Receptor
PDB id Resolution Class Description Source Keywords
4P77 2.04 Å EC: 4.1.99.12 STRUCTURE OF RIBB COMPLEXED WITH SUBSTRATE RU5P VIBRIO CHOLERAE SEROTYPE O1 RIBB RIBOFLVAIN LIGAND COMPLEX CRYSTAL RU5P LYASE
Ref.: STRUCTURAL BASIS FOR COMPETITIVE INHIBITION OF 3,4-DIHYDROXY-2-BUTANONE-4-PHOSPHATE SYNTHASE FROM CHOLERAE. J.BIOL.CHEM. V. 290 11293 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
5RP B:500;
A:301;
 Valid;
Valid;
 none;
none;
 submit data
230.11 C5 H11 O8 P C([C@...
GOL A:302;
 Invalid;
 none;
 submit data
92.094 C3 H8 O3 C(C(C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4P6C 1.86 Å EC: 4.1.99.12 STRUCTURE OF RIBB COMPLEXED WITH INHIBITOR 4PEH VIBRIO CHOLERAE SEROTYPE O1 RIBB DHBPS INHIBITOR RIBOFLAVIN COMPLEX 4PEH LYASE-LYAINHIBITOR COMPLEX
Ref.: STRUCTURAL BASIS FOR COMPETITIVE INHIBITION OF 3,4-DIHYDROXY-2-BUTANONE-4-PHOSPHATE SYNTHASE FROM CHOLERAE. J.BIOL.CHEM. V. 290 11293 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4P6P Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
2 4P6C Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
3 4P77 - 5RP C5 H11 O8 P C([C@H]([C....
4 4P8E - 5RP C5 H11 O8 P C([C@H]([C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4P6P Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
2 4P6C Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
3 4P77 - 5RP C5 H11 O8 P C([C@H]([C....
4 4P8E - 5RP C5 H11 O8 P C([C@H]([C....
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4P6P Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
2 4P6C Ki = 100 uM RES C4 H10 N O8 P C([C@H]([C....
3 4P77 - 5RP C5 H11 O8 P C([C@H]([C....
4 4P8E - 5RP C5 H11 O8 P C([C@H]([C....
5 2RIU - 5RP C5 H11 O8 P C([C@H]([C....
6 1TKU - 5RP C5 H11 O8 P C([C@H]([C....
7 1PVY - 5RP C5 H11 O8 P C([C@H]([C....
8 1SNN - 5RP C5 H11 O8 P C([C@H]([C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 5RP; Similar ligands found: 48
No: Ligand ECFP6 Tc MDL keys Tc
1 5SP 1 1
2 HMS 1 1
3 5RP 1 1
4 RUB 0.657895 0.944444
5 XBP 0.657895 0.944444
6 TG6 0.641026 0.972222
7 F6R 0.641026 0.972222
8 I22 0.609756 0.972222
9 DER 0.594595 0.891892
10 DEZ 0.594595 0.891892
11 DXP 0.578947 0.815789
12 RES 0.536585 0.673469
13 R10 0.512195 0.891892
14 PA5 0.512195 0.891892
15 P6F 0.5 0.944444
16 GOS 0.5 0.916667
17 P6T 0.5 0.944444
18 M2P 0.5 0.916667
19 2FP 0.5 0.944444
20 LG6 0.488372 0.891892
21 6PG 0.488372 0.891892
22 HG3 0.485714 0.783784
23 PAN 0.466667 0.673469
24 9C2 0.456522 0.66
25 4TP 0.452381 0.75
26 A5P 0.45 0.944444
27 LX1 0.45 0.815789
28 DX5 0.45 0.944444
29 LXP 0.45 0.944444
30 RBL 0.444444 0.638889
31 QDK 0.444444 0.638889
32 XUL 0.444444 0.638889
33 S6P 0.439024 0.916667
34 KD0 0.425532 0.891892
35 E4P 0.425 0.861111
36 5FX 0.421053 0.605263
37 DG6 0.418605 0.918919
38 R52 0.418605 0.916667
39 TX4 0.418605 0.632653
40 R5P 0.418605 0.916667
41 3PG 0.410256 0.837838
42 H4P 0.408163 0.772727
43 52L 0.408163 0.723404
44 DG2 0.404762 0.810811
45 O1B 0.403846 0.686275
46 G6Q 0.4 0.916667
47 M6R 0.4 0.75
48 AGP 0.4 0.75
Similar Ligands (3D)
Ligand no: 1; Ligand: 5RP; Similar ligands found: 585
No: Ligand Similarity coefficient
1 1AE 0.9460
2 2JJ 0.9251
3 HSX 0.9231
4 9GB 0.9224
5 D5X 0.9217
6 1X4 0.9198
7 P9E 0.9187
8 HSA 0.9174
9 HC4 0.9172
10 4NP 0.9165
11 0CG 0.9156
12 AZM 0.9153
13 YI6 0.9147
14 P23 0.9132
15 SKF 0.9124
16 4NS 0.9113
17 EGV 0.9110
18 3W8 0.9096
19 F98 0.9089
20 PMV 0.9085
21 MP5 0.9068
22 S0W 0.9065
23 K4V 0.9063
24 PLP 0.9062
25 4XF 0.9058
26 MVH 0.9055
27 P81 0.9053
28 TU0 0.9052
29 JFM 0.9050
30 2O8 0.9044
31 ABF 0.9043
32 GCO 0.9040
33 E8U 0.9036
34 AT3 0.9035
35 5GT 0.9032
36 88L 0.9030
37 4MB 0.9030
38 SG3 0.9026
39 1OS 0.9026
40 58X 0.9022
41 Y3L 0.9017
42 GGG 0.9014
43 RP3 0.9012
44 ZEC 0.9012
45 PTB 0.9010
46 5WN 0.9010
47 STT 0.9008
48 BCH 0.9007
49 TZP 0.9004
50 IS2 0.9002
51 MRU 0.9001
52 MSL 0.9001
53 363 0.8999
54 PLR 0.8995
55 EUE 0.8994
56 2OR 0.8994
57 PNP 0.8990
58 LFC 0.8982
59 9VQ 0.8980
60 UA5 0.8979
61 GRF 0.8974
62 FUD 0.8966
63 1PS 0.8965
64 2FX 0.8962
65 BL0 0.8961
66 TYR 0.8957
67 6C5 0.8956
68 MF3 0.8955
69 B41 0.8952
70 KYN 0.8951
71 EYV 0.8950
72 5LD 0.8947
73 AES 0.8947
74 TRP 0.8945
75 SNO 0.8944
76 P80 0.8939
77 MZM 0.8939
78 657 0.8937
79 7UC 0.8937
80 0F3 0.8937
81 6KT 0.8937
82 RNO 0.8937
83 DMA 0.8936
84 6C9 0.8935
85 LSQ 0.8933
86 EUH 0.8932
87 3VX 0.8932
88 DZA 0.8929
89 LUQ 0.8929
90 GLO 0.8927
91 GB5 0.8927
92 PPK 0.8926
93 DHC 0.8923
94 EVF 0.8919
95 OGA 0.8918
96 1FD 0.8917
97 JA5 0.8917
98 KPA 0.8916
99 RP5 0.8916
100 Q9Z 0.8915
101 LO1 0.8912
102 QIV 0.8912
103 TA6 0.8910
104 N91 0.8910
105 428 0.8909
106 D6P 0.8908
107 6FG 0.8902
108 FOM 0.8900
109 N4E 0.8900
110 A6P 0.8898
111 5OY 0.8896
112 5TO 0.8894
113 BGT 0.8892
114 0CM 0.8891
115 SOR 0.8888
116 8NB 0.8888
117 MAJ 0.8887
118 FER 0.8887
119 PSJ 0.8887
120 JCZ 0.8886
121 HPP 0.8884
122 5OO 0.8884
123 7MW 0.8881
124 RYV 0.8878
125 KLS 0.8878
126 2O6 0.8877
127 0FA 0.8876
128 80G 0.8875
129 IOP 0.8874
130 3VS 0.8872
131 DHM 0.8872
132 C82 0.8872
133 LGT 0.8871
134 XCG 0.8871
135 EPE 0.8869
136 GJK 0.8868
137 LLH 0.8867
138 ALE 0.8863
139 PJL 0.8860
140 BG6 0.8855
141 G6P 0.8855
142 Q03 0.8854
143 SSC 0.8853
144 AM4 0.8852
145 YIP 0.8851
146 4NZ 0.8850
147 492 0.8849
148 Q04 0.8849
149 CFA 0.8847
150 DAH 0.8846
151 STX 0.8846
152 4JE 0.8846
153 DTY 0.8845
154 PPT 0.8842
155 4I8 0.8841
156 N2M 0.8840
157 GRQ 0.8839
158 SYC 0.8839
159 D3G 0.8839
160 4AU 0.8837
161 6C4 0.8836
162 3W3 0.8836
163 3W6 0.8836
164 HPS 0.8836
165 4Z9 0.8835
166 ATX 0.8833
167 9BF 0.8833
168 RA7 0.8832
169 7O4 0.8831
170 F02 0.8830
171 A5Q 0.8830
172 S0E 0.8829
173 NAG 0.8829
174 EQW 0.8828
175 TMG 0.8828
176 EZL 0.8828
177 11C 0.8828
178 D9Z 0.8827
179 6C8 0.8826
180 IPE 0.8824
181 GLR 0.8824
182 36M 0.8824
183 0UL 0.8824
184 CS2 0.8822
185 EYJ 0.8821
186 M1T 0.8821
187 78Y 0.8821
188 4AF 0.8819
189 JBZ 0.8819
190 PMP 0.8817
191 0NX 0.8816
192 CLT 0.8815
193 1HS 0.8815
194 8NX 0.8812
195 13P 0.8810
196 PHE 0.8810
197 ZZU 0.8809
198 GWM 0.8809
199 4CM 0.8808
200 IAC 0.8806
201 GLY GLY GLY 0.8805
202 SOL 0.8805
203 OOG 0.8805
204 I2E 0.8803
205 DA3 0.8802
206 PPN 0.8800
207 Q06 0.8800
208 O45 0.8799
209 G14 0.8798
210 GB4 0.8797
211 BP7 0.8797
212 9J6 0.8796
213 HCA 0.8796
214 9NB 0.8795
215 HXY 0.8793
216 4CF 0.8793
217 4BL 0.8791
218 A7H 0.8790
219 API 0.8790
220 XDK 0.8790
221 SEP 0.8790
222 M28 0.8790
223 VD9 0.8789
224 AKG 0.8788
225 PPY 0.8788
226 KPC 0.8788
227 YIE 0.8787
228 L22 0.8787
229 KDG 0.8786
230 YF3 0.8786
231 IYR 0.8786
232 GO2 0.8786
233 PC 0.8785
234 S24 0.8785
235 1FE 0.8784
236 GAE 0.8784
237 FLC 0.8784
238 AJG 0.8784
239 CIT 0.8782
240 3S5 0.8779
241 K97 0.8779
242 5WZ 0.8778
243 AHL 0.8777
244 VM1 0.8777
245 14W 0.8777
246 VFG 0.8777
247 M6P 0.8775
248 3PO 0.8775
249 MTL 0.8774
250 B85 0.8774
251 EE8 0.8774
252 8SZ 0.8773
253 P93 0.8773
254 N7I 0.8773
255 3ZB 0.8772
256 X1R 0.8770
257 54Z 0.8770
258 R20 0.8770
259 4BY 0.8770
260 LVD 0.8770
261 2GQ 0.8768
262 M3L 0.8768
263 X48 0.8767
264 CIY 0.8766
265 4BX 0.8766
266 8V8 0.8765
267 S7G 0.8764
268 AHN 0.8758
269 SYE 0.8757
270 0W1 0.8757
271 2BX 0.8755
272 VC3 0.8755
273 64Z 0.8754
274 F90 0.8754
275 PHI 0.8754
276 F6P 0.8753
277 3EB 0.8753
278 RCV 0.8751
279 XI7 0.8750
280 ZZA 0.8750
281 92G 0.8750
282 LTN 0.8749
283 ZYX 0.8749
284 HNE 0.8749
285 AOS 0.8748
286 K3D 0.8747
287 3IL 0.8746
288 6Q3 0.8745
289 0A1 0.8745
290 IJ6 0.8745
291 ENO 0.8745
292 NFM 0.8744
293 SG2 0.8744
294 NLG 0.8744
295 DED 0.8743
296 IOS 0.8742
297 1KH 0.8742
298 BZJ 0.8742
299 F4K 0.8742
300 UN1 0.8741
301 4OG 0.8741
302 HJ7 0.8741
303 5B2 0.8738
304 3VQ 0.8737
305 PRO GLY 0.8737
306 NK5 0.8735
307 XOG 0.8734
308 MES 0.8734
309 MD6 0.8734
310 6FB 0.8734
311 2QC 0.8733
312 FF2 0.8731
313 RGP 0.8731
314 EWG 0.8730
315 BSA 0.8729
316 A7Q 0.8728
317 DLT 0.8727
318 5TZ 0.8727
319 ARG 0.8727
320 PO6 0.8725
321 8VE 0.8724
322 7N8 0.8724
323 9ZE 0.8723
324 P7Y 0.8722
325 R1P 0.8721
326 NCD 0.8721
327 1BN 0.8720
328 4FP 0.8719
329 JAH 0.8718
330 AHC 0.8718
331 BGP 0.8718
332 8CC 0.8717
333 N1E 0.8717
334 3VR 0.8716
335 4HP 0.8714
336 TYC 0.8714
337 ZON 0.8713
338 KTW 0.8713
339 YPN 0.8712
340 4BF 0.8711
341 AAN 0.8711
342 EF0 0.8710
343 FBF 0.8710
344 SOJ 0.8710
345 S7S 0.8709
346 HPO 0.8709
347 JP2 0.8709
348 12T 0.8708
349 36E 0.8707
350 QH3 0.8706
351 8WQ 0.8706
352 833 0.8705
353 5FL 0.8705
354 GGB 0.8704
355 795 0.8703
356 J4K 0.8702
357 A5H 0.8700
358 5F8 0.8700
359 S7D 0.8699
360 KMY 0.8699
361 SKM 0.8699
362 SSY 0.8696
363 5UK 0.8695
364 EFF 0.8694
365 PBA 0.8694
366 K82 0.8693
367 M5H 0.8693
368 D6G 0.8691
369 LAO 0.8691
370 E79 0.8691
371 Z13 0.8690
372 TZM 0.8690
373 5F5 0.8690
374 M6H 0.8690
375 ICT 0.8690
376 GLP 0.8690
377 SWX 0.8685
378 GG8 0.8685
379 RD4 0.8685
380 4FF 0.8685
381 ET0 0.8684
382 ENW 0.8684
383 4TB 0.8683
384 3LJ 0.8683
385 TYE 0.8682
386 PXP 0.8682
387 QMP 0.8681
388 FZM 0.8681
389 HNT 0.8679
390 JZA 0.8678
391 ASF 0.8678
392 5O6 0.8678
393 LZ5 0.8677
394 TYL 0.8676
395 DDU 0.8676
396 2FM 0.8676
397 KLV 0.8675
398 DHY 0.8675
399 GZ2 0.8674
400 AMR 0.8674
401 JB8 0.8674
402 WV7 0.8674
403 MJ5 0.8673
404 0LO 0.8673
405 ZHA 0.8672
406 FTV 0.8670
407 DGL 0.8670
408 OHJ 0.8670
409 AZY 0.8669
410 C53 0.8666
411 FOC 0.8666
412 IVL 0.8666
413 E7S 0.8665
414 2D2 0.8665
415 3R4 0.8664
416 2J3 0.8664
417 KAP 0.8664
418 TCA 0.8664
419 HIC 0.8663
420 P4F 0.8663
421 5XB 0.8662
422 1L5 0.8661
423 PLP PMP 0.8661
424 6FR 0.8661
425 FPL 0.8660
426 LJ3 0.8660
427 PSV 0.8660
428 IBP 0.8658
429 QUS 0.8657
430 EXD 0.8656
431 BQ2 0.8656
432 KLE 0.8656
433 G1P 0.8654
434 A7N 0.8653
435 NFZ 0.8652
436 YZM 0.8652
437 27K 0.8650
438 LL1 0.8649
439 86L 0.8648
440 HJH 0.8648
441 F1X 0.8647
442 C26 0.8647
443 HLP 0.8646
444 344 0.8645
445 J6W 0.8645
446 NMH 0.8645
447 2NP 0.8644
448 UNJ 0.8644
449 EZ1 0.8644
450 5E5 0.8644
451 S7V 0.8643
452 ENV 0.8642
453 PFF 0.8641
454 S0F 0.8640
455 DVQ 0.8640
456 0L1 0.8640
457 TCR 0.8639
458 7R4 0.8639
459 6TZ 0.8638
460 6FZ 0.8637
461 4FE 0.8636
462 QME 0.8635
463 CH8 0.8635
464 GP9 0.8633
465 HQJ 0.8632
466 TEG 0.8632
467 JPQ 0.8631
468 AVA 0.8631
469 AEG 0.8630
470 PMF 0.8629
471 GHQ 0.8629
472 AJ1 0.8629
473 4V2 0.8628
474 G3P 0.8626
475 S7A 0.8626
476 RVE 0.8626
477 4LV 0.8625
478 YE7 0.8623
479 IP8 0.8623
480 EYY 0.8621
481 9W5 0.8621
482 CUW 0.8621
483 KWB 0.8621
484 6J5 0.8620
485 FCW 0.8620
486 CSN 0.8620
487 4LW 0.8620
488 PML 0.8619
489 CXH 0.8618
490 IWT 0.8618
491 8D6 0.8617
492 56D 0.8616
493 QMS 0.8616
494 GGL 0.8615
495 6MW 0.8615
496 YTX 0.8615
497 1A7 0.8613
498 CTE 0.8612
499 P58 0.8610
500 PH3 0.8610
501 1QV 0.8609
502 X0U 0.8608
503 HCT 0.8608
504 9FH 0.8607
505 HWD 0.8606
506 D1Y 0.8605
507 GVA 0.8605
508 S0A 0.8605
509 GLU 0.8605
510 MMS 0.8604
511 FCD 0.8603
512 ENG 0.8603
513 NPI 0.8603
514 4JC 0.8602
515 M3C 0.8600
516 HX8 0.8600
517 HBO 0.8599
518 HIS 0.8598
519 M72 0.8598
520 60L 0.8596
521 HA5 0.8596
522 2UZ 0.8594
523 F40 0.8594
524 5DS 0.8593
525 5TT 0.8593
526 9F8 0.8592
527 0JD 0.8592
528 EV2 0.8591
529 15N 0.8591
530 5H6 0.8591
531 NLQ 0.8591
532 LEL 0.8590
533 BGU 0.8590
534 F63 0.8589
535 YE6 0.8588
536 9UL 0.8588
537 7QD 0.8588
538 PAL 0.8588
539 BPY 0.8587
540 MXD 0.8586
541 8GL 0.8585
542 8EU 0.8584
543 FYR 0.8583
544 RYY 0.8580
545 549 0.8580
546 M4S 0.8580
547 3YP 0.8579
548 2IT 0.8576
549 LR5 0.8576
550 SZ7 0.8575
551 LR8 0.8574
552 6ZW 0.8574
553 L14 0.8573
554 RQD 0.8572
555 V2Z 0.8571
556 HJD 0.8570
557 JDN 0.8570
558 P4L 0.8570
559 DST 0.8569
560 2HC 0.8567
561 GDL 0.8566
562 EQA 0.8565
563 GNW 0.8564
564 PGH 0.8562
565 D1G 0.8561
566 72D 0.8561
567 R2P 0.8560
568 G88 0.8560
569 BVA 0.8558
570 P22 0.8557
571 MKN 0.8557
572 BPW 0.8554
573 6DQ 0.8544
574 22F 0.8543
575 GL1 0.8542
576 OA1 0.8538
577 R9J 0.8537
578 ST3 0.8534
579 U7E 0.8526
580 5C1 0.8526
581 L03 0.8524
582 3VW 0.8519
583 XIZ 0.8515
584 A3M 0.8511
585 7L4 0.8506
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4P6C; Ligand: RES; 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: 4p6c.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4P6C; Ligand: RES; 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: 4p6c.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
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