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Receptor
PDB id Resolution Class Description Source Keywords
4LIT 2.4 Å EC: 1.14.11.- STRUCTURE OF YCFD A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COL COMPLEX WITH COBALT AND 2-OXOGLUTARATE. ESCHERICHIA COLI JMJC DOMAIN DIOXYGENASE HYDROXYLATION OXIDOREDUCTASE
Ref.: RIBOSOMAL OXYGENASES ARE STRUCTURALLY CONSERVED FRO PROKARYOTES TO HUMANS. NATURE V. 509 422 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
AKG A:502;
Valid;
none;
submit data
146.098 C5 H6 O5 C(CC(...
CO A:501;
Part of Protein;
none;
submit data
58.933 Co [Co+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4LIT 2.4 Å EC: 1.14.11.- STRUCTURE OF YCFD A RIBOSOMAL OXYGENASE FROM ESCHERICHIA COL COMPLEX WITH COBALT AND 2-OXOGLUTARATE. ESCHERICHIA COLI JMJC DOMAIN DIOXYGENASE HYDROXYLATION OXIDOREDUCTASE
Ref.: RIBOSOMAL OXYGENASES ARE STRUCTURALLY CONSERVED FRO PROKARYOTES TO HUMANS. NATURE V. 509 422 2014
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 31 families.
1 4LIT - AKG C5 H6 O5 C(CC(=O)O)....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 19 families.
1 4LIT - AKG C5 H6 O5 C(CC(=O)O)....
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 17 families.
1 4LIT - AKG C5 H6 O5 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: AKG; Similar ligands found: 7
No: Ligand ECFP6 Tc MDL keys Tc
1 AKG 1 1
2 SIN 0.526316 0.833333
3 OOG 0.5 0.947368
4 69O 0.458333 0.714286
5 2IT 0.423077 0.615385
6 SHF 0.416667 0.666667
7 3PY 0.409091 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4LIT; Ligand: AKG; Similar sites found with APoc: 404
This union binding pocket(no: 1) in the query (biounit: 4lit.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
1 4ITH RCM 1.02041
2 3OPT AKG 1.34048
3 1KPH 10A 1.39373
4 1M15 ARG 1.40056
5 1M15 ADP 1.40056
6 4BG4 ADP 1.40449
7 3FW9 SLX 1.4742
8 1PN0 FAD 1.4742
9 1PN0 IPH 1.4742
10 5F3I 5UJ 1.66667
11 1I06 TZL 1.66667
12 5C3R HMU 1.74927
13 5C3R AKG 1.74927
14 5IXG OTP 1.77515
15 1OPK P16 1.81818
16 5NCJ SIN 1.86567
17 6EOZ 58K 1.94805
18 6EOZ AKG 1.94805
19 5JFS 6K0 1.94805
20 2ET1 GLV 1.99005
21 4D06 NAR 2.12014
22 4V24 GYR 2.15633
23 2A4W BLM 2.17391
24 3IGO ANP 2.2113
25 3ZDS HMQ 2.2113
26 3ZDS M8O 2.2113
27 3ZDS OMD 2.2113
28 4LOO SB4 2.21607
29 4IGQ THR M3L GLN 2.22222
30 4IGQ OGA 2.22222
31 2WBP ZZU 2.23464
32 2WBP SIN 2.23464
33 3OYW TDG 2.23881
34 5AMV ADA ADA ADA 2.25564
35 3NW7 LGV 2.28013
36 4ZS4 ATP 2.28013
37 4WW8 VD9 2.28137
38 2WQP WQP 2.29226
39 4QDC ASD 2.30769
40 4BG1 IVL 2.32558
41 4BG1 OGA 2.32558
42 2YG2 S1P 2.32558
43 2YG2 FLC 2.32558
44 3PG7 PTY 2.34375
45 1S20 TLA 2.35294
46 3B6R ADP 2.3622
47 5Y72 DST 2.38806
48 4NAO AKG 2.45399
49 4KYS VIB 2.457
50 5KD6 6C7 2.457
51 5BRT CH9 2.457
52 2OBD 2OB 2.457
53 5L6G XYP 2.457
54 5KD6 LBU 2.457
55 1DRY AAG 2.46914
56 1DRY AKG 2.46914
57 5IQT AKG 2.53968
58 5IQT 6CU 2.53968
59 1T27 PCW 2.58303
60 5HES 032 2.60586
61 1Y0G 8PP 2.6178
62 3E8N ATP 2.6393
63 3E8N VRA 2.6393
64 4GJ3 0XP 2.64901
65 6GIN IR2 2.65781
66 4IAW LIZ 2.65957
67 1EWF PC1 2.7027
68 5MRH Q9Z 2.7027
69 5LNQ CAA 2.7027
70 4NZN ANP 2.72727
71 4NZN 2OU 2.72727
72 6GQM F8H 2.7439
73 5VC5 96M 2.76817
74 5L9B AKG 2.77778
75 5L9V OGA 2.77778
76 5QIN J2V 2.8481
77 1M13 HYF 2.8481
78 2CWH NDP 2.91545
79 5DQ8 FLF 2.91667
80 1VA6 ADP 2.9484
81 3O2K DST 2.9484
82 3SLS ANP 2.96053
83 1NKI PPF 2.96296
84 3VHE 42Q 3.06407
85 4ASE AV9 3.11615
86 2WEI VGG 3.13589
87 4U0I 0LI 3.1746
88 4WOE ADP 3.1941
89 2A1X AKG 3.24675
90 1LN1 DLP 3.27103
91 1VJY 460 3.30033
92 2A1L PCW 3.33333
93 1ULE GLA GAL NAG 3.33333
94 4GN8 ASO 3.34448
95 4ZU4 4TG 3.37838
96 2DKH 3HB 3.4398
97 4RDL FUC GAL NDG FUC 3.4398
98 3LPF Z77 3.4398
99 5VCV 1N1 3.53698
100 3VPD ANP 3.55872
101 1EYE PMM 3.57143
102 4CSV STI 3.63636
103 5SVV FMN 3.64964
104 1NX4 AKG 3.663
105 4G31 0WH 3.67893
106 1N07 FMN 3.68098
107 1LRH NLA 3.68098
108 1U6R ADP 3.68421
109 6FXR AKG 3.6855
110 4KBA 1QM 3.6855
111 2OJW ADP 3.6855
112 5W4W 9WG 3.6855
113 4QAC KK3 3.68664
114 3H7J PPY 3.7037
115 5DEY 59T 3.7037
116 1R6W 164 3.72671
117 3THR C2F 3.75427
118 3FW3 ETS 3.7594
119 3QP8 HL0 3.80435
120 5A89 ADP 3.84615
121 5A89 FMN 3.84615
122 4PSB GA3 3.87097
123 2Z6C FMN 3.87597
124 4MPO AMP 3.92157
125 4ONA UW1 3.9312
126 2HI4 BHF 3.9312
127 3U6W KIV 3.9312
128 5W1E PHB 3.9312
129 5IVE 6E8 3.93939
130 1KDK DHT 3.9548
131 2GJN NIS 3.96341
132 2GJN FMN 3.96341
133 1OIK AKG 3.98671
134 1OIK C26 3.98671
135 1OIJ AKG 3.98671
136 2CM4 RCL 4
137 6D6L FY4 4.11765
138 4GCZ FMN 4.15584
139 1PK8 ATP 4.1769
140 2WKQ FMN 4.21687
141 4K3H 1OM 4.23729
142 5TZO 7V7 4.25532
143 5M3Z PY6 4.27136
144 5M3Z NLE 4.27136
145 4M1U A2G MBG 4.28571
146 3VQ2 LP4 LP5 MYR DAO 4.29043
147 3PUA OGA 4.33673
148 5YJS SAL 4.35897
149 3W8X FTK 4.4226
150 4U0W 16G 4.47154
151 3MPB FRU 4.47154
152 2OG7 SIN 4.48179
153 2R5V HHH 4.48179
154 2YGN PCF 4.48718
155 1YKD CMP 4.52261
156 5MBC FMN 4.53258
157 1W8S FBP 4.56274
158 4QM9 CYS 4.62428
159 1Q6O LG6 4.62963
160 5O9W AKG 4.63215
161 2H8H H8H 4.6683
162 4I9A NCN 4.6683
163 2RKV COA 4.6683
164 5X7Q GLC GLC GLC GLC 4.6683
165 6FE1 V14 4.66926
166 3T50 FMN 4.6875
167 4OOE NDP 4.70297
168 4OOE FOM 4.70297
169 2GU8 796 4.74777
170 3C2O NTM 4.7619
171 1SDW IYT 4.77707
172 1S4M LUM 4.77816
173 4XV1 904 4.79452
174 3SXS PP2 4.85075
175 2RDQ AKG 4.86111
176 3VRY B43 4.914
177 2GJ5 VD3 4.93827
178 3KFF ZBT 4.93827
179 3KFF XBT 4.93827
180 3NNF AKG 4.94186
181 1OS7 AKG 4.947
182 1OS7 TAU 4.947
183 1YRX FMN 4.95868
184 4MP8 MLI 5.01475
185 4MP8 NAD 5.01475
186 4MNS 2AX 5.03145
187 4CQE CQE 5.03597
188 1ZZ7 S0H 5.05051
189 3SCH TB6 5.05051
190 5IH9 6BF 5.07463
191 4YGF AZM 5.12821
192 1GQG DCD 5.14286
193 3GL0 HXX 5.15759
194 4FHD 0TT 5.16304
195 4FHD EEM 5.16304
196 2YNE YNE 5.20833
197 2YNE NHW 5.20833
198 4P5Z Q7M 5.26316
199 4YRD 3IT 5.29248
200 2FB3 GTP 5.29412
201 1F5F DHT 5.36585
202 5TUF TDC 5.40541
203 5TUF FAD 5.40541
204 1QIN GIP 5.46448
205 1AUX AGS 5.46624
206 4QMN DB8 5.48387
207 2ARC ARA 5.4878
208 1I7L ATP 5.50162
209 4BJ8 BTN 5.55556
210 5MJA 7O3 5.57377
211 4IJP 1EH 5.58659
212 2XK9 XK9 5.59006
213 2IRY DGT 5.61056
214 3SAO NKN 5.625
215 3SAO DBH 5.625
216 1GT4 UNA 5.66038
217 1DZK PRZ 5.73248
218 2ABS ACP 5.74413
219 1UNB AKG 5.78778
220 1UNB PN1 5.78778
221 3B1Q NOS 5.82822
222 3WW2 SF6 5.85938
223 3WW2 LPK 5.85938
224 3GC8 B45 5.94595
225 6ES0 BW8 5.99369
226 5Y80 IRE 6.08108
227 4EES FMN 6.08696
228 3BXO UPP 6.14251
229 4Y8D 49J 6.17647
230 4EWH T77 6.18182
231 3PDT ADP 6.18182
232 5LUN ARG 6.25
233 5LUN OGA 6.25
234 5EOB 5QQ 6.26959
235 1KGI T4A 6.29921
236 1NGP NPA 6.30631
237 3E85 BSU 6.32911
238 5VNF VAL THR SER VAL VAL 6.36943
239 2GC0 PAN 6.38298
240 3LKJ LKJ 6.38298
241 1MJJ HAL 6.39269
242 2JLD AG1 6.42857
243 5HV0 AKG 6.45161
244 3EKK GS2 6.51466
245 1NYW DAU 6.59898
246 1ZHX HC3 6.63391
247 3G5D 1N1 6.64336
248 5HCY 60D 6.64653
249 2YAK OSV 6.66667
250 4H6B 10X 6.66667
251 4H6B 10Y 6.66667
252 5YBN AKG 6.6879
253 5EZU MYR 6.74157
254 4XAC AKG 6.74603
255 1J3R 6PG 6.84211
256 4M26 SIN 6.86813
257 4M26 AKG 6.86813
258 4M26 ZZU 6.86813
259 2ZMF CMP 6.87831
260 1TYU GLA MAN RAM TYV GLA MAN RAM TYV 6.87961
261 5O5Y GLC 6.87961
262 2HZQ STR 6.89655
263 2WLG SOP 6.97674
264 1GP6 QUE 7.02247
265 1GP6 DH2 7.02247
266 1GP6 SIN 7.02247
267 4B1M FRU FRU 7.02703
268 3H22 B53 7.07071
269 4RF7 ARG 7.12531
270 2Y6O 1N1 7.2165
271 5E2N V14 7.22433
272 4XCB HY0 7.27969
273 4XCB AKG 7.27969
274 3TTI KBI 7.37101
275 2HK5 1BM 7.40741
276 1ZB6 DIN 7.49186
277 1ZB6 GST 7.49186
278 5A5W GUO 7.50988
279 6CLV 6MB 7.56014
280 1REQ DCA 7.61671
281 4X6F 3XU 7.61905
282 1P0Z FLC 7.63359
283 2NNQ T4B 7.63359
284 2Y0I AKG 7.67045
285 3PP0 03Q 7.69231
286 5JKG 6LF 7.71704
287 3P3N AKG 7.73639
288 4B7E OGA 7.73639
289 2XUM OGA 7.73639
290 2WA4 069 7.73639
291 3RGA LSB 7.77385
292 3N0Y APC 7.82123
293 4B1L FRU 7.87879
294 1QFT HSM 8
295 4C2V YJA 8.07018
296 4WUP 3UF 8.07692
297 5U98 1KX 8.08081
298 5C9J STE 8.08081
299 1ODM ASV 8.1571
300 1OLM VTQ 8.18859
301 4POW OP1 8.30189
302 5EYK 5U5 8.33333
303 5GLT BGC GAL NAG GAL 8.4507
304 2WT2 GAL NAG GAL NAG GAL NAG 8.45481
305 2JIG PD2 8.48214
306 5FBN 5WF 8.48709
307 5T8O 76Z 8.59599
308 4ZSI 4R1 8.77193
309 4ZSI GLP 8.77193
310 3WVS RRM 8.84521
311 2IXC TRH 8.91089
312 4P25 FUC GAL NAG FUC 8.9404
313 1OPB RET 8.95522
314 5DJT FMN 8.96552
315 5DJU FMN 8.96552
316 5EFW FMN 8.96552
317 5HA0 LTD 8.97436
318 2I6A 5I5 9.09091
319 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 9.18367
320 1M6P M6P 9.21053
321 5BU3 4W9 9.23913
322 4CCO OGA 9.33661
323 2Z77 HE7 9.35252
324 1Y7P RIP 9.41704
325 4CCK OGA 9.58231
326 4Y3O OGA 9.58231
327 4CCN OGA 9.58231
328 3E7O 35F 9.58231
329 4J7Q B7N 9.60961
330 4K55 H6P 9.67742
331 4RYV ZEA 9.67742
332 1DMY AZM 9.67742
333 3A28 NAD 9.68992
334 3STD MQ0 9.69697
335 5W10 CMP 9.74359
336 2P7Q GG6 9.77444
337 5JSP DQY 9.95025
338 4J25 OGA 10.0437
339 2YKL NLD 10.1852
340 5UR1 YY9 10.2894
341 4Q0P 0MK 10.3846
342 5N2D 8J8 10.4167
343 2HFN FMN 10.4575
344 2OFV 242 10.4693
345 3MTX PGT 10.596
346 4PAB THG 10.8108
347 5NIU 8YZ 10.9375
348 5C5T AKG 10.9649
349 4G2R H1L 10.9937
350 5I0U DCY 11
351 4WVO 3UZ 11.0497
352 4F7E 0SH 11.2245
353 3L9R L9R 11.2245
354 3L9R L9Q 11.2245
355 4R3U 3KK 11.3022
356 4R3U 3HC 11.3022
357 5CJF 520 11.4695
358 1ST0 GTG 11.5727
359 4ZU5 THM 11.8056
360 2PR5 FMN 12.1212
361 2V0U FMN 12.3288
362 3P7N FMN 12.4031
363 3T4L ZEA 12.5926
364 2P1M IHP 12.7764
365 6GG9 FMN 12.963
366 2CDO GAL AAL GAL AAL GAL AAL 13.125
367 2E56 MYR 13.1944
368 5FPX GLY SER SER HIS HIS HIS HIS HIS 13.2743
369 2FTB OLA 13.6
370 4OJ8 2TQ 13.9932
371 4OJ8 AKG 13.9932
372 5TFZ 7BC 14
373 2C49 ADN 14.2384
374 4Y24 TD2 14.2857
375 6CZI 38E 14.2857
376 2OVD DAO 14.8352
377 3E2M E2M 15.1351
378 4MLO PAM 15.5797
379 1X0P FAD 16.0839
380 3STK PLM 16.6667
381 3G08 FEE 17.1717
382 3RUG DB6 17.1717
383 3SCM LGN 17.1717
384 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 17.1717
385 3QUZ QUV 17.1717
386 1BHX ASP PHE GLU GLU ILE 17.6871
387 5XEG AKG 18.1818
388 5V3D FCN 18.6207
389 2YJ0 420 18.8406
390 2BYC FMN 18.9781
391 5FLJ QUE 19.3548
392 4XIZ LPP 20
393 4WO4 JLS 20
394 5KEW 6SB 20.1389
395 5FKP 6UL 22.7273
396 3EM0 CHD 23.913
397 5JWP AKG 26.3158
398 4QXB OGA 26.6667
399 1H2M OGA 26.9231
400 6F4T OGA 27.0588
401 2YBP 2HG 33.3333
402 1QY1 PRZ 33.3333
403 1H2K OGA 34.1463
404 2OS2 OGA 36.3636
Pocket No.: 2; Query (leader) PDB : 4LIT; 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: 2) in the query (biounit: 4lit.bio1) has 13 residues
No: Leader PDB Ligand Sequence Similarity
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