Receptor
PDB id Resolution Class Description Source Keywords
5FBD 1.75 Å EC: 3.1.30.1 S1 NUCLEASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH PHOSPHAT DEOXYCYTIDINE ASPERGILLUS ORYZAE RIB40 ENDONUCLEASE ZINC DEPENDENT COMPLEX HYDROLASE
Ref.: STRUCTURAL AND CATALYTIC PROPERTIES OF S1 NUCLEASE ASPERGILLUS ORYZAE RESPONSIBLE FOR SUBSTRATE RECOGN CLEAVAGE, NON-SPECIFICITY, AND INHIBITION. PLOS ONE V. 11 68832 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 A:601;
 Invalid;
 none;
 submit data
94.971 O4 P [O-]P...
ZN A:402;
A:401;
A:403;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
65.409 Zn [Zn+2...
NAG A:501;
 Invalid;
 none;
 submit data
221.208 C8 H15 N O6 CC(=O...
DCZ A:701;
 Valid;
 none;
 submit data
227.217 C9 H13 N3 O4 C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5FBF 1.04 Å EC: 3.1.30.1 S1 NUCLEASE FROM ASPERGILLUS ORYZAE IN COMPLEX WITH TWO MOLE 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE ASPERGILLUS ORYZAE RIB40 ENDONUCLEASE ZINC DEPENDENT COMPLEX HYDROLASE
Ref.: STRUCTURAL AND CATALYTIC PROPERTIES OF S1 NUCLEASE ASPERGILLUS ORYZAE RESPONSIBLE FOR SUBSTRATE RECOGN CLEAVAGE, NON-SPECIFICITY, AND INHIBITION. PLOS ONE V. 11 68832 2016
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
50% Homology Family (6)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5FBB - AMP C10 H14 N5 O7 P c1nc(c2c(n....
2 5FBC - AS C10 H14 N5 O5 P S c1nc(c2c(n....
3 5FBF - DCM C9 H14 N3 O7 P C1[C@@H]([....
4 5FBD - DCZ C9 H13 N3 O4 C1[C@@H]([....
5 5FBG - GNG C10 H13 N5 O4 c1nc2c(n1[....
6 1AK0 - ADS THS THS THS n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: DCZ; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 DCZ 1 1
2 LDC 1 1
3 DCM 0.693548 0.833333
4 DC 0.693548 0.833333
5 YYY 0.641791 0.847222
6 DCP 0.605634 0.847222
7 0KX 0.597222 0.824324
8 DCP MG 0.575342 0.84507
9 3TC 0.557377 0.893939
10 LTT 0.540984 0.907692
11 MCY 0.539683 0.954545
12 5BT 0.539683 0.926471
13 CTN 0.52459 0.907692
14 AR3 0.52459 0.907692
15 B86 0.515625 0.926471
16 GEO 0.5 0.852941
17 DUR 0.483871 0.921875
18 DKZ 0.477612 0.811594
19 I5A 0.46875 0.835821
20 C2P 0.457143 0.794521
21 C3P 0.457143 0.780822
22 DOC 0.450704 0.808219
23 3DT 0.424242 0.84058
24 THM 0.424242 0.880597
25 LLT 0.424242 0.880597
26 CPA 0.415842 0.78481
27 DCT 0.4125 0.821918
28 C 0.410959 0.77027
29 CAR 0.410959 0.77027
30 C5P 0.410959 0.77027
31 CGP 0.4 0.756098
Similar Ligands (3D)
Ligand no: 1; Ligand: DCZ; Similar ligands found: 598
No: Ligand Similarity coefficient
1 THU 0.9875
2 URD 0.9850
3 DDU 0.9792
4 5AE 0.9766
5 0DN 0.9766
6 CTD 0.9740
7 URI 0.9735
8 ID2 0.9701
9 5MD 0.9683
10 2TU 0.9661
11 TYU 0.9652
12 PIR 0.9578
13 UUA 0.9561
14 SCT 0.9538
15 F01 0.9521
16 DHZ 0.9512
17 ZEB 0.9491
18 TMC 0.9474
19 ANU 0.9449
20 3D1 0.9448
21 II4 0.9395
22 MDR 0.9385
23 PF1 0.9362
24 5UD 0.9359
25 5F1 0.9349
26 FPL 0.9337
27 MZR 0.9326
28 AHU 0.9304
29 C0H 0.9300
30 RBV 0.9298
31 PQT 0.9294
32 DNB 0.9290
33 RAB 0.9290
34 6HO 0.9288
35 D1Y 0.9275
36 7D7 0.9258
37 ENG 0.9251
38 FMB 0.9251
39 EN1 0.9244
40 DTY 0.9235
41 TYR 0.9235
42 9DI 0.9234
43 5AD 0.9233
44 B41 0.9231
45 ZYV 0.9230
46 PUR 0.9226
47 PFF 0.9225
48 MJ5 0.9216
49 ADN 0.9214
50 X11 0.9214
51 A 0.9210
52 BRD 0.9209
53 IMH 0.9205
54 NOS 0.9203
55 TIZ 0.9200
56 W29 0.9196
57 TBN 0.9196
58 1DA 0.9194
59 UA2 0.9192
60 0A1 0.9191
61 R9J 0.9190
62 TIA 0.9189
63 KYN 0.9185
64 E0O 0.9179
65 R9G 0.9178
66 CH8 0.9171
67 FTV 0.9161
68 HPR 0.9160
69 PRH 0.9160
70 TRP 0.9150
71 1KN 0.9145
72 YOF 0.9142
73 DBM 0.9139
74 5JT 0.9133
75 XYA 0.9131
76 DAH 0.9131
77 CK2 0.9128
78 A4D 0.9124
79 K80 0.9117
80 YF3 0.9113
81 3L1 0.9112
82 KTJ 0.9110
83 TCC 0.9105
84 FHC 0.9104
85 Y4L 0.9104
86 0GA 0.9094
87 7R7 0.9088
88 9W5 0.9087
89 7QV 0.9080
90 AD3 0.9080
91 TYE 0.9068
92 1QP 0.9063
93 TH4 0.9062
94 ISA 0.9061
95 FB4 0.9059
96 DTR 0.9058
97 EZN 0.9055
98 2GD 0.9053
99 9UL 0.9050
100 NNR 0.9046
101 ZIQ 0.9045
102 UKV 0.9041
103 ENO 0.9040
104 TCL 0.9037
105 TZM 0.9037
106 XIF XYP 0.9035
107 XYP XIF 0.9034
108 6J9 0.9027
109 0XT 0.9025
110 IYR 0.9024
111 AZZ 0.9023
112 7ZL 0.9012
113 QMR 0.9011
114 HNM 0.9011
115 MTH 0.9011
116 HNH 0.9010
117 6MD 0.9008
118 FMC 0.9006
119 N2Y 0.9006
120 L5D 0.9005
121 BPY 0.9004
122 EXR 0.9004
123 1KP 0.9001
124 DX3 0.9001
125 JRB 0.9001
126 RQD 0.9000
127 MTA 0.8996
128 RLG 0.8993
129 5ID 0.8989
130 78U 0.8989
131 15E 0.8989
132 51Y 0.8988
133 9B3 0.8986
134 CL9 0.8986
135 3BH 0.8985
136 2B4 0.8977
137 EKH 0.8977
138 HNK 0.8976
139 BVD 0.8974
140 HWD 0.8972
141 1Z6 0.8969
142 8OE 0.8969
143 CTE 0.8968
144 LL1 0.8967
145 JVQ 0.8962
146 5NB 0.8960
147 HNL 0.8956
148 69K 0.8955
149 M5H 0.8954
150 MTP 0.8952
151 A7Q 0.8946
152 FM1 0.8946
153 GNG 0.8945
154 WOE 0.8942
155 FTU 0.8938
156 RFZ 0.8937
157 CUT 0.8934
158 KP2 0.8931
159 HRM 0.8931
160 OCZ 0.8928
161 54Z 0.8928
162 N1E 0.8919
163 JWS 0.8917
164 TR7 0.8915
165 GMP 0.8915
166 4I5 0.8915
167 CMU 0.8913
168 BZE 0.8912
169 A6H 0.8911
170 BZJ 0.8911
171 DCF 0.8910
172 5I5 0.8910
173 3Y7 0.8908
174 LJ4 0.8906
175 H7S 0.8903
176 MUK 0.8903
177 CDY 0.8903
178 BQ2 0.8896
179 PH3 0.8896
180 PHE 0.8896
181 S0G 0.8895
182 4V2 0.8895
183 CH9 0.8894
184 61M 0.8894
185 EGR 0.8894
186 F63 0.8893
187 2UB 0.8891
188 L22 0.8890
189 ITW 0.8890
190 WSD 0.8890
191 LTN 0.8890
192 ANC 0.8889
193 1WC 0.8889
194 AUV 0.8885
195 J47 0.8885
196 TT4 0.8884
197 4Z1 0.8883
198 M02 0.8881
199 92G 0.8880
200 4OG 0.8879
201 79W 0.8879
202 F2W 0.8879
203 30G 0.8877
204 XDK 0.8876
205 CC5 0.8875
206 FT1 0.8874
207 8DA 0.8873
208 3QO 0.8873
209 1A7 0.8873
210 22L 0.8871
211 8OB 0.8867
212 TI7 0.8866
213 16Z 0.8866
214 S8D 0.8865
215 50C 0.8865
216 BP3 0.8863
217 ROI 0.8862
218 CFA 0.8862
219 27M 0.8861
220 7VY 0.8861
221 DBS 0.8860
222 BGU 0.8860
223 IOP 0.8859
224 9FH 0.8857
225 HBI 0.8856
226 6FB 0.8856
227 ACE TRP 0.8854
228 JZA 0.8853
229 MXD 0.8853
230 9VQ 0.8853
231 8U3 0.8853
232 CNI 0.8851
233 WL3 0.8851
234 FT2 0.8851
235 YIE 0.8851
236 PPN 0.8850
237 N0Z 0.8850
238 6QF 0.8848
239 S60 0.8846
240 XFE 0.8844
241 9FL 0.8843
242 EXL 0.8843
243 M3E 0.8843
244 FQX 0.8843
245 RVD 0.8843
246 F16 0.8840
247 2J5 0.8839
248 4BY 0.8837
249 QTV 0.8837
250 MP5 0.8836
251 CCV 0.8836
252 9BF 0.8835
253 IC9 0.8834
254 C82 0.8834
255 AWE 0.8833
256 XYP AHR 0.8832
257 GNW 0.8831
258 5E4 0.8830
259 IM4 0.8824
260 JF6 0.8824
261 DEW 0.8821
262 5F8 0.8821
263 P9E 0.8820
264 4I8 0.8818
265 GVG 0.8818
266 BP7 0.8815
267 38B 0.8815
268 IWH 0.8814
269 2K8 0.8814
270 HFA 0.8812
271 0A9 0.8812
272 MSR 0.8810
273 I2E 0.8810
274 3VW 0.8809
275 EQA 0.8808
276 JGB 0.8808
277 4G2 0.8807
278 9R5 0.8807
279 WS7 0.8804
280 HX8 0.8802
281 SY4 0.8802
282 2UD 0.8801
283 NIY 0.8799
284 FWD 0.8799
285 848 0.8799
286 L13 0.8796
287 363 0.8796
288 ING 0.8796
289 X48 0.8794
290 Q4G 0.8793
291 ETV 0.8792
292 DTE 0.8791
293 9PL 0.8790
294 6J3 0.8790
295 FDR 0.8790
296 EAJ 0.8788
297 MAJ 0.8788
298 QUS 0.8786
299 3QV 0.8785
300 STT 0.8784
301 EXG 0.8784
302 IMG 0.8784
303 WVV 0.8781
304 AMR 0.8781
305 46P 0.8778
306 HX4 0.8778
307 F4K 0.8777
308 AH9 0.8777
309 AVA 0.8776
310 5GV 0.8775
311 JY4 0.8774
312 C9E 0.8774
313 7UZ 0.8772
314 6HX 0.8771
315 ALN 0.8769
316 APS 0.8768
317 2C2 0.8768
318 NCT 0.8763
319 BZQ 0.8762
320 MPK 0.8762
321 J4K 0.8761
322 IOS 0.8760
323 A5H 0.8760
324 4UO 0.8759
325 B2T 0.8758
326 XDL XYP 0.8757
327 JOV 0.8757
328 49O 0.8756
329 SKF 0.8755
330 344 0.8755
331 C53 0.8752
332 EXD 0.8751
333 M5E 0.8748
334 S0E 0.8747
335 HVE 0.8747
336 U 0.8746
337 36E 0.8745
338 WUB 0.8745
339 IQQ 0.8744
340 Z15 0.8744
341 G14 0.8743
342 C2Y 0.8743
343 6ZW 0.8742
344 CPZ 0.8742
345 X0U 0.8741
346 1VK 0.8740
347 657 0.8740
348 BTM 0.8740
349 6DP 0.8739
350 43F 0.8739
351 CUH 0.8739
352 GWM 0.8739
353 BBY 0.8738
354 SV4 0.8737
355 M01 0.8737
356 MR6 0.8735
357 JF1 0.8735
358 PYU 0.8734
359 OA1 0.8733
360 GSY 0.8733
361 8XL 0.8732
362 BZM 0.8732
363 RUY 0.8732
364 54E 0.8732
365 EYY 0.8732
366 CWD 0.8732
367 XYP XDN 0.8732
368 H4B 0.8731
369 0OL 0.8731
370 GC3 0.8731
371 XDN XYP 0.8729
372 B4O 0.8729
373 PH2 0.8729
374 89J 0.8728
375 8D6 0.8727
376 7Q1 0.8726
377 JAH 0.8725
378 4NS 0.8724
379 ODK 0.8723
380 2F6 0.8723
381 EUE 0.8722
382 2UZ 0.8722
383 Q2S 0.8721
384 TMG 0.8721
385 0JD 0.8720
386 S24 0.8719
387 B2Y 0.8718
388 4WF 0.8717
389 M72 0.8715
390 AN3 0.8715
391 NAG 0.8714
392 78Y 0.8712
393 DHY 0.8712
394 YTX 0.8711
395 4GU 0.8711
396 BRH 0.8710
397 EVF 0.8710
398 1A5 0.8709
399 P2L 0.8709
400 NHT 0.8709
401 CSN 0.8709
402 X0W 0.8707
403 6KT 0.8707
404 BNL 0.8706
405 2WU 0.8703
406 EBP 0.8703
407 M3Q 0.8703
408 2GQ 0.8700
409 X6P 0.8699
410 CB1 0.8698
411 RVB 0.8697
412 7R4 0.8697
413 I3E 0.8697
414 A5E 0.8697
415 ZEC 0.8696
416 TLM 0.8694
417 NGT 0.8692
418 X2M 0.8691
419 ID8 0.8690
420 JG8 0.8689
421 6NT 0.8687
422 4FF 0.8687
423 BZS 0.8687
424 XCG 0.8686
425 HXY 0.8685
426 1FL 0.8685
427 S0F 0.8682
428 0UL 0.8682
429 T2D 0.8680
430 WCU 0.8679
431 OQC 0.8677
432 JF8 0.8676
433 PRL 0.8676
434 9FG 0.8675
435 977 0.8675
436 LL2 0.8675
437 EYV 0.8675
438 QMS 0.8674
439 L1T 0.8674
440 ZZZ 0.8672
441 TZF 0.8671
442 8HG 0.8670
443 FC2 0.8670
444 1F1 0.8670
445 D3G 0.8669
446 33S 0.8667
447 1SF 0.8667
448 3ZB 0.8666
449 535 0.8666
450 5F5 0.8665
451 IWT 0.8664
452 E4P 0.8664
453 TYL 0.8664
454 5GT 0.8663
455 FCD 0.8662
456 WS6 0.8658
457 DBQ 0.8658
458 428 0.8657
459 9AA 0.8655
460 FMQ 0.8655
461 VM1 0.8654
462 UA5 0.8651
463 8NX 0.8651
464 F6P 0.8651
465 JR2 0.8651
466 4BL 0.8650
467 DNQ 0.8648
468 M6H 0.8648
469 XYP XYP 0.8647
470 3NY 0.8646
471 DE3 0.8645
472 N8M 0.8645
473 4HP 0.8644
474 1FD 0.8643
475 SDF 0.8643
476 CP6 0.8643
477 PPT 0.8641
478 3CR 0.8641
479 36Y 0.8641
480 EAT 0.8640
481 23N 0.8639
482 5E5 0.8638
483 AP4 0.8638
484 MOK 0.8638
485 8VR 0.8637
486 AH6 0.8637
487 W8G 0.8636
488 NB1 0.8636
489 PAU 0.8635
490 JMS 0.8635
491 0HN 0.8635
492 SQ4 0.8634
493 HHH 0.8634
494 MPV 0.8632
495 AOJ 0.8632
496 15N 0.8631
497 SNU 0.8630
498 TJM 0.8628
499 IAC 0.8627
500 AOT 0.8623
501 5FL 0.8623
502 AZM 0.8621
503 2QC 0.8620
504 N2Z 0.8619
505 2ZM 0.8619
506 52C 0.8617
507 GNM 0.8617
508 CU8 0.8616
509 6NI 0.8616
510 ESI 0.8615
511 XI7 0.8614
512 4AU 0.8613
513 NCV 0.8613
514 CS2 0.8612
515 9ZE 0.8612
516 ISC 0.8612
517 4FP 0.8611
518 DRG 0.8611
519 G6P 0.8610
520 HA5 0.8609
521 E3X 0.8605
522 TQL 0.8604
523 U5P 0.8604
524 QBS 0.8601
525 SLS 0.8601
526 PPY 0.8599
527 ABF 0.8597
528 B21 0.8597
529 97T 0.8597
530 2LY 0.8596
531 4NP 0.8594
532 2PK 0.8592
533 AX8 0.8588
534 M1Z 0.8588
535 AJD 0.8588
536 J9Q 0.8588
537 DX1 0.8587
538 8P3 0.8587
539 GNV 0.8586
540 GVY 0.8585
541 AV4 0.8585
542 HQJ 0.8585
543 JAW 0.8584
544 JMG 0.8584
545 ESP 0.8583
546 TMP 0.8583
547 IA2 0.8582
548 14N 0.8582
549 UMP 0.8582
550 3R4 0.8581
551 6X9 0.8581
552 5NI 0.8578
553 KYA 0.8578
554 GN6 0.8577
555 46M 0.8577
556 BIO 0.8577
557 3VS 0.8576
558 PIQ 0.8575
559 YZM 0.8574
560 K48 0.8573
561 68A 0.8572
562 DU 0.8572
563 8NB 0.8570
564 LJ3 0.8570
565 4VY 0.8569
566 2O6 0.8567
567 7O4 0.8566
568 JSX 0.8563
569 PLP 0.8562
570 6TZ 0.8561
571 092 0.8560
572 5O5 0.8559
573 XRS 0.8559
574 AKD 0.8558
575 A4V 0.8558
576 XYS XYS 0.8557
577 2JM 0.8556
578 L5V 0.8554
579 R2P 0.8554
580 B23 0.8554
581 7L4 0.8553
582 JB8 0.8553
583 NGO 0.8553
584 UNJ 0.8550
585 LAH 0.8550
586 B1J 0.8549
587 ALE 0.8547
588 5OO 0.8546
589 RK4 0.8544
590 DPN 0.8531
591 2HC 0.8530
592 MZM 0.8527
593 NGW 0.8527
594 3A9 0.8526
595 L03 0.8522
596 LNR 0.8517
597 EV3 0.8513
598 Z21 0.8512
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5FBF; Ligand: DCM; 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: 5fbf.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5FBF; Ligand: DCM; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 5fbf.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
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