Receptor
PDB id Resolution Class Description Source Keywords
5D2K 1.57 Å EC: 4.1.1.77 4-OXALOCROTONATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA G7 - WITH MAGNESIUM AND 2-OXOADIPATE PSEUDOMONAS PUTIDA NAPHTHALENE DEGRADATION LYASE
Ref.: CRYSTAL STRUCTURES OF APO AND LIGANDED 4-OXALOCROTO DECARBOXYLASE UNCOVER A STRUCTURAL BASIS FOR THE METAL-ASSISTED DECARBOXYLATION OF A VINYLOGOUS BETA ACID. BIOCHEMISTRY V. 55 2632 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO B:306;
B:305;
A:307;
B:307;
B:308;
A:304;
A:303;
A:308;
A:309;
A:305;
B:303;
A:306;
B:304;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
62.068 C2 H6 O2 C(CO)...
ACT B:309;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
OOG A:302;
B:302;
Valid;
Valid;
none;
Atoms found MORE than expected: % Diff = 2;
submit data
160.125 C6 H8 O5 C(CC(...
MG B:301;
A:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D2H 1.94 Å EC: 4.1.1.77 4-OXALOCROTONATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA G7 - WITH MAGNESIUM AND ALPHA-KETOGLUTARATE PSEUDOMONAS PUTIDA NAPHTHALENE DEGRADATION LYASE
Ref.: CRYSTAL STRUCTURES OF APO AND LIGANDED 4-OXALOCROTO DECARBOXYLASE UNCOVER A STRUCTURAL BASIS FOR THE METAL-ASSISTED DECARBOXYLATION OF A VINYLOGOUS BETA ACID. BIOCHEMISTRY V. 55 2632 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
2 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
3 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
2 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
3 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
50% 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 2EB5 - OXL C2 O4 C(=O)(C(=O....
2 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
3 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
4 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: OOG; Similar ligands found: 10
No: Ligand ECFP6 Tc MDL keys Tc
1 OOG 1 1
2 GUA 0.590909 0.894737
3 AKG 0.5 0.947368
4 7C3 0.466667 0.642857
5 0L1 0.458333 0.85
6 KPA 0.451613 0.612903
7 PML 0.423077 0.809524
8 AZ1 0.407407 0.772727
9 69O 0.407407 0.681818
10 26P 0.4 0.678571
Similar Ligands (3D)
Ligand no: 1; Ligand: OOG; Similar ligands found: 696
No: Ligand Similarity coefficient
1 UN1 0.9881
2 2FM 0.9702
3 O45 0.9692
4 650 0.9628
5 GLU 0.9570
6 HCI 0.9541
7 LYS 0.9522
8 DLY 0.9522
9 FK8 0.9502
10 LYN 0.9490
11 TCA 0.9489
12 MF3 0.9468
13 11C 0.9464
14 GLN 0.9458
15 HC4 0.9448
16 DAR 0.9441
17 S8V 0.9440
18 Q9Z 0.9437
19 RNO 0.9435
20 7BC 0.9431
21 AHN 0.9420
22 NNH 0.9420
23 SNO 0.9411
24 6HN 0.9409
25 LVD 0.9407
26 HOC 0.9407
27 MLZ 0.9393
28 P81 0.9387
29 HIS 0.9366
30 CXP 0.9361
31 URO 0.9355
32 CLT 0.9355
33 PHE 0.9354
34 5OY 0.9350
35 4HP 0.9349
36 ARG 0.9343
37 DGL 0.9337
38 6JN 0.9325
39 9YT 0.9325
40 GVA 0.9319
41 CCU 0.9318
42 PBA 0.9317
43 ENW 0.9314
44 2JJ 0.9314
45 DHY 0.9313
46 1L5 0.9311
47 XIZ 0.9308
48 PPY 0.9308
49 E79 0.9307
50 8SZ 0.9304
51 OGA 0.9299
52 MLY 0.9295
53 TIH 0.9294
54 DHH 0.9294
55 NPI 0.9294
56 PO6 0.9284
57 AG2 0.9278
58 M6H 0.9268
59 SLZ 0.9267
60 GGB 0.9263
61 JX7 0.9262
62 NFA 0.9262
63 CUW 0.9256
64 PAC 0.9251
65 J0Z 0.9247
66 SSC 0.9243
67 PJL 0.9243
68 HGA 0.9242
69 P80 0.9242
70 ONH 0.9234
71 DIR 0.9229
72 4TP 0.9227
73 1BN 0.9226
74 7OD 0.9224
75 BNL 0.9223
76 DXP 0.9223
77 8OZ 0.9222
78 OCA 0.9220
79 PRO GLY 0.9218
80 011 0.9217
81 3YP 0.9216
82 ACA 0.9215
83 HHI 0.9212
84 DHI 0.9211
85 AOT 0.9204
86 4TB 0.9200
87 6FZ 0.9197
88 URP 0.9196
89 FOM 0.9191
90 ENV 0.9183
91 S2G 0.9183
92 M1T 0.9180
93 PNZ 0.9178
94 2NP 0.9177
95 1N5 0.9177
96 GRQ 0.9177
97 BNF 0.9176
98 F90 0.9176
99 3OM 0.9176
100 3OL 0.9176
101 F98 0.9174
102 LUQ 0.9173
103 LQ2 0.9173
104 B3U 0.9170
105 DXG 0.9169
106 MSR 0.9168
107 HHH 0.9167
108 5XA 0.9167
109 2HG 0.9167
110 XRX 0.9167
111 GVG 0.9166
112 TEG 0.9165
113 M3P 0.9165
114 2IT 0.9164
115 4NB 0.9160
116 DER 0.9159
117 TZM 0.9155
118 4LW 0.9149
119 9RW 0.9149
120 HPN 0.9147
121 L14 0.9146
122 M45 0.9142
123 KPC 0.9139
124 2FX 0.9139
125 3HG 0.9138
126 6J5 0.9138
127 DHC 0.9137
128 MHN 0.9134
129 MES 0.9134
130 KMH 0.9134
131 DI6 0.9133
132 DGN 0.9133
133 DPN 0.9133
134 DLT 0.9132
135 S2P 0.9131
136 N6C 0.9131
137 GB5 0.9129
138 C82 0.9129
139 3LR 0.9127
140 MEQ 0.9126
141 8EW 0.9124
142 YZM 0.9122
143 64Z 0.9120
144 3QO 0.9120
145 ESX 0.9118
146 ANN 0.9116
147 SHV 0.9115
148 N9J 0.9114
149 QUS 0.9114
150 BHH 0.9113
151 TYL 0.9112
152 M5E 0.9111
153 4LV 0.9111
154 PBN 0.9109
155 SEP 0.9109
156 HL4 0.9109
157 J9N 0.9107
158 KMT 0.9106
159 HPP 0.9106
160 EN1 0.9103
161 1PS 0.9103
162 152 0.9103
163 API 0.9102
164 HIC 0.9101
165 ALE 0.9100
166 ENO 0.9099
167 CIR 0.9098
168 DAL DAL 0.9095
169 SD4 0.9095
170 2HC 0.9095
171 GLR 0.9095
172 ALA ALA 0.9094
173 HFA 0.9094
174 RLG 0.9093
175 DZA 0.9092
176 ILO 0.9088
177 KNA 0.9088
178 LGT 0.9088
179 3HP 0.9088
180 RNS 0.9088
181 JB8 0.9086
182 K7M 0.9083
183 173 0.9083
184 KQY 0.9082
185 IVL 0.9080
186 TZP 0.9079
187 HF2 0.9079
188 SHI 0.9078
189 RUJ 0.9078
190 EXY 0.9077
191 TYR 0.9076
192 6NI 0.9074
193 BL0 0.9073
194 DEZ 0.9073
195 Q06 0.9073
196 SNU 0.9072
197 3H2 0.9072
198 KDG 0.9072
199 NYL 0.9071
200 ORN 0.9071
201 MHO 0.9070
202 I1E 0.9070
203 LL2 0.9069
204 URQ 0.9068
205 TYC 0.9067
206 61M 0.9067
207 GCO 0.9064
208 428 0.9064
209 IAR 0.9062
210 XCG 0.9062
211 AHC 0.9061
212 3PG 0.9061
213 M3H 0.9060
214 R2P 0.9054
215 4BF 0.9053
216 B40 0.9052
217 P7Y 0.9050
218 PRA 0.9050
219 HPV 0.9049
220 F4E 0.9047
221 GO2 0.9045
222 ONL 0.9044
223 4ZD 0.9043
224 PPT 0.9043
225 QFJ 0.9042
226 CPZ 0.9042
227 DE5 0.9042
228 HBU 0.9041
229 ESP 0.9039
230 ICB 0.9039
231 LPB 0.9039
232 NCT 0.9038
233 N4B 0.9037
234 FBF 0.9036
235 DHM 0.9035
236 2D8 0.9034
237 YIE 0.9034
238 7UC 0.9029
239 P58 0.9028
240 OHJ 0.9028
241 E4P 0.9026
242 LNO 0.9026
243 SSB 0.9025
244 SZ7 0.9025
245 9GB 0.9025
246 BRH 0.9023
247 M74 0.9022
248 SME 0.9021
249 AAN 0.9021
250 0A9 0.9020
251 56D 0.9019
252 6XA 0.9018
253 9J3 0.9018
254 9ON 0.9017
255 YPN 0.9017
256 JDN 0.9014
257 HXY 0.9013
258 TYE 0.9013
259 GGL 0.9013
260 GZ2 0.9011
261 SMN 0.9009
262 S0W 0.9007
263 BPN 0.9006
264 PH3 0.9004
265 RP3 0.9003
266 2UB 0.9002
267 PCS 0.9002
268 8GL 0.9001
269 HNK 0.9000
270 S0D 0.9000
271 MSL 0.8999
272 92G 0.8999
273 GJZ 0.8998
274 7O4 0.8997
275 GAE 0.8996
276 K4V 0.8996
277 AMH 0.8995
278 MAJ 0.8995
279 6CL 0.8994
280 HL5 0.8994
281 A7N 0.8993
282 AEG 0.8992
283 HNL 0.8990
284 5WZ 0.8990
285 PIM 0.8989
286 5DL 0.8988
287 LSQ 0.8985
288 DHS 0.8985
289 F06 0.8984
290 R9M 0.8984
291 AT3 0.8983
292 7VP 0.8983
293 SDD 0.8983
294 DTY 0.8982
295 HNH 0.8980
296 363 0.8979
297 DYT 0.8977
298 OEG 0.8977
299 HG3 0.8976
300 5TO 0.8976
301 A3M 0.8975
302 1HS 0.8975
303 3C4 0.8974
304 HAR 0.8973
305 IP8 0.8973
306 A5E 0.8973
307 DA3 0.8973
308 MUC 0.8971
309 6C9 0.8970
310 MNP 0.8970
311 4CM 0.8969
312 DX5 0.8969
313 LT1 0.8969
314 OSE 0.8968
315 CS2 0.8968
316 MET 0.8966
317 LX1 0.8964
318 GNW 0.8964
319 AE3 0.8962
320 4NZ 0.8962
321 OTR 0.8960
322 6C5 0.8960
323 ZGL 0.8960
324 8U3 0.8960
325 HSO 0.8958
326 EYV 0.8958
327 5OO 0.8957
328 EGV 0.8956
329 SOR 0.8955
330 B85 0.8955
331 GVY 0.8954
332 3S5 0.8954
333 FUD 0.8954
334 TMG 0.8954
335 K6V 0.8953
336 9X6 0.8953
337 Z70 0.8952
338 YIP 0.8952
339 ZZU 0.8951
340 264 0.8951
341 XOG 0.8951
342 SB7 0.8950
343 492 0.8948
344 XRS 0.8947
345 14W 0.8946
346 MAH 0.8946
347 R20 0.8945
348 IXW 0.8945
349 HX8 0.8945
350 GLO 0.8942
351 4NM 0.8939
352 FHC 0.8938
353 3CR 0.8938
354 268 0.8938
355 HX4 0.8936
356 QH3 0.8935
357 GWM 0.8935
358 F4K 0.8934
359 LPA 0.8934
360 NTU 0.8934
361 NWH 0.8931
362 49F 0.8931
363 36M 0.8931
364 FZM 0.8930
365 EVF 0.8930
366 I38 0.8930
367 CFA 0.8930
368 58X 0.8930
369 F9P 0.8927
370 3VX 0.8925
371 HDH 0.8925
372 LNR 0.8922
373 PFF 0.8918
374 4NP 0.8916
375 AL0 0.8916
376 NOT 0.8916
377 AM4 0.8914
378 HLP 0.8913
379 B41 0.8910
380 E5X 0.8907
381 S0F 0.8907
382 MED 0.8907
383 RBJ 0.8906
384 36Y 0.8906
385 4BZ 0.8905
386 ISA 0.8905
387 13P 0.8904
388 VC3 0.8904
389 6C4 0.8904
390 1X4 0.8902
391 J4K 0.8902
392 SOL 0.8902
393 AMQ 0.8901
394 5SP 0.8901
395 NLE 0.8900
396 P93 0.8899
397 OKG 0.8899
398 TB8 0.8898
399 6ZX 0.8898
400 JF6 0.8896
401 1A7 0.8895
402 HMS 0.8894
403 5LD 0.8894
404 ZZA 0.8894
405 3VQ 0.8893
406 LR5 0.8893
407 GPJ 0.8890
408 NM2 0.8890
409 259 0.8890
410 MSE 0.8890
411 HJH 0.8890
412 XDK 0.8887
413 Q03 0.8887
414 S24 0.8886
415 RP5 0.8884
416 Q04 0.8884
417 LPK 0.8882
418 KLS 0.8880
419 JRB 0.8878
420 6HO 0.8877
421 AFS 0.8877
422 AHL 0.8875
423 H4E 0.8874
424 SAF 0.8874
425 GB4 0.8873
426 2BX 0.8873
427 TAG 0.8871
428 6TZ 0.8870
429 0VT 0.8868
430 GLY GLY 0.8868
431 X48 0.8867
432 TOH 0.8867
433 80G 0.8864
434 DAH 0.8862
435 PHU 0.8862
436 BP7 0.8861
437 CYX 0.8861
438 RES 0.8860
439 I2E 0.8860
440 G3P 0.8859
441 TSR 0.8859
442 PZM 0.8858
443 N2Y 0.8858
444 NF3 0.8858
445 NMH 0.8857
446 XUL 0.8857
447 N91 0.8856
448 MPV 0.8855
449 4NS 0.8855
450 QBM 0.8854
451 VUR 0.8854
452 KTA 0.8854
453 A5P 0.8852
454 263 0.8851
455 11X 0.8851
456 6MW 0.8849
457 3VS 0.8848
458 3AE 0.8848
459 LZ5 0.8848
460 R5P 0.8846
461 MZT 0.8845
462 PNP 0.8844
463 L5V 0.8844
464 CH9 0.8843
465 129 0.8843
466 MMS 0.8842
467 258 0.8840
468 0QW 0.8839
469 CHH 0.8839
470 PHI 0.8839
471 5PV 0.8839
472 NSD 0.8839
473 LY0 0.8839
474 HSX 0.8839
475 A29 0.8838
476 SOJ 0.8837
477 BZQ 0.8837
478 BPW 0.8835
479 IAC 0.8835
480 MD6 0.8834
481 EOU 0.8834
482 RNT 0.8833
483 9ZE 0.8833
484 PUE 0.8831
485 L06 0.8829
486 MPJ 0.8827
487 2BG 0.8826
488 KMY 0.8826
489 TRP 0.8825
490 3QM 0.8825
491 GPF 0.8824
492 G3H 0.8824
493 LTL 0.8824
494 ABF 0.8823
495 MTL 0.8823
496 SYM 0.8822
497 FER 0.8822
498 RTK 0.8822
499 LDP 0.8819
500 YRL 0.8818
501 AZM 0.8817
502 6SD 0.8816
503 2FT 0.8813
504 XI7 0.8813
505 PGH 0.8812
506 C1M 0.8809
507 C53 0.8809
508 4BX 0.8809
509 ODK 0.8808
510 NFM 0.8806
511 41K 0.8806
512 5RP 0.8805
513 1VK 0.8804
514 I3E 0.8804
515 E0O 0.8804
516 FPL 0.8802
517 KTJ 0.8802
518 QDK 0.8801
519 MQB 0.8801
520 XYH 0.8800
521 ATX 0.8797
522 M3L 0.8797
523 6KT 0.8796
524 3VW 0.8795
525 1H1 0.8794
526 4FP 0.8791
527 5XB 0.8791
528 CCD 0.8791
529 YOF 0.8790
530 GP9 0.8789
531 B3M 0.8788
532 JFM 0.8788
533 I4B 0.8788
534 NM3 0.8787
535 ZEC 0.8787
536 GLY GLY GLY 0.8786
537 HQJ 0.8786
538 J6W 0.8785
539 G14 0.8782
540 3BU 0.8782
541 LLH 0.8781
542 OCT 0.8780
543 EUE 0.8777
544 S7A 0.8775
545 16D 0.8774
546 0NX 0.8773
547 BHU 0.8773
548 CCE 0.8772
549 9W5 0.8771
550 4I8 0.8771
551 4PN 0.8769
552 MP5 0.8768
553 Z13 0.8765
554 5LA 0.8765
555 7MW 0.8765
556 OC9 0.8764
557 PG0 0.8761
558 RB5 0.8760
559 FTV 0.8759
560 GVM 0.8758
561 RQD 0.8757
562 FF2 0.8754
563 9SE 0.8754
564 4MB 0.8753
565 QMP 0.8753
566 AMS 0.8753
567 0OL 0.8751
568 RKV 0.8751
569 069 0.8750
570 AOS 0.8748
571 3EB 0.8747
572 6FG 0.8747
573 M4S 0.8745
574 EYJ 0.8745
575 4XF 0.8745
576 RUY 0.8742
577 9J6 0.8741
578 IYR 0.8739
579 NSB 0.8739
580 33S 0.8739
581 PJW 0.8736
582 L99 0.8735
583 AES 0.8734
584 GO8 0.8727
585 PC 0.8726
586 IOS 0.8724
587 GLY ALA 0.8723
588 D3G 0.8723
589 4VY 0.8722
590 4FA 0.8722
591 5FX 0.8721
592 1GP 0.8720
593 CLU 0.8719
594 DII 0.8718
595 4JK 0.8717
596 WT2 0.8717
597 KYN 0.8716
598 HWD 0.8716
599 AEF 0.8716
600 2QC 0.8715
601 1Z6 0.8715
602 SG3 0.8711
603 JMG 0.8711
604 IOP 0.8709
605 EQW 0.8708
606 CXH 0.8704
607 9BF 0.8704
608 CH8 0.8702
609 QME 0.8701
610 6Q3 0.8700
611 A51 0.8698
612 5DS 0.8696
613 OJD 0.8695
614 NVU 0.8695
615 JZA 0.8694
616 DVQ 0.8694
617 MJ5 0.8693
618 4JC 0.8692
619 3KJ 0.8690
620 5H6 0.8688
621 ACH 0.8688
622 HPL 0.8686
623 TU0 0.8685
624 36E 0.8675
625 M5H 0.8674
626 MJW 0.8672
627 X1R 0.8668
628 OMD 0.8667
629 DHR 0.8666
630 N7I 0.8666
631 NLP 0.8665
632 PG3 0.8664
633 GJK 0.8661
634 SKF 0.8661
635 42J 0.8660
636 SPD 0.8658
637 J9Y 0.8656
638 RJY 0.8653
639 PSJ 0.8653
640 3XH 0.8653
641 B09 0.8651
642 4LR 0.8650
643 PQS 0.8648
644 T03 0.8647
645 R9J 0.8647
646 MPH 0.8646
647 APS 0.8645
648 ARP 0.8643
649 PIY 0.8642
650 4FE 0.8641
651 BQ2 0.8639
652 DTR 0.8638
653 K34 0.8635
654 FIX 0.8633
655 JPQ 0.8626
656 PLP 0.8621
657 REL 0.8621
658 DEW 0.8621
659 Y4L 0.8619
660 GOJ 0.8619
661 27K 0.8619
662 3R4 0.8618
663 N1E 0.8617
664 ST3 0.8617
665 6NA 0.8615
666 IPO 0.8610
667 FHV 0.8610
668 MVH 0.8609
669 AVI 0.8606
670 PMV 0.8605
671 6L6 0.8604
672 K80 0.8602
673 8D6 0.8598
674 UA5 0.8591
675 5O6 0.8588
676 SN4 0.8584
677 C4E 0.8581
678 GRF 0.8578
679 EGR 0.8575
680 QBP 0.8575
681 AOY 0.8574
682 ODI 0.8574
683 1YO 0.8573
684 MD0 0.8570
685 2D2 0.8566
686 RAT 0.8562
687 DED 0.8559
688 JCZ 0.8557
689 SHO 0.8555
690 CEE 0.8548
691 HTX 0.8540
692 DAV 0.8539
693 XQI 0.8539
694 S7S 0.8535
695 4FF 0.8526
696 HJD 0.8518
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D2H; Ligand: AKG; 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: 5d2h.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback