Receptor
PDB id Resolution Class Description Source Keywords
2YAJ 1.81 Å EC: 4.1.1.83 CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME WITH BOUND SUBSTR CLOSTRIDIUM SCATOLOGENES LYASE RADICAL CHEMISTRY METALLOENZYME IRON-SULFUR CENTER
Ref.: STRUCTURAL BASIS FOR A KOLBE-TYPE DECARBOXYLATION C BY A GLYCYL RADICAL ENZYME. J.AM.CHEM.SOC. V. 133 14666 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4HP A:1898;
C:1898;
Valid;
Valid;
none;
none;
submit data
152.147 C8 H8 O3 c1cc(...
SF4 B:87;
B:88;
D:87;
D:88;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
351.64 Fe4 S4 [S]12...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2YAJ 1.81 Å EC: 4.1.1.83 CRYSTAL STRUCTURE OF GLYCYL RADICAL ENZYME WITH BOUND SUBSTR CLOSTRIDIUM SCATOLOGENES LYASE RADICAL CHEMISTRY METALLOENZYME IRON-SULFUR CENTER
Ref.: STRUCTURAL BASIS FOR A KOLBE-TYPE DECARBOXYLATION C BY A GLYCYL RADICAL ENZYME. J.AM.CHEM.SOC. V. 133 14666 2011
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YAJ - 4HP C8 H8 O3 c1cc(ccc1C....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YAJ - 4HP C8 H8 O3 c1cc(ccc1C....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2YAJ - 4HP C8 H8 O3 c1cc(ccc1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 4HP; Similar ligands found: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 4HP 1 1
2 ENO 0.625 0.782609
3 HPP 0.545455 0.904762
4 PAC 0.5 0.684211
5 YI6 0.473684 0.75
6 34H 0.459459 0.826087
7 TYR 0.447368 0.642857
8 DTY 0.447368 0.642857
9 DHY 0.432432 0.76
10 IO2 0.422222 0.75
11 3HP 0.421053 0.95
12 3C4 0.410256 0.76
13 PHB 0.40625 0.842105
Similar Ligands (3D)
Ligand no: 1; Ligand: 4HP; Similar ligands found: 751
No: Ligand Similarity coefficient
1 AEG 0.9913
2 TYL 0.9771
3 PO6 0.9729
4 YRL 0.9717
5 4FA 0.9708
6 HHH 0.9689
7 AEF 0.9681
8 RBJ 0.9660
9 TYE 0.9649
10 S24 0.9640
11 YPN 0.9623
12 GWM 0.9614
13 BPW 0.9611
14 QY9 0.9589
15 J0Z 0.9578
16 K7M 0.9569
17 Q9Z 0.9566
18 DHR 0.9556
19 AKG 0.9545
20 I4B 0.9542
21 OTR 0.9539
22 FK8 0.9538
23 HDH 0.9527
24 CXP 0.9522
25 HCI 0.9515
26 M4T 0.9512
27 NFM 0.9508
28 R9S 0.9479
29 BNF 0.9463
30 268 0.9459
31 ICB 0.9458
32 LDP 0.9456
33 HC4 0.9451
34 2BX 0.9434
35 6FZ 0.9431
36 8OZ 0.9428
37 3QM 0.9426
38 PMF 0.9422
39 OGA 0.9421
40 DGL 0.9411
41 URS 0.9408
42 PHE 0.9406
43 4VY 0.9404
44 173 0.9390
45 OHP 0.9390
46 QBM 0.9389
47 S8V 0.9387
48 NYL 0.9387
49 88L 0.9379
50 GLU 0.9379
51 SMN 0.9374
52 M3H 0.9374
53 42J 0.9368
54 258 0.9364
55 1FD 0.9363
56 UA5 0.9363
57 9RW 0.9360
58 TSU 0.9359
59 AHC 0.9359
60 OOG 0.9349
61 HY1 0.9348
62 PPT 0.9345
63 PRA 0.9344
64 M6H 0.9341
65 B85 0.9337
66 SYC 0.9336
67 PBA 0.9325
68 GRO 0.9324
69 I1E 0.9323
70 GJZ 0.9322
71 N4B 0.9322
72 PEL 0.9318
73 LNR 0.9317
74 B40 0.9316
75 S0W 0.9310
76 SAN 0.9310
77 FEH 0.9306
78 1BN 0.9302
79 2IT 0.9298
80 GGL 0.9298
81 4NC 0.9298
82 8U3 0.9297
83 AHN 0.9295
84 DGN 0.9293
85 PPY 0.9293
86 HPS 0.9289
87 GLN 0.9284
88 BHO 0.9278
89 GZQ 0.9277
90 2FY 0.9276
91 ISZ 0.9274
92 AAN 0.9273
93 HL4 0.9272
94 4SX 0.9271
95 NIZ 0.9270
96 IZC 0.9269
97 SSB 0.9268
98 AMH 0.9267
99 TPA 0.9265
100 MSR 0.9263
101 C1M 0.9263
102 CXF 0.9263
103 2UB 0.9263
104 RMN 0.9261
105 PEA 0.9260
106 B41 0.9259
107 TYC 0.9258
108 S2G 0.9256
109 HNK 0.9256
110 HNL 0.9254
111 PFF 0.9253
112 CPZ 0.9253
113 MES 0.9252
114 YIE 0.9248
115 271 0.9246
116 LT1 0.9244
117 QMP 0.9242
118 7BC 0.9232
119 86L 0.9231
120 XIZ 0.9226
121 264 0.9225
122 1DJ 0.9223
123 HF2 0.9220
124 L99 0.9219
125 EYV 0.9216
126 AC6 0.9216
127 4JC 0.9216
128 E4P 0.9215
129 F06 0.9214
130 HXY 0.9213
131 11C 0.9212
132 2LP 0.9211
133 PAB 0.9211
134 CFA 0.9209
135 4BF 0.9208
136 FBM 0.9206
137 JZ7 0.9205
138 JZ4 0.9205
139 MTL 0.9203
140 FCR 0.9200
141 PH3 0.9200
142 KMH 0.9200
143 4PN 0.9199
144 2HG 0.9198
145 PZI 0.9194
146 92K 0.9191
147 LSQ 0.9191
148 NVU 0.9188
149 PBN 0.9187
150 C2B 0.9186
151 3LR 0.9185
152 MP5 0.9183
153 BSX 0.9179
154 KDG 0.9178
155 MXN 0.9178
156 MUC 0.9175
157 5XB 0.9174
158 FBS 0.9174
159 RSO 0.9174
160 4J8 0.9173
161 23J 0.9171
162 9J3 0.9170
163 OHJ 0.9168
164 PHU 0.9168
165 MQB 0.9165
166 49F 0.9164
167 MNN 0.9164
168 DIR 0.9159
169 Q03 0.9159
170 NAG 0.9158
171 RNS 0.9154
172 SSC 0.9153
173 RAT 0.9152
174 7C3 0.9150
175 HBA 0.9150
176 2CL 0.9149
177 PBZ 0.9148
178 NPO 0.9147
179 KTA 0.9145
180 AMS 0.9145
181 MS9 0.9144
182 4JL 0.9143
183 DHS 0.9142
184 I3E 0.9142
185 SEP 0.9142
186 CEE 0.9141
187 PRY 0.9140
188 FA1 0.9137
189 T9G 0.9137
190 CFI 0.9135
191 F90 0.9130
192 IAC 0.9130
193 BHU 0.9125
194 YTX 0.9125
195 FBA 0.9125
196 7WG 0.9124
197 5WZ 0.9123
198 ODO 0.9123
199 DJN 0.9120
200 1SA 0.9117
201 263 0.9117
202 AAS 0.9114
203 RNO 0.9114
204 P72 0.9114
205 A29 0.9113
206 HMS 0.9113
207 HIS 0.9112
208 PHI 0.9111
209 SAF 0.9110
210 3BU 0.9110
211 SYM 0.9107
212 F9P 0.9103
213 DAL DAL 0.9102
214 BCU 0.9100
215 SOR 0.9100
216 HG3 0.9099
217 CS2 0.9098
218 IXW 0.9098
219 3PG 0.9098
220 N9J 0.9097
221 BNL 0.9094
222 HIC 0.9092
223 RLG 0.9092
224 61M 0.9092
225 0A1 0.9090
226 DHI 0.9088
227 B3U 0.9087
228 AOT 0.9086
229 TIH 0.9084
230 0JD 0.9081
231 LYS 0.9081
232 NFA 0.9077
233 1LN 0.9077
234 DZA 0.9077
235 DPN 0.9076
236 O45 0.9075
237 APG 0.9074
238 4XV 0.9073
239 TSS 0.9073
240 P58 0.9072
241 36Y 0.9072
242 FHC 0.9070
243 4VP 0.9069
244 4XS 0.9069
245 RNT 0.9067
246 HFA 0.9066
247 SNU 0.9064
248 57O 0.9064
249 ALE 0.9064
250 NOK 0.9062
251 2FT 0.9061
252 15N 0.9060
253 DEW 0.9059
254 X0V 0.9058
255 XX2 0.9057
256 ISA 0.9055
257 BL0 0.9054
258 PZM 0.9051
259 FUD 0.9051
260 SNO 0.9050
261 SDF 0.9050
262 4MA 0.9049
263 HNH 0.9048
264 A5E 0.9047
265 SPA 0.9047
266 9SE 0.9047
267 269 0.9045
268 3YP 0.9042
269 YOF 0.9041
270 F4E 0.9041
271 0L1 0.9039
272 S2P 0.9038
273 1X4 0.9036
274 XYL 0.9033
275 RB5 0.9033
276 97T 0.9033
277 717 0.9032
278 3HG 0.9031
279 LFC 0.9031
280 41K 0.9030
281 EPR 0.9030
282 HSO 0.9029
283 GLO 0.9029
284 BPN 0.9028
285 TSR 0.9027
286 54Z 0.9026
287 AES 0.9024
288 0LH 0.9023
289 PPN 0.9021
290 APS 0.9020
291 36M 0.9020
292 2AL 0.9020
293 J9N 0.9020
294 GLL 0.9019
295 NCT 0.9019
296 1Y6 0.9017
297 2C2 0.9015
298 2HC 0.9014
299 C82 0.9014
300 HWD 0.9013
301 HBD 0.9012
302 9R5 0.9012
303 DAH 0.9010
304 Z82 0.9008
305 R9J 0.9007
306 PIM 0.9006
307 PIY 0.9006
308 LYL 0.9006
309 4NP 0.9004
310 KP6 0.9002
311 M4S 0.9002
312 449 0.9002
313 BRH 0.9002
314 LVD 0.9000
315 B09 0.9000
316 7A8 0.8999
317 DS0 0.8999
318 HYA 0.8995
319 A3M 0.8994
320 FP1 0.8992
321 NLE 0.8991
322 IYR 0.8991
323 ARP 0.8990
324 ASC 0.8989
325 KOJ 0.8989
326 M5E 0.8987
327 MEQ 0.8987
328 XIY 0.8987
329 INO 0.8986
330 TZM 0.8985
331 1L5 0.8985
332 HQ9 0.8984
333 OMD 0.8984
334 EHM 0.8984
335 52C 0.8984
336 URP 0.8983
337 YF3 0.8983
338 MED 0.8981
339 261 0.8981
340 DHC 0.8981
341 ZBT 0.8980
342 TZL 0.8980
343 R9M 0.8980
344 HHT 0.8979
345 E5X 0.8978
346 ORN 0.8977
347 EKZ 0.8977
348 MET 0.8976
349 4P5 0.8975
350 J9Q 0.8974
351 4NS 0.8972
352 BHH 0.8971
353 SBK 0.8971
354 XUL 0.8970
355 GLY GLY 0.8970
356 9VQ 0.8968
357 2QC 0.8964
358 069 0.8964
359 2CO 0.8963
360 HJH 0.8962
361 ZON 0.8962
362 FB2 0.8962
363 ST3 0.8961
364 P81 0.8961
365 CLU 0.8960
366 F4K 0.8960
367 TZE 0.8958
368 SOL 0.8956
369 MLT 0.8956
370 PEP 0.8955
371 QH3 0.8955
372 2BG 0.8953
373 IFP 0.8951
374 4NM 0.8951
375 CXH 0.8950
376 QUS 0.8950
377 YZM 0.8948
378 N2Z 0.8943
379 ANN 0.8943
380 FBV 0.8941
381 PNZ 0.8941
382 HMH 0.8937
383 F52 0.8936
384 4FH 0.8936
385 HSM 0.8936
386 PGH 0.8931
387 FBJ 0.8931
388 URO 0.8931
389 M74 0.8929
390 0HO 0.8929
391 SN4 0.8926
392 5FX 0.8925
393 IOM 0.8924
394 AL0 0.8922
395 MMS 0.8921
396 KMT 0.8921
397 A09 0.8919
398 BP9 0.8917
399 IOS 0.8915
400 S7A 0.8914
401 826 0.8913
402 MR1 0.8912
403 PMB 0.8912
404 13P 0.8911
405 9BF 0.8908
406 HHI 0.8906
407 IP8 0.8905
408 OEG 0.8905
409 TAG 0.8904
410 36E 0.8903
411 24B 0.8902
412 DOB 0.8899
413 4TB 0.8898
414 8WO 0.8898
415 GUA 0.8896
416 DHB 0.8895
417 6NT 0.8894
418 FA3 0.8894
419 HNM 0.8894
420 XXG 0.8892
421 SHI 0.8891
422 174 0.8891
423 OAA 0.8889
424 L5V 0.8885
425 PCS 0.8884
426 LX1 0.8884
427 M45 0.8883
428 GVM 0.8878
429 MPV 0.8878
430 XM0 0.8877
431 SW7 0.8877
432 AEH 0.8877
433 PNP 0.8874
434 FOC 0.8873
435 0HN 0.8872
436 GVG 0.8872
437 GOJ 0.8871
438 7QS 0.8871
439 TZF 0.8871
440 4WL 0.8870
441 2O8 0.8869
442 56D 0.8869
443 33S 0.8868
444 GCO 0.8864
445 JF6 0.8864
446 2HO 0.8864
447 JRB 0.8863
448 UFV 0.8860
449 E0O 0.8859
450 EOL 0.8859
451 PEQ 0.8858
452 G3H 0.8854
453 Z13 0.8854
454 9RH 0.8854
455 Y4L 0.8854
456 ABF 0.8853
457 IOP 0.8852
458 2ZM 0.8852
459 XQI 0.8851
460 HSX 0.8850
461 MNP 0.8848
462 6ZX 0.8848
463 1F1 0.8847
464 3A9 0.8847
465 7N0 0.8846
466 NNO 0.8846
467 H7Y 0.8846
468 1WC 0.8843
469 QIC 0.8843
470 P9P 0.8842
471 TLA 0.8842
472 ISD 0.8842
473 51F 0.8841
474 TCA 0.8841
475 PBC 0.8840
476 152 0.8840
477 MJ5 0.8840
478 NF3 0.8840
479 H8N 0.8839
480 SYG 0.8839
481 J9T 0.8838
482 CH8 0.8838
483 4BZ 0.8838
484 IPB 0.8838
485 FF3 0.8838
486 ABI 0.8837
487 M58 0.8837
488 1M2 0.8836
489 HX8 0.8835
490 GZ3 0.8834
491 92G 0.8834
492 HMU 0.8833
493 0QW 0.8833
494 NSP 0.8831
495 GP9 0.8831
496 SRT 0.8829
497 6NI 0.8829
498 NDG 0.8828
499 129 0.8828
500 GZL 0.8827
501 DDU 0.8827
502 SG3 0.8825
503 MAJ 0.8824
504 TH7 0.8824
505 2A9 0.8824
506 BZ2 0.8822
507 DVQ 0.8820
508 BEZ 0.8820
509 3QO 0.8819
510 XLS 0.8819
511 MYJ 0.8818
512 COI 0.8818
513 K34 0.8816
514 8XL 0.8815
515 JDN 0.8814
516 FAN 0.8813
517 93K 0.8813
518 JAW 0.8811
519 4ZA 0.8810
520 IHB 0.8810
521 BEN 0.8810
522 SQV 0.8808
523 3NY 0.8804
524 50C 0.8803
525 EYJ 0.8803
526 PCA 0.8802
527 PRZ 0.8800
528 0V5 0.8799
529 QSB 0.8796
530 4FP 0.8796
531 MAH 0.8795
532 FPL 0.8795
533 KBZ 0.8794
534 CLT 0.8793
535 FHB 0.8792
536 SS1 0.8791
537 80G 0.8789
538 HQJ 0.8786
539 9TW 0.8786
540 259 0.8784
541 DE5 0.8783
542 4A3 0.8783
543 CCD 0.8781
544 8K2 0.8780
545 CHB 0.8779
546 TAR 0.8779
547 LNO 0.8779
548 2PG 0.8778
549 JB8 0.8778
550 2K8 0.8777
551 LTT 0.8777
552 BAM 0.8775
553 FB1 0.8773
554 1DV 0.8772
555 ASP 0.8770
556 6PC 0.8770
557 YCP 0.8770
558 K5W 0.8768
559 ZZT 0.8768
560 NCA 0.8767
561 AX3 0.8767
562 ZXD 0.8766
563 J4K 0.8764
564 TRP 0.8760
565 DHK 0.8759
566 3S5 0.8758
567 505 0.8758
568 FA0 0.8758
569 4SD 0.8756
570 535 0.8755
571 7VP 0.8753
572 3HM 0.8753
573 NGA 0.8752
574 FBW 0.8751
575 PF1 0.8751
576 RHU 0.8749
577 4YO 0.8749
578 1P8 0.8749
579 DC5 0.8747
580 RP5 0.8746
581 X1P 0.8746
582 GLR 0.8746
583 PPR 0.8744
584 9KH 0.8741
585 JLZ 0.8740
586 7Q1 0.8740
587 AG2 0.8739
588 CRN 0.8738
589 1SV 0.8738
590 3V4 0.8738
591 A2G 0.8737
592 5CU 0.8737
593 L13 0.8736
594 AMQ 0.8733
595 BHA 0.8732
596 3PF 0.8729
597 OCA 0.8728
598 G3P 0.8728
599 RQD 0.8728
600 SNE 0.8726
601 GLC 0.8723
602 657 0.8723
603 FOM 0.8722
604 5NI 0.8722
605 SIN 0.8722
606 AT3 0.8721
607 DXG 0.8720
608 4M0 0.8719
609 3CR 0.8717
610 5RP 0.8714
611 BNS 0.8714
612 DQA 0.8712
613 ORO 0.8712
614 EV0 0.8712
615 4LR 0.8710
616 QSC 0.8709
617 SPV 0.8709
618 SKM 0.8708
619 RM1 0.8708
620 BWD 0.8708
621 EDR 0.8706
622 MRZ 0.8706
623 NGT 0.8705
624 NGW 0.8705
625 C5A 0.8704
626 NIO 0.8703
627 9X7 0.8701
628 IWD 0.8701
629 3SL 0.8700
630 TIU 0.8700
631 5OB 0.8699
632 5OO 0.8699
633 92P 0.8699
634 CWD 0.8699
635 HA7 0.8697
636 PYU 0.8697
637 FWD 0.8697
638 5XC 0.8696
639 LMR 0.8695
640 R20 0.8694
641 PC 0.8693
642 MZW 0.8689
643 L14 0.8688
644 AS3 0.8687
645 SYN 0.8687
646 5NU 0.8687
647 UNU 0.8683
648 4JT 0.8681
649 NOJ 0.8681
650 5XA 0.8680
651 ABN 0.8680
652 40F 0.8678
653 6HO 0.8677
654 G4D 0.8677
655 3DM 0.8674
656 BPY 0.8673
657 NPA 0.8672
658 1AB 0.8671
659 PYJ 0.8671
660 SR1 0.8669
661 428 0.8669
662 DGJ 0.8668
663 GT4 0.8668
664 ASO 0.8665
665 SVD 0.8659
666 BZ3 0.8659
667 FBF 0.8659
668 SS2 0.8656
669 15E 0.8655
670 R2B 0.8654
671 9CL 0.8654
672 FBB 0.8652
673 9ZE 0.8652
674 2AS 0.8650
675 TL6 0.8649
676 3OC 0.8648
677 0OC 0.8647
678 OQC 0.8647
679 M6W 0.8645
680 DCZ 0.8644
681 OVM 0.8643
682 PZA 0.8643
683 B24 0.8641
684 GF4 0.8640
685 5LA 0.8640
686 DER 0.8639
687 4AA 0.8638
688 2HU 0.8638
689 ADA 0.8636
690 GDE 0.8632
691 NTN 0.8632
692 K2T 0.8630
693 15L 0.8630
694 1P3 0.8629
695 DOR 0.8629
696 GXY 0.8629
697 SYE 0.8628
698 SQ7 0.8627
699 GBN 0.8627
700 XEN 0.8627
701 XCZ 0.8626
702 CWJ 0.8626
703 MEV 0.8625
704 GAB 0.8622
705 CN0 0.8622
706 APY 0.8622
707 FYU 0.8618
708 IF7 0.8614
709 J6W 0.8611
710 BDP 0.8610
711 NMM 0.8610
712 7MK 0.8609
713 SOJ 0.8606
714 FQI 0.8606
715 12T 0.8606
716 51R 0.8605
717 DFB 0.8604
718 HYP 0.8603
719 4CS 0.8601
720 ESX 0.8596
721 ES2 0.8595
722 S7J 0.8592
723 LT2 0.8591
724 ESP 0.8591
725 TGX 0.8591
726 AVI 0.8589
727 1A5 0.8587
728 AM4 0.8585
729 PGA 0.8584
730 TOH 0.8577
731 NBE 0.8575
732 OK7 0.8574
733 NM2 0.8572
734 LEU 0.8570
735 Q06 0.8570
736 LCN 0.8569
737 94W 0.8567
738 JND 0.8566
739 GAL 0.8559
740 S0F 0.8559
741 3MF 0.8557
742 CIT 0.8556
743 6NA 0.8553
744 BE2 0.8549
745 N4E 0.8541
746 SJ5 0.8535
747 HHA 0.8535
748 P4B 0.8534
749 44V 0.8530
750 NSG 0.8526
751 5GU 0.8524
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2YAJ; Ligand: 4HP; 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: 2yaj.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2YAJ; Ligand: 4HP; 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: 2yaj.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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