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Receptor
PDB id Resolution Class Description Source Keywords
4YDU 2.33 Å EC: 2.6.99.4 CRYSTAL STRUCTURE OF E. COLI YGJD-YEAZ HETERODIMER IN COMPLE ESCHERICHIA COLI YGJD-YEAZ COMPLEX T6A TRANSFERASE TRANSFERASE
Ref.: THE ATP-MEDIATED FORMATION OF THE YGJD-YEAZ-YJEE CO REQUIRED FOR THE BIOSYNTHESIS OF TRNA T6A IN ESCHER COLI. NUCLEIC ACIDS RES. V. 43 1804 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ACT D:303;
D:305;
C:302;
D:306;
A:405;
B:404;
A:404;
D:304;
B:405;
D:302;
A:407;
A:406;
C:303;
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
59.044 C2 H3 O2 CC(=O...
ADP B:401;
D:301;
A:401;
C:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
427.201 C10 H15 N5 O10 P2 c1nc(...
MG A:402;
B:402;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
FE A:403;
B:403;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+3...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4YDU 2.33 Å EC: 2.6.99.4 CRYSTAL STRUCTURE OF E. COLI YGJD-YEAZ HETERODIMER IN COMPLE ESCHERICHIA COLI YGJD-YEAZ COMPLEX T6A TRANSFERASE TRANSFERASE
Ref.: THE ATP-MEDIATED FORMATION OF THE YGJD-YEAZ-YJEE CO REQUIRED FOR THE BIOSYNTHESIS OF TRNA T6A IN ESCHER COLI. NUCLEIC ACIDS RES. V. 43 1804 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4WQ4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4YDU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4WQ5 - ATP C10 H16 N5 O13 P3 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 1 families.
1 4WQ4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4YDU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4WQ5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3ZEU - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
5 3ZET - 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 1 families.
1 4WQ4 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
2 4YDU - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 4WQ5 - ATP C10 H16 N5 O13 P3 c1nc(c2c(n....
4 3ZEU - AGS C10 H16 N5 O12 P3 S c1nc(c2c(n....
5 3ZET - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: ADP; Similar ligands found: 452
No: Ligand ECFP6 Tc MDL keys Tc
1 ADP 1 1
2 HEJ 0.9 1
3 ATP 0.9 1
4 A2D 0.895522 0.971831
5 5FA 0.887324 1
6 AQP 0.887324 1
7 AP5 0.884058 0.971831
8 B4P 0.884058 0.971831
9 BA3 0.869565 0.971831
10 AN2 0.84507 0.985915
11 AT4 0.84507 0.958904
12 M33 0.833333 0.958333
13 ACQ 0.826667 0.972222
14 A 0.823529 0.971429
15 AMP 0.823529 0.971429
16 ACP 0.821918 0.972222
17 6YZ 0.818182 0.972222
18 APR 0.810811 0.971831
19 AR6 0.810811 0.971831
20 ANP 0.802632 0.972222
21 SAP 0.8 0.945946
22 AGS 0.8 0.945946
23 AD9 0.8 0.972222
24 ADX 0.783784 0.873418
25 CA0 0.783784 0.945205
26 TAT 0.779221 0.958904
27 T99 0.779221 0.958904
28 50T 0.773333 0.958333
29 ABM 0.763889 0.917808
30 APC 0.763158 0.958904
31 PRX 0.763158 0.893333
32 ATF 0.759494 0.958904
33 A22 0.753086 0.985915
34 AP2 0.743243 0.958904
35 A12 0.743243 0.958904
36 SRA 0.736111 0.918919
37 ADQ 0.73494 0.945205
38 25L 0.732558 0.985915
39 5AL 0.725 0.931507
40 2A5 0.717949 0.918919
41 A1R 0.714286 0.907895
42 AU1 0.714286 0.972222
43 A3R 0.714286 0.907895
44 ATR 0.708861 0.971429
45 ADP PO3 0.708861 0.943662
46 PAP 0.708861 0.985714
47 SRP 0.707317 0.906667
48 7D3 0.706667 0.905405
49 25A 0.702381 0.971831
50 9X8 0.697674 0.92
51 OAD 0.697674 0.945205
52 RBY 0.6875 0.932432
53 ADV 0.6875 0.932432
54 00A 0.686047 0.883117
55 OOB 0.682353 0.931507
56 5SV 0.682353 0.848101
57 8QN 0.682353 0.931507
58 3OD 0.681818 0.945205
59 BIS 0.681818 0.933333
60 ALF ADP 0.674699 0.87013
61 ADP ALF 0.674699 0.87013
62 AMO 0.674419 0.932432
63 4AD 0.674419 0.92
64 PAJ 0.674419 0.884615
65 GAP 0.670732 0.893333
66 MAP 0.670588 0.945946
67 AHX 0.666667 0.896104
68 VO4 ADP 0.666667 0.931507
69 DLL 0.666667 0.931507
70 ADP VO4 0.666667 0.931507
71 PTJ 0.662921 0.896104
72 3UK 0.659091 0.918919
73 SON 0.658228 0.932432
74 LMS 0.653333 0.82716
75 LAD 0.651685 0.860759
76 WAQ 0.651685 0.883117
77 B5V 0.651685 0.906667
78 PR8 0.651685 0.85
79 ITT 0.65 0.943662
80 7D4 0.65 0.905405
81 G5P 0.648936 0.921053
82 XYA 0.647059 0.84507
83 ADN 0.647059 0.84507
84 RAB 0.647059 0.84507
85 1ZZ 0.644444 0.839506
86 ME8 0.644444 0.839506
87 FYA 0.644444 0.905405
88 NB8 0.644444 0.896104
89 TXA 0.644444 0.932432
90 6AD 0.642857 0.909091
91 ADP BMA 0.640449 0.918919
92 G3A 0.638298 0.921053
93 DAL AMP 0.632184 0.905405
94 AFH 0.631579 0.884615
95 9SN 0.630435 0.871795
96 9ZA 0.625 0.907895
97 DQV 0.625 0.958333
98 9ZD 0.625 0.907895
99 GTA 0.625 0.886076
100 YAP 0.623656 0.894737
101 B5M 0.623656 0.894737
102 FA5 0.623656 0.906667
103 B5Y 0.623656 0.894737
104 UP5 0.622449 0.92
105 HFD 0.619048 0.945946
106 XAH 0.617021 0.839506
107 AV2 0.616279 0.917808
108 AOC 0.615385 0.821918
109 48N 0.612245 0.896104
110 4UV 0.610526 0.894737
111 6V0 0.606061 0.896104
112 NAI 0.606061 0.907895
113 DND 0.606061 0.932432
114 NAX 0.606061 0.873418
115 NXX 0.606061 0.932432
116 TXD 0.606061 0.907895
117 5N5 0.605634 0.819444
118 5AS 0.604938 0.77907
119 A4P 0.60396 0.843373
120 DAT 0.60241 0.905405
121 A2R 0.602273 0.985915
122 TXE 0.6 0.907895
123 OMR 0.6 0.851852
124 4UU 0.597938 0.894737
125 GA7 0.597938 0.906667
126 A A 0.597826 0.944444
127 A4D 0.597222 0.819444
128 5CD 0.597222 0.805556
129 AP0 0.594059 0.896104
130 4TC 0.594059 0.896104
131 A3P 0.592593 0.971429
132 T5A 0.592233 0.841463
133 139 0.592233 0.873418
134 7D5 0.592105 0.878378
135 ATP A A A 0.589474 0.930556
136 LAQ 0.585859 0.839506
137 MYR AMP 0.585106 0.817073
138 F2R 0.580952 0.864198
139 YLP 0.58 0.819277
140 UPA 0.578431 0.907895
141 7DD 0.578313 0.985714
142 3AM 0.576923 0.929577
143 ADJ 0.576923 0.851852
144 COD 0.575472 0.811765
145 NAD 0.575472 0.931507
146 3AT 0.574713 0.971831
147 JB6 0.574468 0.883117
148 4UW 0.574257 0.860759
149 EP4 0.573333 0.753247
150 A2P 0.573171 0.957143
151 CNA 0.571429 0.932432
152 TYM 0.568627 0.906667
153 PPS 0.568182 0.873418
154 DTA 0.565789 0.786667
155 M2T 0.565789 0.734177
156 AR6 AR6 0.565657 0.917808
157 A3D 0.564815 0.918919
158 80F 0.564815 0.841463
159 3DH 0.564103 0.773333
160 G5A 0.563218 0.77907
161 YLB 0.563107 0.819277
162 YLC 0.563107 0.839506
163 AMP DBH 0.561224 0.893333
164 TYR AMP 0.561224 0.87013
165 MTA 0.558442 0.773333
166 DTP 0.556818 0.905405
167 AHZ 0.554455 0.817073
168 NA7 0.553191 0.958904
169 IOT 0.552381 0.831325
170 ZAS 0.55 0.766234
171 7MD 0.55 0.8625
172 ARG AMP 0.55 0.829268
173 IMO 0.548781 0.929577
174 YLA 0.54717 0.819277
175 NAE 0.544643 0.894737
176 TAD 0.544554 0.884615
177 A5A 0.544444 0.807229
178 2AM 0.544304 0.943662
179 TSB 0.543478 0.819277
180 6RE 0.54321 0.759494
181 AYB 0.542056 0.809524
182 NAQ 0.539823 0.871795
183 V3L 0.539326 0.971831
184 SSA 0.538462 0.8
185 AF3 ADP 3PG 0.538462 0.8375
186 ZID 0.535088 0.918919
187 LPA AMP 0.533981 0.817073
188 52H 0.532609 0.77907
189 VMS 0.532609 0.788235
190 54H 0.532609 0.788235
191 BTX 0.53211 0.841463
192 A3N 0.53012 0.786667
193 J7C 0.53012 0.769231
194 5X8 0.528736 0.763158
195 BT5 0.527273 0.831325
196 8X1 0.526882 0.752809
197 5CA 0.526882 0.8
198 53H 0.526882 0.77907
199 ARU 0.526316 0.860759
200 EAD 0.525862 0.873418
201 RGT 0.525253 0.958904
202 OVE 0.52439 0.905405
203 S4M 0.52381 0.666667
204 7DT 0.522727 0.985714
205 GDP 0.522222 0.92
206 DDS 0.522222 0.878378
207 AVV 0.521277 0.896104
208 NDE 0.521008 0.932432
209 7MC 0.518868 0.841463
210 DSH 0.518072 0.725
211 MAO 0.517647 0.759036
212 NSS 0.515789 0.8
213 DSZ 0.515789 0.8
214 LSS 0.515789 0.761364
215 P5A 0.515464 0.744444
216 DZD 0.513514 0.884615
217 NVA LMS 0.510417 0.752809
218 9K8 0.510204 0.714286
219 12D 0.509615 0.785714
220 M24 0.508772 0.85
221 YLY 0.508772 0.809524
222 P1H 0.508333 0.851852
223 5AD 0.506849 0.746479
224 GJV 0.505882 0.75
225 LEU LMS 0.505155 0.752809
226 AMP NAD 0.504505 0.905405
227 4TA 0.504505 0.807229
228 G A A A 0.504505 0.871795
229 NAJ PZO 0.504425 0.848101
230 GSU 0.5 0.77907
231 128 0.5 0.776471
232 KAA 0.5 0.752809
233 71V 0.5 0.907895
234 A3G 0.5 0.8
235 NDC 0.5 0.871795
236 7D7 0.5 0.743243
237 N0B 0.495726 0.819277
238 NJP 0.495495 0.945946
239 ODP 0.495495 0.909091
240 2SA 0.494624 0.932432
241 6C6 0.494505 0.881579
242 SFG 0.494382 0.75
243 0WD 0.491071 0.921053
244 YSA 0.490196 0.77907
245 PO4 PO4 A A A A PO4 0.489796 0.902778
246 SAM 0.48913 0.690476
247 6IA 0.48913 0.8375
248 A7D 0.488636 0.776316
249 6FA 0.488 0.841463
250 FB0 0.487805 0.804598
251 NAJ PYZ 0.487179 0.807229
252 A5D 0.483516 0.786667
253 IDP 0.483516 0.918919
254 SA8 0.483516 0.707317
255 PGS 0.483146 0.883117
256 MHZ 0.483146 0.697674
257 DA 0.482353 0.878378
258 D5M 0.482353 0.878378
259 NEC 0.482353 0.746667
260 NIA 0.481928 0.822785
261 Y3J 0.480519 0.726027
262 8PZ 0.480392 0.8
263 FAD 0.480315 0.851852
264 FAS 0.480315 0.851852
265 FDA 0.48 0.833333
266 N6P 0.479592 0.915493
267 GGZ 0.479167 0.825
268 U A 0.478261 0.907895
269 SAH 0.478261 0.74359
270 SAI 0.478261 0.734177
271 A G 0.477876 0.883117
272 NPW 0.477477 0.886076
273 NDP 0.477477 0.921053
274 AAM 0.476744 0.971429
275 C2R 0.47561 0.90411
276 AMZ 0.47561 0.916667
277 A A A 0.474747 0.905405
278 GTP 0.473684 0.92
279 U A G G 0.473684 0.883117
280 SMM 0.473684 0.686047
281 NZQ 0.473214 0.909091
282 TXP 0.473214 0.921053
283 A3S 0.47191 0.810811
284 SFD 0.46875 0.734043
285 AIR 0.468354 0.901408
286 AAT 0.468085 0.707317
287 EEM 0.468085 0.690476
288 J7V 0.466667 0.833333
289 Z5A 0.466667 0.77907
290 7C5 0.466667 0.818182
291 62F 0.465649 0.8625
292 HDV 0.463158 0.893333
293 FAY 0.462121 0.8625
294 A3T 0.461538 0.821918
295 ETB 0.461538 0.833333
296 DCA 0.461538 0.823529
297 A6D 0.46 0.722892
298 A U 0.459459 0.87013
299 GEK 0.459184 0.7375
300 6K6 0.459184 0.930556
301 RFL 0.458647 0.821429
302 NAP 0.458333 0.945205
303 S7M 0.458333 0.690476
304 4YB 0.457944 0.761364
305 WSA 0.454545 0.788235
306 TAP 0.454545 0.907895
307 FNK 0.454545 0.804598
308 COA 0.453782 0.823529
309 0T1 0.453782 0.823529
310 101 0.453488 0.878378
311 XNP 0.452174 0.873418
312 NA0 0.45082 0.932432
313 7RP 0.448276 0.928571
314 GP3 0.446809 0.921053
315 TM1 0.446602 0.77381
316 APU 0.446429 0.894737
317 PUA 0.445378 0.884615
318 V1N 0.443396 0.917808
319 7RA 0.443182 0.957747
320 COS 0.442623 0.804598
321 AMX 0.442623 0.833333
322 30N 0.442623 0.752688
323 CAO 0.442623 0.795455
324 QQY 0.44186 0.815789
325 ACK 0.44186 0.861111
326 649 0.441441 0.744444
327 0UM 0.44 0.698795
328 NHD 0.439655 0.905405
329 CMX 0.439024 0.823529
330 SCO 0.439024 0.823529
331 GCP 0.438776 0.896104
332 8BR 0.438202 0.906667
333 GNH 0.4375 0.907895
334 8Q2 0.4375 0.772727
335 3AD 0.4375 0.805556
336 NVA 2AD 0.43617 0.759494
337 62X 0.435644 0.666667
338 FCX 0.435484 0.795455
339 ACO 0.435484 0.795455
340 FAM 0.435484 0.804598
341 9JJ 0.434783 0.8625
342 GNP 0.434343 0.896104
343 9GM 0.434343 0.896104
344 NMX 0.433071 0.76087
345 MGP 0.43299 0.884615
346 26A 0.432099 0.763158
347 HAX 0.432 0.804598
348 K15 0.431373 0.682353
349 DG1 0.430894 0.921053
350 1DG 0.430894 0.921053
351 QQX 0.430233 0.805195
352 2VA 0.430108 0.8
353 S8M 0.43 0.759494
354 2MC 0.429688 0.769231
355 6G0 0.428571 0.884615
356 P5F 0.428571 0.823529
357 FYN 0.428571 0.823529
358 3KK 0.428571 0.804598
359 A C A C 0.428571 0.848101
360 7L1 0.427419 0.795455
361 FAI 0.426966 0.916667
362 RMB 0.426966 0.873239
363 AS 0.426966 0.833333
364 1RB 0.425287 0.885714
365 CA6 0.425197 0.729167
366 SOP 0.425197 0.804598
367 OXK 0.425197 0.804598
368 MCD 0.425197 0.804598
369 COK 0.425197 0.804598
370 G1R 0.424242 0.907895
371 SXZ 0.423077 0.710843
372 CC5 0.423077 0.816901
373 F2N 0.422535 0.813953
374 EO7 0.422222 0.788235
375 ANZ 0.422018 0.8
376 1VU 0.421875 0.795455
377 CMC 0.421875 0.804598
378 CO6 0.421875 0.804598
379 ZDA 0.421053 0.864865
380 GKE 0.420561 0.884615
381 GDC 0.420561 0.884615
382 GDD 0.420561 0.884615
383 NFD 0.420168 0.883117
384 GSP 0.42 0.873418
385 D3Y 0.42 0.789474
386 MC4 0.419847 0.76087
387 3D1 0.419753 0.773333
388 3L1 0.419753 0.773333
389 FA9 0.41958 0.864198
390 5GP 0.419355 0.906667
391 G 0.419355 0.906667
392 KB1 0.419048 0.698795
393 CAJ 0.418605 0.804598
394 SCD 0.418605 0.823529
395 CMP 0.417582 0.901408
396 2BA 0.417582 0.915493
397 SO8 0.416667 0.789474
398 VRT 0.416667 0.769231
399 N01 0.416667 0.905405
400 IVC 0.415385 0.813953
401 1HE 0.415385 0.786517
402 A1S 0.415385 0.804598
403 BCO 0.415385 0.804598
404 3HC 0.415385 0.813953
405 MLC 0.415385 0.804598
406 NMN AMP PO4 0.415254 0.87013
407 2FA 0.414634 0.813333
408 MGO 0.414141 0.860759
409 3NZ 0.413462 0.782051
410 COO 0.412214 0.804598
411 MCA 0.412214 0.795455
412 YE1 0.412214 0.813953
413 CAA 0.412214 0.813953
414 GAV 0.411765 0.884615
415 PRT 0.411215 0.931507
416 JLN 0.411111 0.890411
417 P2P 0.411111 0.902778
418 ZZB 0.410256 0.77381
419 SP1 0.409091 0.842105
420 RP1 0.409091 0.842105
421 2CP 0.409091 0.795455
422 SCA 0.409091 0.804598
423 103 0.409091 0.837838
424 PAX 0.408 0.829268
425 FAD NBT 0.407143 0.75
426 COW 0.406015 0.795455
427 3CP 0.406015 0.804598
428 IRC 0.406015 0.813953
429 BYC 0.406015 0.804598
430 CA8 0.406015 0.729167
431 1GZ 0.406015 0.795455
432 COF 0.406015 0.786517
433 HGG 0.406015 0.804598
434 2KQ 0.406015 0.786517
435 G2P 0.405941 0.884615
436 SLU 0.404959 0.770115
437 U A C C 0.404959 0.858974
438 RBZ 0.404494 0.849315
439 1CZ 0.404412 0.795455
440 FAQ 0.402985 0.804598
441 BCA 0.402985 0.795455
442 4CA 0.402985 0.795455
443 MTP 0.402439 0.730769
444 8OD 0.402062 0.945205
445 CO7 0.401515 0.804598
446 GRA 0.4 0.804598
447 G2R 0.4 0.884615
448 ENQ 0.4 0.916667
449 CNV FAD 0.4 0.8
450 GMV 0.4 0.896104
451 HXC 0.4 0.786517
452 HF7 0.4 0.893333
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4YDU; Ligand: ADP; Similar sites found with APoc: 49
This union binding pocket(no: 1) in the query (biounit: 4ydu.bio1) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 1ZMT RNO 2.95359
2 3NC9 TR3 2.95359
3 5ZKC 3C0 3.37553
4 1V1A ADP 3.37553
5 1T8U UAP SGN IDS SGN 3.67647
6 1T8U A3P 3.67647
7 2ZMF CMP 3.7037
8 3FYS PLM 3.79747
9 3WBF API 3.79747
10 3WBF NAP 3.79747
11 2J7T 274 3.79747
12 2VMG MBG 3.82166
13 5O0J 8BR 4.21941
14 2AGD UDH 4.21941
15 2I7C AAT 4.59364
16 1UA4 AMP 4.64135
17 5OD2 5ID 5.06329
18 2WOJ ADP ALF 5.06329
19 5W10 CMP 6.15385
20 3TO7 COA 6.32911
21 4WNK 453 6.32911
22 6ALW BNV 7.173
23 6ALW BMJ 7.173
24 6AMI TRP 7.28863
25 1FIQ MTE 8.01688
26 1FIQ SAL 8.01688
27 4RHE FMN 8.13397
28 1RYI FAD 8.43882
29 1RYI GOA 8.43882
30 3ZM6 2GN 8.43882
31 3NRZ HPA 8.53659
32 3NRZ MTE 8.53659
33 1MGP PLM 8.86076
34 1VPV PLM 8.86076
35 3IQE F42 9.2827
36 3HRD MCN 10
37 4LIK CIT 10.1266
38 4YJI TYL 10.5485
39 1PZX PLM 10.9705
40 4WUJ FMN 12.9252
41 1UWK URO 13.0802
42 1UWK NAD 13.0802
43 2C3H GLC GLC 14.2857
44 4KOT CE3 15.4321
45 4EHU ANP 17.7536
46 1WUW TSU 20
47 1ZRH A3P 21.8978
48 4PYA 2X3 22.9814
49 1N62 MCN 29.5181
Pocket No.: 2; Query (leader) PDB : 4YDU; Ligand: ADP; Similar sites found with APoc: 169
This union binding pocket(no: 2) in the query (biounit: 4ydu.bio1) has 24 residues
No: Leader PDB Ligand Sequence Similarity
1 1Q9I FAD 2.53165
2 1Q9I TEO 2.53165
3 2IID PHE 2.62391
4 2IID FAD 2.62391
5 5TS5 FAD 2.62391
6 1FX8 BOG 2.84698
7 2YCH ATP 2.95359
8 2WPF FAD 2.95359
9 2JIG PD2 3.125
10 1P77 ATR 3.30882
11 4GN8 ASO 3.34448
12 5OBU ANP 3.37553
13 2ZGY GDP 3.37553
14 4A62 ANP 3.37553
15 2IU8 PLM 3.47594
16 2E2P ADP 3.67893
17 1NSA BEN 3.79009
18 3WQT ANP 3.79747
19 2W41 ADP 3.79747
20 2QXL ATP 3.79747
21 1BW9 NAD 3.79747
22 4M26 AKG 3.79747
23 6MVU K4V 3.79747
24 1M2Z BOG 3.89105
25 2Z9I GLY ALA THR VAL 4.01235
26 5FPE 3TR 4.21941
27 3LDQ 3P1 4.21941
28 2BUP ADP 4.21941
29 2BUP ATP 4.21941
30 4MO4 ACP 4.21941
31 4M52 M52 4.21941
32 5FPN KYD 4.21941
33 6CB2 OLC 4.43686
34 3LM9 ADP 4.63576
35 3LM9 FRU 4.63576
36 1SAZ ACP 4.64135
37 5WGR FAD 4.66472
38 5AR0 GB8 4.82234
39 4GNI ATP 4.95627
40 1D4D FAD 4.95627
41 6G3R ADP 5
42 4RW3 SHV 5.06329
43 4J56 FAD 5.06329
44 1ZDQ MSM 5.35714
45 2HK9 ATR 5.45455
46 4XH4 PPI 5.48523
47 5O22 C3R 5.48523
48 4XH4 ANP 5.48523
49 1ZEI CRS 5.66038
50 1J71 THR ILE THR SER 5.68862
51 6EOF ADP 5.90717
52 4C3Y FAD 5.90717
53 3QFA FAD 5.90717
54 3G4Q MCH 6.16438
55 3GUZ PAF 6.25
56 6ASY ATP 6.32911
57 5OBY ANP 6.32911
58 5EXW 7DT 6.32911
59 2BRY FAD 6.32911
60 2PHT MAN MAN MAN 6.34921
61 1Q8O MAN MMA 6.34921
62 2GNM MAN 6.34921
63 2PHU MAN MAN 6.34921
64 2GND MAN 6.34921
65 2PHR MAN MAN BMA MAN 6.34921
66 1Q8V MAN MAN 6.34921
67 2PHF MAN MAN BMA MAN 6.34921
68 2PHX MAN MAN MAN MAN 6.34921
69 1H74 ILE 6.41892
70 3WUR O4B 6.43275
71 5W1E PHB 6.75105
72 5G3U FDA 6.75105
73 4TXI FAD 6.75105
74 3E3U NVC 7.1066
75 4JNE ATP 7.173
76 3EF0 ALF 7.173
77 3FAL REA 7.59494
78 5HTX ADP 8.01688
79 4BV6 FAD 8.01688
80 1T0S BML 8.13953
81 3VGL ANP 8.16327
82 4ZLU 4PW 8.2774
83 4ZLU ADP 8.2774
84 1GPM CIT 8.45481
85 4CZG QH3 8.62069
86 4CZG ADP 8.62069
87 3ZVS MLI 8.75
88 1COY FAD 9.0379
89 6H3O FAD 9.0379
90 2F7A BEZ 9.05172
91 4FBL SPD 9.25267
92 1T9D PYD 9.2827
93 3ITJ FAD 9.32945
94 3FXU TSU 9.5082
95 1O8B ABF 9.58904
96 2CE7 ADP 9.70464
97 5LJW ANP 9.91254
98 4DHY GLC 9.91254
99 5EOU ATP 9.94624
100 2DTJ THR 10.1124
101 4B9Q ATP 10.1266
102 4IV9 TSR 10.2041
103 3MN7 ATP 10.5485
104 3MN6 ATP 10.5485
105 3MN9 ATP 10.5485
106 3U4L ATP 10.5485
107 3CIP ATP 10.5485
108 2QWO ADP 10.8696
109 4Z94 ATP 10.9705
110 4CBX ATP 10.9705
111 1SQK ADP 10.9705
112 4B1X ATP 10.9705
113 4PL8 ATP 10.9705
114 2A3Z ATP 10.9705
115 2PAV ATP 10.9705
116 2A42 ATP 10.9705
117 3SJH ATP 10.9705
118 2A40 ATP 10.9705
119 4B1V ATP 10.9705
120 4B1V LAB 10.9705
121 2FXU ATP 10.9705
122 1YAG ATP 10.9705
123 2V51 ATP 10.9705
124 4B1W ATP 10.9705
125 5YEE ATP 10.9705
126 4PKI ATP 10.9705
127 1KXP ATP 10.9705
128 4H03 LAR 10.9705
129 2Q97 ATP 10.9705
130 4CBU ATP 10.9705
131 2D1K ATP 10.9705
132 3TDC 0EU 10.9705
133 3SJH LAR 10.9705
134 4PL7 ATP 10.9705
135 4H03 ATP 10.9705
136 5ZZB ATP 11.0294
137 1TUU AMP 11.0787
138 1TUU ADP 11.0787
139 1TUU PIS 11.0787
140 3NRR D16 11.0787
141 3AYI HCI 11.0787
142 3AYI FAD 11.0787
143 2FF6 ATP 11.3333
144 2FF3 ATP 11.3333
145 4A2B AGS 11.3703
146 4LCQ URQ 11.8143
147 2D0O ADP 12
148 3PH4 AOS 12.426
149 2V7Y ADP 13.0802
150 1MUU SUC 13.0802
151 3QFU ADP 13.1195
152 5ZZA ATP 13.2231
153 3TTC ADP 13.7026
154 3HEE R5P 14.094
155 4BGB ADP 14.1538
156 4PKG ATP 14.5161
157 4EFH ADP 15.1515
158 3U9Z ADP 15.5172
159 1LVW TYD 16.4557
160 5C1M OLC 20
161 3MN5 ATP 21.0526
162 2PBD ATP 23.2558
163 4OGQ 7PH 24.1379
164 1FQJ ALF 25.1701
165 3VET TOY 33.5277
166 3VET ADP 33.5277
167 3VET CP 33.5277
168 5YPU ATP 40.9091
169 5LY3 ADP 43.75
Pocket No.: 3; Query (leader) PDB : 4YDU; Ligand: ADP; Similar sites found with APoc: 24
This union binding pocket(no: 3) in the query (biounit: 4ydu.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
1 2OEM 1AE 2.95359
2 2Z3U CRR 3.37553
3 6F97 FAD 3.37553
4 1JG0 UMP 3.40909
5 1GPE FAD 3.49854
6 1ON3 DXX 3.79009
7 5HCF BGC 3.79747
8 4LSJ LSJ 3.87597
9 3G5S FAD 4.64135
10 3I7S PYR 4.64135
11 1PFK ADP 5.06329
12 2O1C PPV 5.33333
13 1NAA ABL 5.48523
14 2J83 BAT 5.90717
15 2WBV SIA 8.99471
16 4YVN EBS 9.62099
17 2HFK E4H 10.1266
18 3C8F MT2 11.0204
19 5W7B MYR 12.766
20 2UXR ICT 12.828
21 3KIF GDL 14.1509
22 2RC8 DSN 15.3061
23 3ZCB ATP 17.7419
24 1APZ ASP 18.5185
Pocket No.: 4; Query (leader) PDB : 4YDU; Ligand: ADP; Similar sites found with APoc: 20
This union binding pocket(no: 4) in the query (biounit: 4ydu.bio2) has 14 residues
No: Leader PDB Ligand Sequence Similarity
1 3O9Z NAD 2.5641
2 3O9Z AKG 2.5641
3 5B4B LP5 3.79747
4 2PT9 S4M 4.04984
5 5XJ7 87O 4.47761
6 4X9X OLA 4.68227
7 1VKJ A3P 4.91228
8 3Q9N COA 5.06329
9 1RX0 2MC 5.53936
10 1V97 MTE 5.90717
11 3ET1 ET1 6.18557
12 4A1O JLN 6.75105
13 3I9L N1C 6.97674
14 2YC5 6BC 7.89474
15 1RPN NDP 9.2827
16 1U7Z PMT 9.29204
17 2B8W ALF 5GP 10.9705
18 1I1D 16G 11.1801
19 1I1D COA 11.1801
20 1RM6 PCD 16.4557
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