC 0.425532 0.8625
242 GEK 0.424779 0.753086
243 2VA 0.424528 0.815789
244 4TA 0.423077 0.821429
245 G A A A 0.423077 0.839506
246 5AD 0.422222 0.739726
247 MCD 0.421429 0.818182
248 DCA 0.421053 0.816092
249 ETB 0.421053 0.825581
250 FAD 0.42069 0.865854
251 FAS 0.42069 0.865854
252 FCX 0.42029 0.808989
253 CMC 0.41844 0.818182
254 C2R 0.418367 0.893333
255 AAT 0.418182 0.682353
256 A5D 0.416667 0.75641
257 GGZ 0.415929 0.795181
258 OVE 0.415842 0.846154
259 P5F 0.415584 0.837209
260 NJP 0.415385 0.909091
261 ODP 0.415385 0.875
262 KB1 0.415254 0.714286
263 0T1 0.414815 0.816092
264 COA 0.414815 0.816092
265 KH3 0.414634 0.709302
266 AV2 0.414414 0.857143
267 SCO 0.413043 0.837209
268 CMX 0.413043 0.837209
269 SO8 0.412844 0.805195
270 6C6 0.412844 0.825
271 0WD 0.412214 0.886076
272 OXK 0.411348 0.818182
273 SOP 0.411348 0.797753
274 DAT 0.411215 0.846154
275 NPW 0.410853 0.853659
276 FAM 0.410072 0.797753
277 MCA 0.409722 0.808989
278 62F 0.409396 0.853659
279 DTP 0.409091 0.846154
280 U A G G 0.409091 0.85
281 TXP 0.407692 0.886076
282 2CP 0.406897 0.808989
283 FAY 0.406667 0.876543
284 COS 0.405797 0.797753
285 AMX 0.405797 0.825581
286 30N 0.405797 0.747368
287 CAO 0.405797 0.788889
288 2MC 0.405594 0.763441
289 Y3J 0.404255 0.697368
290 AMZ 0.40404 0.88
291 RFL 0.403974 0.835294
292 PGS 0.401869 0.82716
293 A A A 0.401709 0.87013
294 F2N 0.401274 0.806818
295 ACO 0.4 0.788889
296 VRT 0.4 0.78481
297 NDP 0.4 0.886076
298 71V 0.4 0.85
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2EQA; Ligand: AMP; Similar sites found: 32
This union binding pocket(no: 1) in the query (biounit: 2eqa.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2B9J ADP 0.009568 0.40951 1.42045
2 2B9I ADP 0.009999 0.40515 1.42045
3 4NFN 2KC 0.01312 0.40316 2.589
4 1ULE GLA GAL NAG 0.008928 0.42544 2.66667
5 1HQL GLA MBG 0.02912 0.40201 3.11284
6 2CFC KPC 0.0106 0.43104 3.6
7 3DAK ANP 0.01149 0.40242 3.7931
8 5BVE 4VG 0.02036 0.40432 4.15512
9 3ZGJ RMN 0.005106 0.44451 4.26136
10 4JH6 FCN 0.02151 0.40764 4.34783
11 3SHR CMP 0.01286 0.41482 4.68227
12 3IHB GLU 0.02607 0.40544 4.82955
13 4OFG PCG 0.01396 0.40912 4.86111
14 4AVB CMP 0.009567 0.41707 5.1051
15 4YVN EBS 0.003859 0.45249 5.11364
16 4A91 GLU 0.004946 0.44245 5.36913
17 2WHL MAN BMA BMA 0.02913 0.40463 5.44218
18 4GJY OGA 0.02683 0.40297 5.53191
19 4E1Z 0MX 0.002017 0.42178 5.84192
20 3PNA CMP 0.02012 0.40912 5.84416
21 4ZYB 4SQ 0.01417 0.4088 5.97015
22 4I9A NCN 0.007928 0.40972 6.25
23 4JUI EGR 0.03557 0.40155 6.81818
24 2XG5 EC5 0.0203 0.42228 8.25688
25 2XG5 EC2 0.0203 0.42228 8.25688
26 1BHX ASP PHE GLU GLU ILE 0.0238 0.40149 10
27 1V9T SIN ALA PRO ALA NIT 0.01471 0.42051 10.241
28 3OF1 CMP 0.01681 0.40902 11.3821
29 3BFF FPM 0.04849 0.40057 12.2137
30 3LGS ADE 0.0151 0.42103 13.1086
31 2A19 ANP 0.01041 0.41938 13.1429
32 3TTC ADP 0.0000004605 0.55423 16.7614
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