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Receptor
PDB id Resolution Class Description Source Keywords
4YJK 1.68 Å EC: 2.4.2.3 CRYSTAL STRUCTURE OF C212S MUTANT OF SHEWANELLA ONEIDENSIS M URIDINE PHOSPHORYLASE SHEWANELLA ONEIDENSIS (STRAIN MR-1) URACIL S212C MUTANT URIDINE PHOSPHORYLASE TRANSFERASE
Ref.: CONCERTED ACTION OF TWO SUBUNITS OF THE FUNCTIONAL SHEWANELLA ONEIDENSIS MR-1 URIDINE PHOSPHORYLASE DE FROM A COMPARISON OF THE C212S MUTANT AND THE WILD-ENZYME. ACTA CRYSTALLOGR D STRUCT V. 72 203 2016 BIOL
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 B:301;
E:301;
F:302;
A:302;
C:301;
D:302;
D:304;
E:302;
D:303;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
URA F:301;
D:301;
A:301;
Valid;
Valid;
Valid;
none;
none;
none;
submit data
112.087 C4 H4 N2 O2 C1=CN...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YJK 1.68 Å EC: 2.4.2.3 CRYSTAL STRUCTURE OF C212S MUTANT OF SHEWANELLA ONEIDENSIS M URIDINE PHOSPHORYLASE SHEWANELLA ONEIDENSIS (STRAIN MR-1) URACIL S212C MUTANT URIDINE PHOSPHORYLASE TRANSFERASE
Ref.: CONCERTED ACTION OF TWO SUBUNITS OF THE FUNCTIONAL SHEWANELLA ONEIDENSIS MR-1 URIDINE PHOSPHORYLASE DE FROM A COMPARISON OF THE C212S MUTANT AND THE WILD-ENZYME. ACTA CRYSTALLOGR D STRUCT V. 72 203 2016 BIOL
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
70% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1U1G - BBB C21 H22 N2 O6 c1ccc(cc1)....
2 1RXC - R1P C5 H11 O8 P C([C@@H]1[....
3 1TGY - R1P C5 H11 O8 P C([C@@H]1[....
4 4E1V - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 1U1E - 182 C13 H14 N2 O4 Se c1ccc(cc1)....
6 3KVV - URF C4 H3 F N2 O2 C1=C(C(=O)....
7 1U1D - 181 C13 H14 N2 O4 S c1ccc(cc1)....
8 1U1C Ki ~ 4300 nM BAU C14 H16 N2 O4 c1ccc(cc1)....
9 3FWP - ANU C9 H10 N2 O5 C1=CN2[C@H....
10 1TGV - 5UD C9 H11 F N2 O6 C1=C(C(=O)....
11 1U1F Ki ~ 680 nM 183 C21 H22 N2 O5 c1ccc(cc1)....
12 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1U1G - BBB C21 H22 N2 O6 c1ccc(cc1)....
2 1RXC - R1P C5 H11 O8 P C([C@@H]1[....
3 1TGY - R1P C5 H11 O8 P C([C@@H]1[....
4 4E1V - URF C4 H3 F N2 O2 C1=C(C(=O)....
5 1U1E - 182 C13 H14 N2 O4 Se c1ccc(cc1)....
6 3KVV - URF C4 H3 F N2 O2 C1=C(C(=O)....
7 1U1D - 181 C13 H14 N2 O4 S c1ccc(cc1)....
8 1U1C Ki ~ 4300 nM BAU C14 H16 N2 O4 c1ccc(cc1)....
9 3FWP - ANU C9 H10 N2 O5 C1=CN2[C@H....
10 1TGV - 5UD C9 H11 F N2 O6 C1=C(C(=O)....
11 1U1F Ki ~ 680 nM 183 C21 H22 N2 O5 c1ccc(cc1)....
12 4YJK - URA C4 H4 N2 O2 C1=CNC(=O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: URA; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 URA 1 1
2 TUL 0.5 0.725
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YJK; Ligand: URA; Similar sites found with APoc: 342
This union binding pocket(no: 1) in the query (biounit: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5YSI NCA None
2 5N2F 8HW None
3 5N2D 8J8 None
4 5NIU 8YZ None
5 2NSJ C2R None
6 2FWP ICR None
7 5AHW CMP None
8 5DX8 SFG 0.793651
9 5DX0 SFG 0.793651
10 3DAA PDD 1.19048
11 6GFK SAH 1.19522
12 4J3L AJ5 1.42857
13 5J75 6GQ 1.51515
14 2WLG SOP 1.86047
15 5U3F 7TS 1.98413
16 1X7D ORN 1.98413
17 6ECT SAM 1.98413
18 3VKX T3 1.98413
19 3KJD 78P 1.98413
20 6ECU SAH 1.98413
21 6CEP NAD 1.98413
22 5Y4R C2E 2.06897
23 5LX6 78P 2.09424
24 3DUW SAH 2.24215
25 5XLY C2E 2.25564
26 6G96 ACO 2.27273
27 3LGS ADE 2.38095
28 3LGS SAH 2.38095
29 4GLJ RHB 2.38095
30 2PWY SAH 2.38095
31 5N5S NAP 2.38095
32 1I9G SAM 2.38095
33 1RKD RIB 2.38095
34 1RKD ADP 2.38095
35 5LHT TIH 2.38095
36 6MJF SAH 2.38095
37 5FA8 SAM 2.48447
38 3LF0 ATP 2.63158
39 3EEL 53T 2.64317
40 5KJZ PCG 2.66667
41 1NFS DED 2.73224
42 4ZVV NAD 2.77778
43 2XIQ MLC 2.77778
44 4ZVV GN0 2.77778
45 2PCU PHE ASN ARG PRO VAL 2.77778
46 3X0D SAH 2.77778
47 5YU3 NAD 2.77778
48 5YU3 PRO 2.77778
49 6B2M COA 2.77778
50 4ZH7 FUC GAL NAG GAL FUC 2.77778
51 3VYW SAM 2.77778
52 3GC8 B45 2.77778
53 5VN0 NAI 2.77778
54 4GQB 0XU 2.77778
55 4Z9D NAD 2.85714
56 1D1G NDP 2.97619
57 4QAR ADE 2.98507
58 5EWK P34 3
59 5LYH 7B8 3.10881
60 1L3I SAH 3.125
61 1QL9 ZEN 3.13901
62 1K27 MTM 3.1746
63 1PJS SAH 3.1746
64 5KJW 53C 3.1746
65 2YB9 HA0 3.1746
66 2ZRU FMN 3.1746
67 4AZW SAM 3.1746
68 2Y6Q I7T 3.1746
69 2C6Q IMP 3.1746
70 5OLK DTP 3.1746
71 3IES M24 3.1746
72 1NE7 16G 3.1746
73 5W75 SUC 3.1746
74 5N5D SAM 3.53982
75 5F7J ADE 3.57143
76 5IFK HPA 3.57143
77 1WOR RED 3.57143
78 4H03 NAD 3.57143
79 6BWL NAD 3.57143
80 2WN6 NDP 3.57143
81 1GAD NAD 3.57143
82 3CMC NAD 3.57143
83 1Q19 APC 3.57143
84 6APL C5P 3.57143
85 4PLT OXM 3.57143
86 2J8Z NAP 3.57143
87 4PLT NAI 3.57143
88 5MJI 7O6 3.57143
89 3OKP GDD 3.57143
90 4GV4 MEJ 3.57143
91 4I8P NAD 3.57143
92 4KIB SAH 3.57143
93 1LL2 UPG 3.57143
94 2E7Z MGD 3.57143
95 6GEW SFG 3.57143
96 6GEW SAH 3.57143
97 4XTX 590 3.57143
98 3DLA NXX 3.57143
99 3T4L ZEA 3.57143
100 3H8V ATP 3.57143
101 5N0O SAM 3.57143
102 5OFW 9TW 3.58744
103 3FIU AMP 3.61446
104 5DYO FLU 3.66972
105 4YC0 5OF 3.76569
106 1GZF NAD 3.79147
107 1GZF ADP 3.79147
108 1GZF NIR 3.79147
109 4FK7 P34 3.93013
110 4B2Z P5S 3.96825
111 6MPT C30 3.96825
112 3MB5 SAM 3.96825
113 2VYN NAD 3.96825
114 1C3X 8IG 3.96825
115 1VJO PLP 3.96825
116 5K3W PLP 3.96825
117 6BQC LOP 3.96825
118 1Z45 NAD 3.96825
119 4I54 1C1 3.96825
120 2HJR APR 3.96825
121 2Q1S NAI 3.96825
122 3O8M BGC 3.96825
123 3O8M GLC 3.96825
124 4K91 SIN 3.96825
125 2E0N SAH 3.96825
126 3VSE SAH 3.96825
127 2YAK OSV 3.96825
128 4GYW UDP 3.96825
129 1SOW NAD 3.96825
130 5W5R PYR 3.96825
131 1TU3 GNP 4.09357
132 1R2Q GNP 4.11765
133 2ZMF CMP 4.2328
134 3KYF 5GP 5GP 4.329
135 3CTL S6P 4.329
136 2P4S DIH 4.36508
137 1G2O IMH 4.36508
138 4CE5 PDG 4.36508
139 5ERG SAM 4.36508
140 4UUG PXG 4.36508
141 1REQ DCA 4.36508
142 1PZG A3D 4.36508
143 1T26 NAI 4.36508
144 1T26 GBD 4.36508
145 3VZ3 SSN 4.36508
146 3VZ3 NAP 4.36508
147 4AVB ACO 4.36508
148 5LD5 NAD 4.36508
149 1EFY BZC 4.36508
150 2IHT TPP 4.36508
151 4L2I NAD 4.36508
152 3GE7 AFQ 4.36508
153 3VPH OXM 4.36508
154 1UPA TPP 4.36508
155 3VPH NAD 4.36508
156 4ZCC FAD 4.36508
157 1Y8Q ATP 4.36508
158 5HJM MTA 4.36508
159 2IHU TP9 4.36508
160 2IO8 ADP 4.36508
161 1TMM APC 4.43038
162 4POO SAM 4.5
163 4XDA RIB 4.53074
164 4XDA ADP 4.53074
165 3SM2 478 4.54545
166 2A5F NAD 4.66321
167 4DEC 3PG 4.7619
168 4DEC UDP 4.7619
169 6BHV DQV 4.7619
170 4R0M FA5 4.7619
171 4YWV SSN 4.7619
172 4PJT 2YQ 4.7619
173 5M3E APR 4.84848
174 1S7N COA 4.94506
175 1VMK GUN 5.05415
176 5N53 8NB 5.12821
177 3EFS BTN 5.15021
178 4I9A NCN 5.15873
179 1RM0 D6P 5.15873
180 1RM0 NAI 5.15873
181 4C4A SAH 5.15873
182 1O5R FR9 5.15873
183 1TDF FAD 5.15873
184 2BLE 5GP 5.15873
185 5I7A 68Q 5.15873
186 6ACS CIT 5.15873
187 5APK 76E 5.15873
188 4MO4 ACP 5.15873
189 2NXE SAM 5.15873
190 3IWJ NAD 5.15873
191 2CYE COA 5.26316
192 2FLI DX5 5.45455
193 4XSH NAI 5.47945
194 4PAB THG 5.55556
195 2IVD ACJ 5.55556
196 1QRD FAD 5.55556
197 4LH0 GLV 5.55556
198 5X62 SAH 5.55556
199 4M37 SAH 5.55556
200 3RDE OYP 5.55556
201 2RDE C2E 5.57769
202 4R3U 3KK 5.95238
203 4R3U 3HC 5.95238
204 1VKO NAD 5.95238
205 2H21 SAM 5.95238
206 1YKD CMP 5.95238
207 5UAV NDP 5.95238
208 3BOF HCS 5.95238
209 1Q8A HCS 5.95238
210 3PPM JG1 5.95238
211 3DXY SAM 5.9633
212 4QAC KK3 5.99078
213 2QBU SAH 6.03448
214 5LLT DND 6.10329
215 3KYG 5GP 5GP 6.1674
216 1AJQ SPA 6.2201
217 1O94 AMP 6.34921
218 2YBQ UP2 6.34921
219 2OQ2 A3P 6.34921
220 5KVA SAM 6.47482
221 5UKL SIX 6.48968
222 4O9S 2RY 6.51163
223 1OJZ NAD 6.60377
224 1RJW ETF 6.74603
225 4I9B NAD 6.74603
226 1VBH PEP 6.74603
227 5ZJ5 NAI 6.79012
228 4M7V NAP 6.85714
229 2A9K NAD 6.95187
230 5MRH Q9Z 7.14286
231 4RPL 3UC 7.14286
232 4RPL FAD 7.14286
233 4R84 CSF 7.14286
234 3OJO NAD 7.14286
235 1RSG FAD 7.14286
236 4NV7 COA 7.14286
237 3FHI ANP 7.14286
238 2JLD ALA GLY GLY ALA ALA ALA ALA ALA 7.14286
239 4ZFL 4NK 7.26496
240 1MJH ATP 7.40741
241 1OG1 TAD 7.52212
242 1Q0S SAH 7.53968
243 1XNG ATP 7.53968
244 4IXH IMP 7.53968
245 2A0W DIH 7.93651
246 1B8O IMH 7.93651
247 5ETJ IM5 7.93651
248 1DR1 HBI 7.93651
249 1DR1 NAP 7.93651
250 2QQF A1R 7.93651
251 3OV6 MK0 7.93651
252 1E6E FAD 7.93651
253 3OQJ 3CX 7.93651
254 1D4D FAD 7.93651
255 3WOL VAL TYR 7.93651
256 5JWI ARG GLU 7.93651
257 5NWD 9C8 8.16327
258 1F5F DHT 8.29268
259 3NRR D16 8.33333
260 2ZW5 COA 8.33333
261 4I3V NAD 8.33333
262 5LOG SAH 8.58369
263 4XUC 43G 8.7156
264 4XUC SAM 8.7156
265 2R5N RP5 8.73016
266 2R5N R5P 8.73016
267 2R5N TPP 8.73016
268 4PLG OXM 8.73016
269 4PLG NAI 8.73016
270 2HNK SAH 8.78661
271 4DR9 BB2 8.85417
272 2A92 NAI 9.12698
273 1L1E SAH 9.12698
274 3QWB NDP 9.12698
275 4DQ2 BTX 9.12698
276 1KYZ SAH 9.12698
277 3AWJ COA 9.12698
278 3BGD SAH 9.12698
279 3BGD PM6 9.12698
280 3QOX SAH 9.12698
281 3L9R L9R 9.18367
282 4F7E 0SH 9.18367
283 3HVJ 705 9.50226
284 4MIG G3F 9.52381
285 3JSX CC2 9.52381
286 3JSX FAD 9.52381
287 4FC7 NAP 9.52381
288 4FC7 COA 9.52381
289 1Q3Q ANP 9.52381
290 4BGB ADP 9.52381
291 1KDK DHT 9.60452
292 3KJS DQ1 10.3175
293 3KJS NAP 10.3175
294 4WKC BIG 10.6122
295 1JG3 ADN 10.6383
296 1KOL NAD 11.0553
297 5TBS ADE 11.1111
298 1IYE PGU 11.1111
299 5F7N NAG GAL FUC FUC A2G 11.6667
300 5F7Y GLC GAL NAG GAL FUC A2G 11.6667
301 2A8Y MTA 11.9048
302 1T90 NAD 11.9048
303 5OVK NDP 11.9048
304 1VKF CIT 12.234
305 4WKB TDI 12.2951
306 3DJF BC3 12.6984
307 5ZW3 SAH 12.8889
308 3CBG SAH 13.0952
309 1GV0 NAD 13.0952
310 4YMH SAH 13.3333
311 2XXP DSL 13.4921
312 3BL6 FMC 13.913
313 1HDG NAD 14.6825
314 6D6L FY4 14.7059
315 1QAW TRP 14.8649
316 2F59 INI 15.9236
317 4RT1 C2E 16.0714
318 2WA4 069 16.6667
319 5FVJ ACO 16.8675
320 3ZZS TRP 16.9231
321 3ZZQ TRP 16.9231
322 2XZ9 PYR 17.8571
323 1WXI AMP 18.6508
324 6AM8 PLT 19.0476
325 1TT8 PHB 23.7805
326 6AYR BIG 26.8908
327 4BMX ADE 27.0916
328 4FFS BIG 28.0335
329 3KVY URA 33.3333
330 3KVY R2B 33.3333
331 1ZOS MTM 33.913
332 1NW4 IMH 37.3016
333 4DA6 GA2 38.8889
334 1ODJ GMP 40.8511
335 2AC7 ADN 40.8511
336 3BJE URA 40.873
337 1VHW ADN 40.873
338 3U40 ADN 43.3884
339 6F4W FMC 43.7768
340 1JE1 GMP 44.4915
341 1A69 FMB 44.5378
342 1Z34 2FD 45.9574
Pocket No.: 2; Query (leader) PDB : 4YJK; Ligand: URA; Similar sites found with APoc: 90
This union binding pocket(no: 2) in the query (biounit: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 5JY4 ISC 0.793651
2 4MSG 2C6 1.38249
3 1YY5 FAD 1.5873
4 5I60 67W 1.98413
5 3WMX NAD 1.98413
6 4BLW SAH 1.98413
7 4QC6 30N 2.23464
8 1EK6 NAI 2.38095
9 1EK6 UPG 2.38095
10 6AIN FAD 2.38095
11 1GUZ NAD 2.38095
12 4YZC STU 2.38095
13 1US5 GLU 2.38095
14 5VN0 FAD 2.77778
15 5WS9 AMP 2.77778
16 3O9L LPN 3.01205
17 1KDO C 3.0837
18 2C6Q NDP 3.1746
19 3L4S 3PG 3.1746
20 3L4S NAD 3.1746
21 1KOR ANP 3.1746
22 1KOR ARG 3.1746
23 1KOR SIN 3.1746
24 1NV8 SAM 3.1746
25 1S4M LUM 3.1746
26 2OEG UPG 3.1746
27 4NP3 2L2 3.33333
28 4KQ6 DLZ 3.35196
29 4FXQ G9L 3.57143
30 5BYK A3P 3.57143
31 5BYK OAQ 3.57143
32 1CER NAD 3.57143
33 1QO8 FAD 3.57143
34 4IVG ANP 3.57143
35 5X68 FAD 3.57143
36 2AQX ATP 3.57143
37 1WDK NAD 3.57143
38 4OR7 NAP 3.63636
39 5N87 N66 3.96825
40 1TKB N1T 3.96825
41 1CSI CMX 3.96825
42 1CSI OAA 3.96825
43 3MJH GTP 4.16667
44 3WYJ H78 4.36508
45 5GSN NAP 4.36508
46 5E72 SAM 4.36508
47 3BXF FBP 4.7619
48 5MM0 GDD 4.7619
49 4PIO SAH 5.15873
50 4PIO AVI 5.15873
51 2CI5 HCS 5.15873
52 4R74 F6P 5.15873
53 3B20 NAD 5.15873
54 1VM6 NAD 5.26316
55 3PD2 A3S 5.44218
56 4DSG FAD 5.55556
57 4DSG UDP 5.55556
58 2ADA HPR 5.55556
59 2X3F APC 5.55556
60 5AHM IMP 5.55556
61 4R5Z SIN 5.95238
62 3WCA FPS 5.95238
63 5UAV TFB 5.95238
64 2DT5 NAD 6.16114
65 3FW3 ETS 6.34921
66 5FPE 3TR 6.74603
67 3E9I XAH 6.74603
68 1UXG FUM 7.44337
69 1UXG NAD 7.44337
70 4LWP SAH 7.53968
71 4L9Z COA 7.53968
72 1KY8 NAP 7.93651
73 2RKV COA 7.93651
74 1U2Z SAH 8.33333
75 5XU2 F6R 8.73016
76 5XU2 TPP 8.73016
77 5XU2 8EL 8.73016
78 1PJ6 FOL 8.73016
79 2QTR NXX 9.52381
80 6FA4 D1W 10.4046
81 5IM3 DTP 11.1111
82 1JGT CMA 11.1111
83 1JGT APC 11.1111
84 4JEM C5P 11.1765
85 1XSE NDP 11.5079
86 5JZI LYS LEU VAL ALA LEU GLY ILE ASN ALA VAL 11.8483
87 3Q9T FAY 13.0952
88 1WAP TRP 14.6667
89 3A5Z KAA 15.1832
90 1Z4O GL1 15.8371
Pocket No.: 3; Query (leader) PDB : 4YJK; Ligand: URA; Similar sites found with APoc: 48
This union binding pocket(no: 3) in the query (biounit: 4yjk.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
1 4BUY F37 1.25
2 1HDR NAD 1.63934
3 2FK8 SAM 1.98413
4 1OMO NAD 2.38095
5 3JZ4 NAP 2.38095
6 1J49 NAD 2.38095
7 1CT9 AMP 2.38095
8 3L02 SN0 2.38095
9 3L02 CP 2.38095
10 1E3W NAD 2.38095
11 4J7H TLO 2.38095
12 6B92 SAH 3.1746
13 2V77 PAY 3.1746
14 1PFY MSP 3.1746
15 4R6W SAH 3.1746
16 5Z2F NAP 3.1746
17 2QV6 GTP 3.1746
18 1TOX NAD 3.1746
19 4WB6 ATP 3.57143
20 3ESS 18N 3.91304
21 5JY6 NAD 3.96825
22 5ZCT ANP 3.96825
23 2YAB AMP 3.96825
24 5YLT SFG 4.36508
25 2QCS ANP 4.36508
26 1PL6 NAD 4.36508
27 1PL6 572 4.36508
28 3G89 SAM 4.41767
29 4MOP 2H5 4.42338
30 6EK3 OUL 4.52489
31 2JHP SAH 4.7619
32 2ZFU SAH 5.11628
33 4EYG VNL 5.15873
34 4R1S NAP 5.15873
35 4A0M NAD 5.15873
36 1TPY SAH 5.55556
37 3RHJ NAP 5.55556
38 3KLJ FAD 5.55556
39 4M38 SAH 5.55556
40 1OFL NGK GCD 5.55556
41 6DW2 HD4 6.66667
42 3QV1 NAD 6.74603
43 2HFN FMN 7.18954
44 5W10 CMP 7.69231
45 4I53 1C1 8.33333
46 2XVF FAD 11.9048
47 2BJU IH4 14.2857
48 2IVF MGD 17.8571
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