Receptor
PDB id Resolution Class Description Source Keywords
5OO4 1.6 Å EC: 5.-.-.- STREPTOMYCES PAC13 WITH URIDINE STREPTOMYCES COERULEORUBIDUS PAC13 DEHYDRATASE PACIDAMYCIN BIOSYNTHETIC PROTEIN
Ref.: PAC13 IS A SMALL, MONOMERIC DEHYDRATASE THAT MEDIAT FORMATION OF THE 3'-DEOXY NUCLEOSIDE OF PACIDAMYCIN ANGEW. CHEM. INT. ED. ENGL. V. 56 12492 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
URI A:201;
Valid;
none;
submit data
244.201 C9 H12 N2 O6 C1=CN...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5OO5 1.78 Å EC: 5.-.-.- STREPTOMYCES PAC13 WITH URIDINE URONIC ACID STREPTOMYCES COERULEORUBIDUS PAC13 DEHYDRATASE PACIDAMYCIN BIOSYNTHETIC PROTEIN
Ref.: PAC13 IS A SMALL, MONOMERIC DEHYDRATASE THAT MEDIAT FORMATION OF THE 3'-DEOXY NUCLEOSIDE OF PACIDAMYCIN ANGEW. CHEM. INT. ED. ENGL. V. 56 12492 2017
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 30 families.
1 5OO8 - URI C9 H12 N2 O6 C1=CN(C(=O....
2 5OO5 - UUA C9 H10 N2 O7 C1=CN(C(=O....
3 5OOA - URI C9 H12 N2 O6 C1=CN(C(=O....
4 5OO9 - URI C9 H12 N2 O6 C1=CN(C(=O....
5 5OO4 - URI C9 H12 N2 O6 C1=CN(C(=O....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 29 families.
1 5OO8 - URI C9 H12 N2 O6 C1=CN(C(=O....
2 5OO5 - UUA C9 H10 N2 O7 C1=CN(C(=O....
3 5OOA - URI C9 H12 N2 O6 C1=CN(C(=O....
4 5OO9 - URI C9 H12 N2 O6 C1=CN(C(=O....
5 5OO4 - URI C9 H12 N2 O6 C1=CN(C(=O....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 5OO8 - URI C9 H12 N2 O6 C1=CN(C(=O....
2 5OO5 - UUA C9 H10 N2 O7 C1=CN(C(=O....
3 5OOA - URI C9 H12 N2 O6 C1=CN(C(=O....
4 5OO9 - URI C9 H12 N2 O6 C1=CN(C(=O....
5 5OO4 - URI C9 H12 N2 O6 C1=CN(C(=O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: URI; Similar ligands found: 92
No: Ligand ECFP6 Tc MDL keys Tc
1 URI 1 1
2 CJB 0.895833 0.949153
3 DKX 0.709091 0.857143
4 2TU 0.666667 0.888889
5 U5P 0.661017 0.848485
6 U 0.661017 0.848485
7 U4S 0.65 0.833333
8 U3P 0.644068 0.833333
9 UA3 0.644068 0.833333
10 U3S 0.629032 0.833333
11 U2S 0.629032 0.848485
12 UDP 0.625 0.863636
13 44P 0.603175 0.826087
14 UPU 0.6 0.863636
15 UTP 0.597015 0.863636
16 U2P 0.590164 0.848485
17 U5F 0.588235 0.863636
18 UDP UDP 0.575758 0.861538
19 2KH 0.565217 0.838235
20 UUA 0.561404 0.864407
21 ZEB 0.553571 0.966102
22 URM 0.552632 0.852941
23 660 0.552632 0.852941
24 UFM 0.552632 0.865672
25 GDU 0.552632 0.865672
26 UPG 0.552632 0.865672
27 UNP 0.549296 0.838235
28 Y6W 0.545455 0.816901
29 N3E 0.544118 0.835821
30 DHZ 0.534483 0.966102
31 UPF 0.531646 0.816901
32 U2F 0.531646 0.816901
33 UDP GAL 0.531646 0.865672
34 UMF 0.53125 0.757143
35 U1S 0.527027 0.8
36 BRD 0.525424 0.915254
37 FZK 0.52 0.734177
38 UVC 0.515625 0.782609
39 UFG 0.5125 0.816901
40 DUR 0.508475 0.903226
41 AR3 0.5 0.919355
42 UPP 0.5 0.838235
43 UDH 0.5 0.794521
44 5UD 0.5 0.920635
45 CTN 0.5 0.919355
46 URD 0.491525 0.881356
47 CTD 0.491525 0.9
48 UDM 0.488372 0.84058
49 CSQ 0.488372 0.780822
50 CSV 0.488372 0.780822
51 3UC 0.488095 0.816901
52 AWU 0.4875 0.838235
53 UD2 0.477273 0.852941
54 UD1 0.477273 0.852941
55 UDX 0.47561 0.838235
56 UAD 0.47561 0.838235
57 LSU 0.475 0.674699
58 USQ 0.464286 0.730769
59 UGA 0.464286 0.850746
60 UGB 0.464286 0.850746
61 GPQ 0.460317 0.875
62 G3N 0.458824 0.814286
63 UGF 0.458824 0.802817
64 PUP 0.457831 0.811594
65 GPK 0.453125 0.875
66 GPU 0.446154 0.875
67 YSU 0.436782 0.682927
68 6SY 0.43662 0.80597
69 0YQ 0.435897 0.835821
70 EPZ 0.428571 0.84058
71 D1M 0.426471 0.903226
72 UM3 0.426471 0.782609
73 HWU 0.425532 0.828571
74 12V 0.425532 0.828571
75 D1J 0.424658 0.848485
76 EPU 0.424242 0.828571
77 EEB 0.424242 0.828571
78 UTP U U U 0.421687 0.818182
79 HP7 0.419355 0.838235
80 UD7 0.419355 0.826087
81 MJZ 0.414894 0.814286
82 5AE 0.412698 0.887097
83 F5P 0.410526 0.814286
84 F5G 0.410526 0.826087
85 UD4 0.410526 0.814286
86 DU 0.408451 0.771429
87 UMP 0.408451 0.771429
88 UP5 0.408163 0.76
89 DDU 0.403226 0.793651
90 IUG 0.402062 0.721519
91 DUS 0.4 0.701299
92 4TC 0.4 0.74026
Similar Ligands (3D)
Ligand no: 1; Ligand: URI; Similar ligands found: 489
No: Ligand Similarity coefficient
1 TYU 0.9947
2 DCZ 0.9735
3 GEO 0.9729
4 THU 0.9704
5 I5A 0.9703
6 F01 0.9690
7 PIR 0.9626
8 NOS 0.9582
9 THM 0.9562
10 0DN 0.9535
11 5MD 0.9511
12 B86 0.9505
13 MCY 0.9499
14 PUR 0.9489
15 K80 0.9477
16 A 0.9462
17 ADN 0.9462
18 1DA 0.9455
19 5N5 0.9449
20 9DI 0.9446
21 ID2 0.9443
22 5BT 0.9442
23 TBN 0.9417
24 5CD 0.9414
25 A4D 0.9405
26 FMB 0.9395
27 TIZ 0.9393
28 PRH 0.9386
29 HPR 0.9386
30 FMC 0.9362
31 MDR 0.9359
32 DNB 0.9356
33 5FD 0.9355
34 5AD 0.9355
35 XYA 0.9351
36 MZR 0.9342
37 TMC 0.9342
38 RAB 0.9341
39 TAL 0.9338
40 1KN 0.9335
41 3D1 0.9332
42 RBV 0.9327
43 IMH 0.9320
44 Y3J 0.9310
45 NWW 0.9299
46 DBM 0.9297
47 NNR 0.9296
48 UA2 0.9294
49 3AD 0.9285
50 3DT 0.9278
51 SCT 0.9267
52 6MD 0.9254
53 3BH 0.9236
54 5NB 0.9235
55 RPP 0.9227
56 AD3 0.9225
57 MTI 0.9214
58 TIA 0.9213
59 PF1 0.9206
60 MTM 0.9205
61 FM1 0.9204
62 MTA 0.9201
63 W29 0.9195
64 FTU 0.9188
65 5ID 0.9187
66 16Z 0.9187
67 LDC 0.9183
68 ZYV 0.9175
69 EKH 0.9172
70 DKZ 0.9170
71 IWH 0.9162
72 FM2 0.9158
73 SNI 0.9154
74 MTH 0.9153
75 38B 0.9152
76 7FF 0.9132
77 TCC 0.9131
78 AHU 0.9124
79 TCL 0.9114
80 1SF 0.9112
81 R9G 0.9100
82 GMP 0.9098
83 MTP 0.9095
84 WVV 0.9094
85 AUV 0.9092
86 TI7 0.9090
87 9UL 0.9090
88 Z15 0.9085
89 7D7 0.9085
90 PQT 0.9077
91 EAT 0.9070
92 Z57 0.9067
93 TR7 0.9066
94 WS6 0.9065
95 9W5 0.9057
96 2GD 0.9052
97 IM4 0.9052
98 TH4 0.9050
99 7ZL 0.9046
100 LTT 0.9046
101 DK4 0.9045
102 FC2 0.9044
103 RFZ 0.9039
104 B2T 0.9034
105 QTV 0.9030
106 ANU 0.9030
107 78U 0.9029
108 8OB 0.9028
109 NWQ 0.9028
110 4I5 0.9025
111 FB4 0.9020
112 A7K 0.9020
113 5I5 0.9019
114 ENG 0.9018
115 8OE 0.9016
116 C0H 0.9015
117 X11 0.9009
118 WSD 0.9008
119 1FL 0.8997
120 6HX 0.8997
121 IMG 0.8995
122 JVQ 0.8994
123 LLT 0.8994
124 DCN 0.8991
125 6J3 0.8990
126 2FA 0.8988
127 AP4 0.8985
128 A4G 0.8984
129 J47 0.8976
130 27M 0.8976
131 HNL 0.8975
132 CL9 0.8968
133 6CR 0.8966
134 0FR 0.8963
135 WOE 0.8956
136 CC5 0.8955
137 WS7 0.8955
138 QTS 0.8954
139 HNK 0.8953
140 43F 0.8952
141 N1Y 0.8952
142 H7S 0.8952
143 FTV 0.8950
144 1Z6 0.8949
145 50C 0.8948
146 5JT 0.8943
147 C6Z 0.8940
148 RQD 0.8932
149 92G 0.8932
150 G6P 0.8931
151 SQV 0.8930
152 CUT 0.8930
153 A4N 0.8929
154 KYN 0.8929
155 AX8 0.8928
156 3TC 0.8928
157 KTJ 0.8926
158 DCF 0.8924
159 TYR 0.8923
160 KWH 0.8919
161 IQQ 0.8918
162 79W 0.8918
163 BBY 0.8917
164 MEX 0.8915
165 ZAS 0.8913
166 FPL 0.8910
167 FT1 0.8909
168 E0O 0.8909
169 OCZ 0.8908
170 GNG 0.8907
171 AZC 0.8906
172 A6H 0.8904
173 CH8 0.8904
174 N8M 0.8903
175 L13 0.8902
176 CP6 0.8901
177 XIF XYP 0.8899
178 XYP XIF 0.8897
179 R8Y 0.8896
180 KWQ 0.8896
181 TRP 0.8894
182 L5D 0.8893
183 EXR 0.8892
184 RLG 0.8891
185 AZZ 0.8891
186 OA1 0.8890
187 FCW 0.8888
188 JFS 0.8888
189 FT3 0.8887
190 FCD 0.8886
191 4MP 0.8884
192 ZIQ 0.8883
193 EAJ 0.8882
194 ITW 0.8882
195 ID8 0.8878
196 VBC 0.8878
197 S1D 0.8878
198 DIF 0.8875
199 DTR 0.8873
200 Q2S 0.8872
201 EZN 0.8871
202 FMQ 0.8871
203 JSX 0.8871
204 MJ5 0.8870
205 FHI 0.8869
206 QMR 0.8869
207 4UO 0.8867
208 HNM 0.8864
209 QBS 0.8864
210 HNH 0.8863
211 JF8 0.8860
212 A9O 0.8860
213 LTN 0.8859
214 CMU 0.8858
215 AVA 0.8856
216 XIL 0.8855
217 A7Q 0.8853
218 1ER 0.8853
219 3B4 0.8851
220 XDL XYP 0.8848
221 B4O 0.8848
222 2J2 0.8848
223 HX8 0.8846
224 JP2 0.8845
225 LAH 0.8844
226 IC9 0.8843
227 VIB 0.8840
228 OX2 0.8840
229 Y4L 0.8840
230 F16 0.8839
231 HBO 0.8838
232 4OG 0.8837
233 ENO 0.8835
234 FT2 0.8834
235 MCF 0.8830
236 1CY 0.8830
237 RVE 0.8828
238 6NZ 0.8828
239 A4T 0.8824
240 HWD 0.8824
241 8UY 0.8823
242 BP3 0.8822
243 28B 0.8822
244 SY4 0.8821
245 F63 0.8820
246 N2Y 0.8819
247 X6P 0.8817
248 ETV 0.8817
249 ISC 0.8816
250 XDK 0.8816
251 30G 0.8813
252 9FG 0.8812
253 XK0 0.8809
254 A4Q 0.8808
255 FUZ 0.8808
256 EXG 0.8807
257 YF3 0.8805
258 H70 0.8804
259 YE6 0.8802
260 U2Z 0.8801
261 BVD 0.8795
262 M02 0.8795
263 RUG 0.8793
264 4EU 0.8793
265 7UZ 0.8793
266 A4B 0.8790
267 0OY 0.8790
268 C2M 0.8790
269 P2L 0.8790
270 AWE 0.8789
271 3Y7 0.8787
272 M2T 0.8787
273 SOJ 0.8787
274 HJ8 0.8787
275 5VL 0.8786
276 4E5 0.8786
277 2JM 0.8786
278 SV4 0.8786
279 BPY 0.8785
280 CUH 0.8784
281 M3E 0.8782
282 5F8 0.8782
283 DAH 0.8781
284 JMQ 0.8780
285 6J9 0.8778
286 JRB 0.8777
287 FWD 0.8775
288 ISJ 0.8775
289 F6P 0.8774
290 GNW 0.8773
291 QQX 0.8771
292 XYP XYP 0.8771
293 MUK 0.8769
294 CC7 0.8769
295 C5P 0.8768
296 C 0.8767
297 PBQ 0.8766
298 V1T 0.8765
299 BTM 0.8764
300 TT4 0.8764
301 MBY 0.8764
302 NAL 0.8763
303 1A7 0.8762
304 H2U 0.8760
305 2JX 0.8758
306 54E 0.8757
307 7QV 0.8757
308 B21 0.8756
309 1Z8 0.8756
310 EBP 0.8755
311 EN1 0.8755
312 HVE 0.8754
313 26C 0.8753
314 FN5 0.8753
315 9VZ 0.8753
316 AOJ 0.8752
317 CH 0.8752
318 3VW 0.8750
319 B23 0.8750
320 2K8 0.8747
321 S0F 0.8747
322 TQL 0.8746
323 MOK 0.8743
324 7R7 0.8742
325 ERZ 0.8742
326 K48 0.8741
327 JD7 0.8740
328 U4J 0.8740
329 SLY 0.8740
330 HJH 0.8740
331 3IL 0.8739
332 JF2 0.8739
333 51Y 0.8739
334 UP6 0.8739
335 FNA 0.8737
336 BZM 0.8736
337 Q4G 0.8736
338 NIY 0.8735
339 XYP XDN 0.8734
340 XDN XYP 0.8734
341 9PL 0.8733
342 AH9 0.8733
343 F0C 0.8732
344 MXD 0.8732
345 5E4 0.8730
346 CWD 0.8728
347 1U7 0.8728
348 8CB 0.8727
349 BCK 0.8727
350 T2D 0.8726
351 EQW 0.8725
352 BZE 0.8724
353 KW8 0.8724
354 M01 0.8723
355 XM5 0.8722
356 ACK 0.8721
357 MIL 0.8720
358 A8Q 0.8719
359 JO8 0.8719
360 JMS 0.8719
361 8HG 0.8717
362 BQ5 0.8717
363 9AA 0.8717
364 EV2 0.8716
365 JF1 0.8715
366 GT4 0.8714
367 LFQ 0.8714
368 4WF 0.8714
369 KP2 0.8713
370 CTE 0.8713
371 DBQ 0.8710
372 46P 0.8708
373 BC3 0.8707
374 A5H 0.8703
375 ZEA 0.8702
376 BWD 0.8702
377 SQ4 0.8702
378 QUS 0.8700
379 AJD 0.8699
380 S0G 0.8697
381 EXL 0.8697
382 X0W 0.8697
383 A1Y 0.8696
384 QQY 0.8695
385 NI9 0.8693
386 IWD 0.8692
387 3CR 0.8692
388 DTY 0.8692
389 EV3 0.8690
390 9FH 0.8688
391 X48 0.8687
392 4I8 0.8686
393 5FL 0.8684
394 17C 0.8683
395 BP6 0.8683
396 IMQ 0.8682
397 BRH 0.8682
398 HRX 0.8681
399 GN6 0.8681
400 1XA 0.8681
401 CH9 0.8680
402 3VO 0.8679
403 61M 0.8679
404 MPK 0.8677
405 GFE 0.8672
406 4FF 0.8672
407 B2Y 0.8671
408 JAH 0.8671
409 ING 0.8670
410 GSY 0.8670
411 AMR 0.8669
412 42R 0.8668
413 977 0.8668
414 SQ7 0.8668
415 A7M 0.8668
416 DCM 0.8668
417 AVX 0.8668
418 ALN 0.8667
419 7MK 0.8666
420 FHC 0.8665
421 22L 0.8661
422 HVJ 0.8661
423 BMP 0.8659
424 4CF 0.8659
425 1VK 0.8657
426 FC3 0.8657
427 PFF 0.8656
428 NE1 0.8656
429 1WC 0.8652
430 2J5 0.8650
431 DBE 0.8645
432 GAT 0.8642
433 XYP AHR 0.8638
434 CR1 0.8636
435 7G1 0.8636
436 GTC 0.8632
437 FLF 0.8629
438 FUB FUB 0.8628
439 JZA 0.8627
440 M5H 0.8627
441 5P3 0.8626
442 XFE 0.8626
443 AMQ 0.8620
444 89J 0.8615
445 S2T 0.8612
446 G14 0.8612
447 2OH 0.8612
448 DTE 0.8607
449 IKY 0.8604
450 F2W 0.8603
451 SQP 0.8598
452 NCT 0.8595
453 PH3 0.8594
454 BP7 0.8594
455 0OL 0.8592
456 ROI 0.8592
457 JF6 0.8591
458 CMP 0.8589
459 F4K 0.8588
460 A05 0.8588
461 YIE 0.8587
462 4FP 0.8585
463 N1E 0.8578
464 CFA 0.8574
465 W8G 0.8573
466 JG8 0.8570
467 7R4 0.8568
468 15Q 0.8567
469 6ZW 0.8565
470 GVG 0.8561
471 J27 0.8561
472 HBI 0.8559
473 CEG 0.8556
474 M2E 0.8551
475 PJW 0.8548
476 I2E 0.8547
477 L1T 0.8545
478 LJ3 0.8543
479 AU8 0.8540
480 P58 0.8539
481 EF2 0.8538
482 C3P 0.8533
483 7QS 0.8529
484 DDN 0.8527
485 C82 0.8526
486 H4B 0.8515
487 M5E 0.8511
488 XYS XYS 0.8507
489 5GV 0.8502
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5OO5; Ligand: UUA; 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: 5oo5.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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