Receptor
PDB id Resolution Class Description Source Keywords
6HDW 2.3 Å EC: 6.2.1.- CRYSTAL STRUCTURE OF 2-HYDROXYISOBUTYRYL-COA LIGASE (HCL) IN POSTADENYLATION STATE IN COMPLEX WITH 2-HIB-AMP AQUINCOLA TERTIARICARBONIS LIGASE 2-HYDROXYISOBUTYRATE COA
Ref.: STRUCTURES OF 2-HYDROXYISOBUTYRIC ACID-COA LIGASE R DETERMINANTS OF SUBSTRATE SPECIFICITY AND DESCRIBE MULTI-CONFORMATIONAL CATALYTIC CYCLE. J.MOL.BIOL. V. 431 2747 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SO4 A:1002;
A:1004;
A:1003;
Invalid;
Invalid;
Invalid;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
8LE A:1001;
Valid;
none;
submit data
433.31 C14 H20 N5 O9 P CC(C)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6HE2 2.3 Å EC: 6.2.1.- CRYSTAL STRUCTURE OF AN OPEN CONFORMATION OF 2-HYDROXYISOBUT LIGASE (HCL) IN COMPLEX WITH 2-HIB-AMP AND COA AQUINCOLA TERTIARICARBONIS LIGASE 2-HYDROXYISOBUTYRATE COA
Ref.: STRUCTURES OF 2-HYDROXYISOBUTYRIC ACID-COA LIGASE R DETERMINANTS OF SUBSTRATE SPECIFICITY AND DESCRIBE MULTI-CONFORMATIONAL CATALYTIC CYCLE. J.MOL.BIOL. V. 431 2747 2019
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6HDW - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
2 6HDY - 3HL C4 H8 O3 C[C@@H](CC....
3 6HDX - 8LH C14 H20 N5 O9 P C[C@H](CO)....
4 6HE0 - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
5 6HE2 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 6HDW - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
2 6HDY - 3HL C4 H8 O3 C[C@@H](CC....
3 6HDX - 8LH C14 H20 N5 O9 P C[C@H](CO)....
4 6HE0 - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
5 6HE2 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 6HDW - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
2 6HDY - 3HL C4 H8 O3 C[C@@H](CC....
3 6HDX - 8LH C14 H20 N5 O9 P C[C@H](CO)....
4 6HE0 - 8LE C14 H20 N5 O9 P CC(C)(C(=O....
5 6HE2 - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 8LE; Similar ligands found: 449
No: Ligand ECFP6 Tc MDL keys Tc
1 8LE 1 1
2 KG4 0.807692 0.921053
3 CA0 0.794872 0.921053
4 5AL 0.759036 0.959459
5 A2D 0.753247 0.894737
6 8LH 0.741176 0.934211
7 AT4 0.7375 0.860759
8 AN2 0.7375 0.883117
9 BA3 0.734177 0.894737
10 M33 0.728395 0.907895
11 PAJ 0.727273 0.961039
12 AP5 0.725 0.894737
13 B4P 0.725 0.894737
14 ADP 0.725 0.894737
15 8LQ 0.724138 0.934211
16 QA7 0.724138 0.973333
17 SRP 0.72093 0.909091
18 OOB 0.715909 0.933333
19 8QN 0.715909 0.959459
20 A 0.714286 0.893333
21 AMP 0.714286 0.893333
22 PRX 0.710843 0.871795
23 45A 0.708861 0.894737
24 ABM 0.708861 0.894737
25 ADX 0.707317 0.809524
26 DLL 0.7 0.933333
27 ACP 0.698795 0.871795
28 HEJ 0.698795 0.894737
29 ATP 0.698795 0.894737
30 50T 0.698795 0.858974
31 PTJ 0.695652 0.973684
32 3UK 0.692308 0.921053
33 AQP 0.690476 0.894737
34 APR 0.690476 0.92
35 5FA 0.690476 0.894737
36 AR6 0.690476 0.92
37 4AD 0.688889 0.897436
38 AMO 0.688889 0.909091
39 B5V 0.684783 0.909091
40 PR8 0.684783 0.853659
41 AMP MG 0.683544 0.88
42 AGS 0.682353 0.85
43 AD9 0.682353 0.871795
44 00A 0.681319 0.886076
45 ME8 0.677419 0.865854
46 1ZZ 0.677419 0.865854
47 TXA 0.677419 0.934211
48 FA5 0.673684 0.909091
49 A12 0.670732 0.860759
50 AP2 0.670732 0.860759
51 ATF 0.670455 0.860759
52 ACQ 0.666667 0.871795
53 ANP 0.666667 0.871795
54 WAQ 0.666667 0.886076
55 LAD 0.666667 0.864198
56 9SN 0.663158 0.875
57 SRA 0.6625 0.848101
58 4UV 0.659794 0.897436
59 NB8 0.659574 0.875
60 3OD 0.659574 0.946667
61 B5Y 0.65625 0.922078
62 B5M 0.65625 0.922078
63 OAD 0.655914 0.946667
64 GAP 0.647727 0.896104
65 AU1 0.647059 0.871795
66 AHX 0.645161 0.851852
67 6YZ 0.644444 0.871795
68 5SV 0.641304 0.829268
69 V2G 0.640449 0.875
70 9X8 0.638298 0.897436
71 HQG 0.637363 0.907895
72 ADP MG 0.635294 0.893333
73 SON 0.635294 0.909091
74 ADP BEF 0.635294 0.893333
75 APC 0.632184 0.860759
76 DAL AMP 0.630435 0.933333
77 A22 0.630435 0.883117
78 T99 0.629214 0.860759
79 TAT 0.629214 0.860759
80 RBY 0.625 0.884615
81 ADV 0.625 0.884615
82 9ZA 0.623656 0.935065
83 25A 0.623656 0.894737
84 9ZD 0.623656 0.935065
85 OZV 0.623656 0.894737
86 LAQ 0.617647 0.843373
87 A1R 0.617021 0.839506
88 ADQ 0.617021 0.896104
89 A3R 0.617021 0.839506
90 4UU 0.613861 0.897436
91 YLP 0.61165 0.845238
92 JNT 0.610526 0.871795
93 FYA 0.608247 0.858974
94 BIS 0.608247 0.839506
95 ATP MG 0.606742 0.893333
96 ADP PO3 0.606742 0.893333
97 APC MG 0.606742 0.87013
98 4UW 0.605769 0.8875
99 BEF ADP 0.6 0.87013
100 XAH 0.6 0.821429
101 TYM 0.6 0.909091
102 YLB 0.59434 0.845238
103 YLC 0.59434 0.865854
104 LMS 0.590361 0.788235
105 KMQ 0.59 0.909091
106 MYR AMP 0.585859 0.843373
107 25L 0.585859 0.883117
108 IOT 0.583333 0.813953
109 48N 0.580952 0.898734
110 VO4 ADP 0.580645 0.871795
111 ANP MG 0.580645 0.883117
112 ALF ADP 0.580645 0.82716
113 MAP 0.578947 0.85
114 DQV 0.576923 0.907895
115 COD 0.576577 0.858824
116 NAX 0.575472 0.831325
117 G3A 0.572816 0.851852
118 AYB 0.572727 0.835294
119 CNA 0.572727 0.884615
120 OMR 0.570093 0.855422
121 5AS 0.568182 0.764045
122 GA7 0.567308 0.860759
123 G5P 0.567308 0.851852
124 YLA 0.563636 0.823529
125 TSB 0.5625 0.802326
126 GTA 0.561905 0.843373
127 6V0 0.560748 0.851852
128 NAI 0.560748 0.8625
129 DND 0.560748 0.909091
130 TXD 0.560748 0.8625
131 RAB 0.558442 0.776316
132 ADN 0.558442 0.776316
133 XYA 0.558442 0.776316
134 AOC 0.55814 0.779221
135 5CD 0.556962 0.763158
136 TXE 0.555556 0.8625
137 ADP BMA 0.555556 0.871795
138 AFH 0.552381 0.841463
139 52H 0.552083 0.847059
140 54H 0.552083 0.835294
141 VMS 0.552083 0.835294
142 YLY 0.551724 0.835294
143 L3W 0.550459 0.884615
144 G5A 0.548387 0.764045
145 A5A 0.547368 0.811765
146 53H 0.546392 0.847059
147 5N5 0.544304 0.753247
148 BT5 0.54386 0.813953
149 2A5 0.543478 0.825
150 AHZ 0.542056 0.843373
151 F2R 0.539823 0.823529
152 A3D 0.53913 0.921053
153 M24 0.538462 0.853659
154 ARG AMP 0.537736 0.811765
155 A4D 0.5375 0.753247
156 LPA AMP 0.537037 0.821429
157 EP4 0.536585 0.782051
158 AP0 0.536364 0.851852
159 T5A 0.535714 0.823529
160 TAD 0.53271 0.841463
161 UP5 0.53211 0.873418
162 8X1 0.530612 0.73913
163 M2T 0.53012 0.7625
164 DTA 0.53012 0.746835
165 3DH 0.529412 0.75641
166 JB6 0.529412 0.839506
167 6RE 0.528736 0.702381
168 SSA 0.525773 0.764045
169 MTA 0.52381 0.75641
170 7MD 0.523364 0.843373
171 AR6 AR6 0.523364 0.894737
172 3AM 0.523256 0.855263
173 UPA 0.522523 0.8625
174 4TC 0.522523 0.851852
175 A3P 0.522222 0.893333
176 NAD 0.521739 0.907895
177 PAP 0.521277 0.881579
178 ATR 0.521277 0.868421
179 D4F 0.521008 0.843373
180 LSS 0.52 0.806818
181 P5A 0.519608 0.731183
182 AMP DBH 0.518868 0.848101
183 A4P 0.517857 0.784091
184 7D5 0.517647 0.810127
185 J7C 0.516854 0.710843
186 H1Q 0.516129 0.857143
187 5CA 0.515152 0.764045
188 NVA LMS 0.514852 0.758242
189 9K8 0.514563 0.73913
190 ATP A A A 0.514286 0.881579
191 ATP A 0.514286 0.881579
192 80F 0.512821 0.823529
193 N0B 0.512397 0.823529
194 7D3 0.511111 0.8125
195 LEU LMS 0.509804 0.795455
196 NAD IBO 0.508929 0.894737
197 7MC 0.508929 0.845238
198 NAD TDB 0.508929 0.894737
199 139 0.508772 0.831325
200 ADJ 0.508772 0.811765
201 NAE 0.508333 0.897436
202 A2P 0.505495 0.88
203 ITT 0.505376 0.844156
204 7D4 0.505376 0.8125
205 6AD 0.505155 0.841463
206 PPS 0.505155 0.788235
207 A2R 0.50505 0.907895
208 NSS 0.504951 0.764045
209 DSZ 0.504951 0.784091
210 NAQ 0.504132 0.898734
211 5X8 0.5 0.769231
212 NWW 0.5 0.72
213 AF3 ADP 3PG 0.5 0.841463
214 ALF ADP 3PG 0.5 0.841463
215 ARU 0.5 0.819277
216 BTX 0.495726 0.802326
217 AMP NAD 0.495726 0.907895
218 SMM 0.494949 0.732558
219 V3L 0.494845 0.92
220 S4M 0.494505 0.655556
221 6MZ 0.494505 0.881579
222 NDC 0.492188 0.851852
223 EAD 0.491935 0.853659
224 DZD 0.491525 0.841463
225 GSU 0.490385 0.784091
226 KAA 0.490385 0.73913
227 EEM 0.489796 0.717647
228 SA8 0.489583 0.73494
229 A5D 0.489583 0.746835
230 MAO 0.48913 0.744186
231 NEC 0.488889 0.730769
232 ZID 0.487805 0.896104
233 8PZ 0.485981 0.764045
234 HFD 0.484536 0.85
235 JSQ 0.484536 0.85
236 SFG 0.484211 0.75641
237 A3N 0.483516 0.725
238 IMO 0.483516 0.855263
239 NAJ PZO 0.483333 0.829268
240 ZAS 0.483146 0.728395
241 B1U 0.481481 0.723404
242 YSA 0.481481 0.764045
243 SAM 0.479592 0.717647
244 GJV 0.478261 0.694118
245 2AM 0.477273 0.844156
246 P1H 0.476562 0.833333
247 5AD 0.475 0.72973
248 DSH 0.472527 0.690476
249 A3G 0.472527 0.759494
250 SAH 0.469388 0.75
251 SAI 0.469388 0.740741
252 O02 0.469388 0.829268
253 FB0 0.469231 0.788889
254 KOY 0.469027 0.807692
255 CUU 0.46875 0.87013
256 NAJ PYZ 0.467742 0.790698
257 DCA 0.467213 0.848837
258 NA7 0.466667 0.860759
259 QXP 0.466019 0.730337
260 V47 0.465347 0.789474
261 S7M 0.465347 0.717647
262 NDE 0.465116 0.884615
263 3AT 0.464646 0.87013
264 4YB 0.464286 0.766667
265 J4G 0.462264 0.897436
266 OVE 0.461538 0.8125
267 WSA 0.46087 0.772727
268 NO7 0.460784 0.8375
269 NWQ 0.460674 0.723684
270 7C5 0.459459 0.8
271 MHZ 0.458333 0.685393
272 4TA 0.458333 0.811765
273 N5O 0.456522 0.725
274 2SA 0.455446 0.884615
275 AV2 0.455446 0.822785
276 ETB 0.455285 0.858824
277 LQJ 0.454545 0.87013
278 6C6 0.454545 0.814815
279 A3T 0.453608 0.802632
280 DAT 0.453608 0.8125
281 QXG 0.45283 0.722222
282 38V 0.452381 0.821429
283 AVV 0.451923 0.829268
284 ODP 0.45 0.841463
285 NJP 0.45 0.873418
286 6IA 0.45 0.841463
287 DTP 0.45 0.8125
288 C2R 0.449438 0.857143
289 AMZ 0.449438 0.844156
290 649 0.448276 0.731183
291 COA 0.448 0.848837
292 0T1 0.448 0.848837
293 A7D 0.447917 0.7375
294 A3S 0.447917 0.769231
295 6FA 0.447761 0.845238
296 0UM 0.447619 0.72619
297 0WD 0.446281 0.851852
298 3KK 0.446154 0.829545
299 AAT 0.445545 0.674419
300 K3K 0.445455 0.740741
301 NPW 0.445378 0.821429
302 NVA 2AD 0.444444 0.743902
303 62X 0.443396 0.732558
304 GGZ 0.442308 0.764706
305 71V 0.442105 0.817073
306 FAS 0.441176 0.855422
307 FAD 0.441176 0.855422
308 9JJ 0.440559 0.821429
309 FDA 0.440298 0.816092
310 K15 0.439252 0.709302
311 A6D 0.439252 0.689655
312 FNK 0.438849 0.808989
313 GEK 0.438095 0.743902
314 S8M 0.438095 0.722892
315 COS 0.4375 0.829545
316 CAO 0.4375 0.820225
317 30N 0.4375 0.776596
318 K3E 0.4375 0.731707
319 AMX 0.4375 0.858824
320 Y3J 0.435294 0.688312
321 R2V 0.435185 0.730337
322 NAD BBN 0.434783 0.802326
323 SCO 0.434109 0.870588
324 CMX 0.434109 0.870588
325 7D7 0.433735 0.705128
326 NDP 0.433333 0.851852
327 8Q2 0.432203 0.73913
328 COK 0.431818 0.829545
329 N5A 0.431579 0.7
330 SXZ 0.431193 0.780488
331 FCX 0.430769 0.840909
332 ACO 0.430769 0.820225
333 FAM 0.430769 0.829545
334 SFD 0.430657 0.739583
335 N6P 0.429907 0.842105
336 TXP 0.429752 0.851852
337 NZQ 0.429752 0.841463
338 PGS 0.428571 0.795181
339 HAX 0.427481 0.829545
340 Z5A 0.426357 0.784091
341 PO4 PO4 A A A A PO4 0.425926 0.855263
342 DA 0.425532 0.810127
343 FAY 0.425532 0.843373
344 D5M 0.425532 0.810127
345 2MC 0.425373 0.793478
346 AIR 0.425287 0.828947
347 V1N 0.424779 0.894737
348 FYN 0.424242 0.848837
349 2VA 0.424242 0.828947
350 N01 0.424 0.907895
351 NIA 0.423913 0.761905
352 KGA 0.423358 0.787234
353 7L1 0.423077 0.820225
354 NA0 0.423077 0.909091
355 XNP 0.422764 0.809524
356 RFL 0.422535 0.847059
357 KGJ 0.422222 0.776596
358 NX8 0.421569 0.682353
359 DDS 0.421569 0.7875
360 OXK 0.421053 0.850575
361 FAI 0.421053 0.844156
362 AAM 0.421053 0.893333
363 SOP 0.421053 0.829545
364 KGP 0.421053 0.752577
365 CA6 0.421053 0.752577
366 YZS 0.421053 0.752577
367 MCD 0.421053 0.850575
368 F2N 0.418919 0.797753
369 62F 0.41844 0.843373
370 NAD CJ3 0.41844 0.775281
371 7DD 0.418367 0.881579
372 K2R 0.418182 0.858974
373 1VU 0.41791 0.820225
374 CMC 0.41791 0.850575
375 CO6 0.41791 0.829545
376 NMX 0.41791 0.784946
377 K2H 0.416667 0.719512
378 APU 0.416667 0.85
379 J7V 0.415385 0.837209
380 KY2 0.415094 0.678161
381 P5F 0.414966 0.827586
382 SCD 0.414815 0.870588
383 CAJ 0.414815 0.850575
384 KB1 0.414414 0.705882
385 KXW 0.413793 0.714286
386 BYC 0.413043 0.829545
387 COW 0.413043 0.820225
388 KFV 0.413043 0.760417
389 CA8 0.413043 0.752577
390 2KQ 0.413043 0.831461
391 3HC 0.411765 0.83908
392 BCO 0.411765 0.829545
393 1HE 0.411765 0.811111
394 A1S 0.411765 0.829545
395 IVC 0.411765 0.83908
396 SO8 0.411765 0.794872
397 MLC 0.411765 0.850575
398 VRT 0.411765 0.753086
399 1CZ 0.411348 0.840909
400 6K6 0.411215 0.857143
401 COA FLC 0.410853 0.837209
402 FAQ 0.410072 0.829545
403 K2K 0.409091 0.682353
404 3NZ 0.409091 0.765432
405 YE1 0.408759 0.83908
406 LCV 0.408759 0.762887
407 MCA 0.408759 0.840909
408 CAA 0.408759 0.83908
409 COO 0.408759 0.829545
410 SO5 0.408759 0.762887
411 NAP 0.407692 0.896104
412 KYB 0.407407 0.678161
413 HXC 0.407143 0.811111
414 GRA 0.407143 0.850575
415 RGT 0.40708 0.884615
416 OZP 0.40678 0.73494
417 FA9 0.406667 0.86747
418 7RA 0.40625 0.881579
419 7DT 0.405941 0.881579
420 NWZ 0.405941 0.670588
421 MC4 0.405797 0.784946
422 SCA 0.405797 0.850575
423 YXS 0.405797 0.752577
424 2CP 0.405797 0.840909
425 YXR 0.405797 0.752577
426 O05 0.405405 0.764045
427 GNH 0.403846 0.839506
428 KYE 0.403509 0.701149
429 K2W 0.403509 0.686047
430 K3H 0.403509 0.714286
431 3CP 0.402878 0.850575
432 COF 0.402878 0.811111
433 1GZ 0.402878 0.820225
434 HGG 0.402878 0.850575
435 IRC 0.402878 0.83908
436 D3Y 0.401869 0.75
437 KY5 0.401786 0.690476
438 KH3 0.401709 0.701149
439 SLU 0.401575 0.755556
440 PLP AAD 0.401575 0.73913
441 2NE 0.401408 0.811111
442 CO8 0.401408 0.811111
443 S0N 0.401408 0.850575
444 CIC 0.401408 0.850575
445 BCA 0.4 0.820225
446 101 0.4 0.810127
447 4CA 0.4 0.820225
448 NMN AMP PO4 0.4 0.85
449 NHD 0.4 0.883117
Similar Ligands (3D)
Ligand no: 1; Ligand: 8LE; Similar ligands found: 4
No: Ligand Similarity coefficient
1 GDP 0.9188
2 IDP 0.8940
3 GDP MG 0.8750
4 DZ4 0.8672
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6HE2; Ligand: COA; 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: 6he2.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6HE2; Ligand: 8LE; 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: 6he2.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6HE2; Ligand: COA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6he2.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6HE2; Ligand: AMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6he2.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6HE2; Ligand: AMP; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6he2.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 6HE2; Ligand: 8LE; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 6he2.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
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