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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 1443 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 1205 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 1039 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: 313
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 AP5 0.644444 0.932432
13 ADP 0.644444 0.932432
14 B4P 0.644444 0.932432
15 9ZD 0.642857 0.922078
16 OOB 0.642857 0.945946
17 9ZA 0.642857 0.922078
18 ACP 0.641304 0.907895
19 AT4 0.637363 0.896104
20 AN2 0.637363 0.92
21 4AD 0.636364 0.934211
22 PRX 0.634409 0.883117
23 LAD 0.633663 0.875
24 WAQ 0.633663 0.897436
25 A 0.632184 0.905405
26 AMP 0.632184 0.905405
27 ADX 0.630435 0.841463
28 00A 0.63 0.897436
29 DLL 0.63 0.945946
30 ABM 0.629214 0.906667
31 NB8 0.627451 0.910256
32 ME8 0.627451 0.876543
33 1ZZ 0.627451 0.876543
34 50T 0.623656 0.894737
35 HEJ 0.623656 0.932432
36 ATP 0.623656 0.932432
37 5FA 0.617021 0.932432
38 APR 0.617021 0.958904
39 AQP 0.617021 0.932432
40 AR6 0.617021 0.958904
41 48N 0.614679 0.935065
42 ANP 0.614583 0.907895
43 AHX 0.613861 0.886076
44 AU1 0.612903 0.907895
45 SAP 0.610526 0.884615
46 AD9 0.610526 0.907895
47 AGS 0.610526 0.884615
48 B5Y 0.609524 0.934211
49 3UK 0.607843 0.933333
50 LAQ 0.605505 0.853659
51 B5V 0.601942 0.921053
52 PR8 0.601942 0.864198
53 DAL AMP 0.6 0.945946
54 ACQ 0.597938 0.907895
55 A12 0.597826 0.896104
56 AP2 0.597826 0.896104
57 FA5 0.59434 0.921053
58 YAP 0.59434 0.909091
59 B5M 0.59434 0.934211
60 OAD 0.592233 0.986301
61 SRA 0.588889 0.858974
62 XAH 0.588785 0.831325
63 IOT 0.587719 0.823529
64 ATF 0.585859 0.896104
65 YLP 0.585586 0.855422
66 9SN 0.584906 0.886076
67 TSB 0.584158 0.833333
68 GAP 0.581633 0.907895
69 3OD 0.580952 0.986301
70 6YZ 0.58 0.907895
71 5SV 0.578431 0.839506
72 9X8 0.576923 0.934211
73 A3R 0.572816 0.873418
74 4UU 0.572727 0.909091
75 YLB 0.570175 0.855422
76 YLC 0.570175 0.876543
77 YLA 0.568965 0.855422
78 4UV 0.568807 0.909091
79 A22 0.568627 0.92
80 SON 0.568421 0.921053
81 APC 0.56701 0.896104
82 4UW 0.566372 0.898734
83 T99 0.565657 0.896104
84 TAT 0.565657 0.896104
85 AYB 0.564103 0.86747
86 25A 0.563107 0.906667
87 ADV 0.561224 0.921053
88 RBY 0.561224 0.921053
89 F2R 0.559322 0.855422
90 GA7 0.558559 0.896104
91 ADQ 0.557692 0.933333
92 A1R 0.557692 0.873418
93 A5A 0.554455 0.821429
94 DQV 0.553571 0.945946
95 FYA 0.551402 0.87013
96 BIS 0.551402 0.873418
97 BT5 0.55 0.823529
98 OMR 0.547826 0.888889
99 TYM 0.547826 0.921053
100 MYR AMP 0.546296 0.853659
101 ADP PO3 0.545455 0.905405
102 VMS 0.543689 0.802326
103 54H 0.543689 0.802326
104 52H 0.543689 0.793103
105 LMS 0.543478 0.797619
106 5AS 0.541667 0.772727
107 G5A 0.54 0.772727
108 ADP ALF 0.539216 0.8375
109 ALF ADP 0.539216 0.8375
110 MAP 0.538462 0.884615
111 53H 0.538462 0.793103
112 TXE 0.534483 0.897436
113 YLY 0.532258 0.845238
114 25L 0.53211 0.92
115 ARG AMP 0.530973 0.821429
116 AFH 0.530973 0.875
117 7MD 0.530973 0.876543
118 LPA AMP 0.530435 0.831325
119 AP0 0.529915 0.886076
120 7MC 0.529915 0.878049
121 COD 0.528926 0.825581
122 LSS 0.528302 0.775281
123 NAX 0.525862 0.864198
124 TXD 0.525862 0.897436
125 NXX 0.525862 0.946667
126 DND 0.525862 0.946667
127 JB6 0.522936 0.85
128 G3A 0.522124 0.886076
129 SSA 0.519231 0.793103
130 VO4 ADP 0.519231 0.894737
131 ADP VO4 0.519231 0.894737
132 LEU LMS 0.518519 0.766667
133 G5P 0.517544 0.886076
134 DSZ 0.514019 0.813953
135 TYR AMP 0.513274 0.884615
136 GTA 0.513043 0.876543
137 NAI 0.512821 0.897436
138 6V0 0.512821 0.886076
139 5CA 0.509434 0.793103
140 NVA LMS 0.509259 0.766667
141 80F 0.508065 0.855422
142 N0B 0.507812 0.855422
143 ADP BMA 0.504587 0.907895
144 ADJ 0.504132 0.843373
145 GSU 0.5 0.793103
146 NSS 0.5 0.793103
147 NAQ 0.5 0.886076
148 A4P 0.5 0.813953
149 CNA 0.5 0.921053
150 5N5 0.5 0.786667
151 A A 0.5 0.881579
152 AOC 0.5 0.789474
153 TAD 0.5 0.875
154 KAA 0.5 0.747253
155 FB0 0.5 0.797753
156 AMP DBH 0.5 0.883117
157 A3D 0.496 0.933333
158 AF3 ADP 3PG 0.495798 0.851852
159 AHZ 0.495726 0.853659
160 8X1 0.495327 0.747253
161 5X8 0.49505 0.779221
162 5CD 0.494382 0.773333
163 ADN 0.494253 0.810811
164 RAB 0.494253 0.810811
165 XYA 0.494253 0.810811
166 BTX 0.491935 0.811765
167 T5A 0.491803 0.855422
168 6RE 0.489583 0.710843
169 3DH 0.489362 0.766234
170 UP5 0.487395 0.909091
171 P5A 0.486486 0.73913
172 SA8 0.485437 0.743902
173 M24 0.484375 0.864198
174 SXZ 0.482143 0.746988
175 A3T 0.480392 0.837838
176 SFG 0.480392 0.766234
177 NAD 0.48 0.92
178 4TC 0.479339 0.886076
179 UPA 0.479339 0.897436
180 7D5 0.478723 0.820513
181 EP4 0.478261 0.746835
182 YSA 0.478261 0.772727
183 A4D 0.477778 0.786667
184 S7M 0.476636 0.72619
185 DZD 0.47619 0.875
186 2A5 0.475728 0.858974
187 7D3 0.474747 0.846154
188 M2T 0.473118 0.728395
189 DTA 0.473118 0.75641
190 EEM 0.471698 0.72619
191 ATR 0.471154 0.905405
192 PAP 0.471154 0.918919
193 7D4 0.470588 0.846154
194 A3P 0.47 0.905405
195 ATP A A A 0.469565 0.893333
196 8PZ 0.469565 0.793103
197 NAE 0.469231 0.909091
198 9K8 0.469027 0.747253
199 MTA 0.468085 0.766234
200 139 0.467742 0.864198
201 2SA 0.46729 0.921053
202 SAH 0.466667 0.759494
203 SAI 0.466667 0.75
204 EAD 0.466165 0.8875
205 AR6 AR6 0.466102 0.906667
206 J7C 0.464646 0.719512
207 NDE 0.463235 0.896104
208 SMM 0.462963 0.72093
209 SAM 0.462264 0.72619
210 4YB 0.462185 0.775281
211 ZID 0.462121 0.907895
212 S4M 0.46 0.662921
213 GJV 0.46 0.702381
214 0UM 0.459459 0.73494
215 A2R 0.458716 0.945946
216 6AD 0.457944 0.875
217 PPS 0.457944 0.819277
218 ITT 0.456311 0.88
219 A2P 0.455446 0.891892
220 62X 0.455357 0.701149
221 A3G 0.454545 0.792208
222 3AM 0.453608 0.866667
223 HFD 0.45283 0.884615
224 P1H 0.452555 0.865854
225 A3N 0.45 0.75641
226 6IA 0.448598 0.807229
227 V3L 0.448598 0.932432
228 WSA 0.447154 0.781609
229 AMP NAD 0.445312 0.92
230 ARU 0.442478 0.829268
231 MAO 0.441176 0.752941
232 NEC 0.44 0.763158
233 DSH 0.44 0.698795
234 FDA 0.439716 0.825581
235 NA7 0.438596 0.896104
236 K15 0.438596 0.717647
237 FNK 0.438356 0.797753
238 AVV 0.4375 0.8625
239 6FA 0.43662 0.855422
240 IMO 0.435644 0.866667
241 649 0.435484 0.73913
242 3AT 0.435185 0.906667
243 NAJ PZO 0.435115 0.839506
244 ZAS 0.434343 0.7375
245 7C5 0.433333 0.810127
246 A3S 0.432692 0.802632
247 A7D 0.432692 0.746835
248 8Q2 0.432 0.766667
249 SFD 0.430556 0.747368
250 2AM 0.428571 0.88
251 MHZ 0.428571 0.693182
252 NDC 0.425532 0.8625
253 GEK 0.424779 0.753086
254 2VA 0.424528 0.815789
255 4TA 0.423077 0.821429
256 G A A A 0.423077 0.839506
257 NAJ PYZ 0.422222 0.8
258 5AD 0.422222 0.739726
259 MCD 0.421429 0.818182
260 DCA 0.421053 0.816092
261 ETB 0.421053 0.825581
262 FAS 0.42069 0.865854
263 FAD 0.42069 0.865854
264 FCX 0.42029 0.808989
265 CMC 0.41844 0.818182
266 C2R 0.418367 0.893333
267 AAT 0.418182 0.682353
268 A5D 0.416667 0.75641
269 NVA 2AD 0.416667 0.775
270 GGZ 0.415929 0.795181
271 OVE 0.415842 0.846154
272 P5F 0.415584 0.837209
273 ODP 0.415385 0.875
274 NJP 0.415385 0.909091
275 KB1 0.415254 0.714286
276 COA 0.414815 0.816092
277 0T1 0.414815 0.816092
278 KH3 0.414634 0.709302
279 AV2 0.414414 0.857143
280 SCO 0.413043 0.837209
281 CMX 0.413043 0.837209
282 6C6 0.412844 0.825
283 SO8 0.412844 0.805195
284 A G 0.412214 0.85
285 0WD 0.412214 0.886076
286 SOP 0.411348 0.797753
287 OXK 0.411348 0.818182
288 DAT 0.411215 0.846154
289 NPW 0.410853 0.853659
290 FAM 0.410072 0.797753
291 MCA 0.409722 0.808989
292 62F 0.409396 0.853659
293 DTP 0.409091 0.846154
294 U A G G 0.409091 0.85
295 TXP 0.407692 0.886076
296 2CP 0.406897 0.808989
297 FAY 0.406667 0.876543
298 30N 0.405797 0.747368
299 COS 0.405797 0.797753
300 AMX 0.405797 0.825581
301 CAO 0.405797 0.788889
302 2MC 0.405594 0.763441
303 Y3J 0.404255 0.697368
304 AMZ 0.40404 0.88
305 RFL 0.403974 0.835294
306 U A 0.402985 0.873418
307 PGS 0.401869 0.82716
308 A A A 0.401709 0.87013
309 F2N 0.401274 0.806818
310 NDP 0.4 0.886076
311 ACO 0.4 0.788889
312 VRT 0.4 0.78481
313 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 with APoc: 92
This union binding pocket(no: 1) in the query (biounit: 2eqa.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 2B9J ADP 1.42045
2 2B9I ADP 1.42045
3 3HAV ATP 1.67224
4 5VAD PRO 1.98864
5 4C2W ANP 2.15054
6 4D52 GXL 2.22222
7 4D52 GIV 2.22222
8 4D4U FUC GAL NAG 2.22222
9 3VET CP 2.27273
10 3VET ADP 2.27273
11 3VET TOY 2.27273
12 5C03 AGS 2.33918
13 5X7Q GLC GLC 2.55682
14 6AC9 ANP 2.55682
15 4YGF AZM 2.5641
16 4NFN 2KC 2.589
17 1VKF CIT 2.65957
18 1ULE GLA GAL NAG 2.66667
19 1ELI PYC 2.84091
20 2P7Q GG6 3.00752
21 4BXF AKG 3.125
22 2QX0 PH2 3.14465
23 1VHW ADN 3.16206
24 5F90 GLA GAL BGC 5VQ 3.20513
25 5ZA2 NXL 3.40909
26 5C8W PCG 3.4965
27 2CFC KPC 3.6
28 4JGP PYR 3.68664
29 2ZUX RAM 3.69318
30 3DAK ANP 3.7931
31 5B09 4MX 3.84615
32 5JOG 6LT 3.89105
33 1SWG BTN 3.90625
34 1EU1 GLC 3.97727
35 3T2W BTN 4.09836
36 5BVE 4VG 4.15512
37 3ZGJ RMN 4.26136
38 4JH6 FCN 4.34783
39 2BOS GLA GAL GLC NBU 4.41176
40 5L2R MLA 4.54545
41 5KJZ PCG 4.66667
42 3SHR CMP 4.68227
43 5TCI MLI 4.71014
44 5XQW 8EU 4.73934
45 1JPA ANP 4.80769
46 4NZF ARB 4.82955
47 3IHB GLU 4.82955
48 4OFG PCG 4.86111
49 5GLT BGC GAL NAG GAL 4.92958
50 1R1Q ACE ARG GLU PTR VAL ASN VAL 5
51 4AVB CMP 5.1051
52 4YVN EBS 5.11364
53 3BJE URA 5.15759
54 4A91 GLU 5.36913
55 3HQP OXL 5.39773
56 2WHL MAN BMA BMA 5.44218
57 5ZMY TAR 5.73248
58 1OFZ FUC 5.76923
59 1ZTH ADP 5.81395
60 4E1Z 0MX 5.84192
61 3PNA CMP 5.84416
62 4LUS TCE 5.96591
63 4I9A NCN 6.25
64 2QQC AG2 6.25
65 3A51 VDY 6.53409
66 4JUI EGR 6.81818
67 4QXB OGA 7.35294
68 4RF7 ARG 7.38636
69 4WOE 3S5 7.95455
70 5FYR INS 8.05369
71 6GNO XDI 8.14815
72 1KKR 2AS 8.23864
73 2XG5 EC5 8.25688
74 2XG5 EC2 8.25688
75 1KJ1 MAN 8.25688
76 3EW2 BTN 9.62963
77 1BHX ASP PHE GLU GLU ILE 10
78 1RJW ETF 10.0295
79 2DT9 THR 10.1796
80 1V9T SIN ALA PRO ALA NIT 10.241
81 4OIT MAN 10.6195
82 3OF1 CMP 11.3821
83 3BFF FPM 12.2137
84 1OYJ GSH 12.5541
85 3LGS ADE 13.1086
86 2A19 ANP 13.1429
87 3OCP CMP 13.6691
88 3K0T BGC 16.0839
89 3TTC ADP 16.7614
90 3WIR BGC 17.6136
91 5F7J ADE 18.4375
92 5YZ2 AMP 23.6111
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