-->
Receptor
PDB id Resolution Class Description Source Keywords
5K53 1.8 Å EC: 1.-.-.- CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM OSCILLATORIA SP. KNUA011 OSCILLATORIA SP. FERRITIN-LIKE DI-IRON PROTEIN METAL BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGEN LIMNOTHRIX SP. KNUA012 AND OSCILLATORIA SP. KNUA011 BIOCHEM.BIOPHYS.RES.COMMUN. V. 477 395 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:501;
A:500;
B:500;
B:501;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
55.845 Fe [Fe+3...
STE A:502;
B:502;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0;
Atoms found LESS than expected: % Diff = 0;
submit data
284.477 C18 H36 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K53 1.8 Å EC: 1.-.-.- CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM OSCILLATORIA SP. KNUA011 OSCILLATORIA SP. FERRITIN-LIKE DI-IRON PROTEIN METAL BINDING PROTEIN
Ref.: CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGEN LIMNOTHRIX SP. KNUA012 AND OSCILLATORIA SP. KNUA011 BIOCHEM.BIOPHYS.RES.COMMUN. V. 477 395 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 318 families.
1 5K53 - STE C18 H36 O2 CCCCCCCCCC....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 280 families.
1 5K53 - STE C18 H36 O2 CCCCCCCCCC....
2 4RC7 - PL3 C16 H34 O CCCCCCCCCC....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4PG1 - Y39 C13 H24 O2 CCCCCCCCC[....
2 4PGK - Y69 C17 H34 O4 CCOCCOCCOC....
3 4PGI - Y69 C17 H34 O4 CCOCCOCCOC....
4 4TW3 - STE C18 H36 O2 CCCCCCCCCC....
5 4PG0 - Y39 C13 H24 O2 CCCCCCCCC[....
6 4KVS - 6NA C6 H12 O2 CCCCCC(=O)....
7 4KVQ - PLM C16 H32 O2 CCCCCCCCCC....
8 4KVR - 6NA C6 H12 O2 CCCCCC(=O)....
9 5K53 - STE C18 H36 O2 CCCCCCCCCC....
10 4RC7 - PL3 C16 H34 O CCCCCCCCCC....
11 4QUW - PL3 C16 H34 O CCCCCCCCCC....
12 4RC5 - PL3 C16 H34 O CCCCCCCCCC....
13 4RC8 - STE C18 H36 O2 CCCCCCCCCC....
14 5K52 - OCD C18 H36 O CCCCCCCCCC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: STE; Similar ligands found: 62
No: Ligand ECFP6 Tc MDL keys Tc
1 MYR 1 1
2 EW8 1 1
3 TDA 1 1
4 F15 1 1
5 PLM 1 1
6 STE 1 1
7 X90 1 1
8 DAO 1 1
9 KNA 1 1
10 DCR 1 1
11 F23 1 1
12 11A 1 1
13 DKA 1 1
14 OCA 0.956522 1
15 SHV 0.833333 0.952381
16 KTC 0.793103 0.875
17 AZ1 0.73913 0.64
18 6NA 0.72 0.904762
19 ELA 0.71875 0.954545
20 OLA 0.71875 0.954545
21 NER 0.71875 0.954545
22 VCA 0.666667 0.954545
23 PAM 0.666667 0.954545
24 PML 0.625 0.6
25 3LA 0.606061 0.8
26 LEA 0.6 0.809524
27 MYZ 0.588235 0.909091
28 12H 0.586207 0.615385
29 ODD 0.567568 0.913043
30 BRC 0.566667 0.666667
31 14V 0.555556 0.740741
32 M12 0.545455 0.869565
33 14U 0.542857 0.703704
34 EIC 0.538462 0.913043
35 EOD 0.538462 0.7
36 D0G 0.5 0.954545
37 BMJ 0.5 0.954545
38 BNV 0.5 0.954545
39 BUA 0.48 0.666667
40 RCL 0.468085 0.84
41 FTT 0.459459 0.807692
42 HXD 0.459459 0.807692
43 56S 0.459459 0.653846
44 ODT 0.452381 0.782609
45 3X1 0.444444 0.818182
46 LNL 0.44186 0.826087
47 9J6 0.441176 0.666667
48 OOA 0.441176 0.76
49 CUY 0.435897 0.68
50 6UL 0.435897 0.68
51 CNS 0.435897 0.68
52 5UF 0.432432 0.807692
53 243 0.428571 0.807692
54 1QW 0.418605 0.606061
55 GYM 0.418605 0.606061
56 O8N 0.413793 0.75
57 1DO 0.413793 0.75
58 PL3 0.413793 0.75
59 OC9 0.413793 0.75
60 DE1 0.413793 0.75
61 F09 0.413793 0.75
62 T25 0.403846 0.677419
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K53; Ligand: STE; Similar sites found with APoc: 377
This union binding pocket(no: 1) in the query (biounit: 5k53.bio2) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1NU4 MLA None
2 1UO5 PIH None
3 1JGS SAL None
4 1XXA ARG None
5 1B4B ARG None
6 5IJJ I6P None
7 5NNT DPV None
8 4WG0 CHD None
9 1MT1 AG2 None
10 2ZFZ ARG None
11 1G27 BB1 None
12 5N8V KZZ None
13 5ET3 60C None
14 6CAY ERG None
15 2GBB CIT None
16 5C1M OLC 0.763359
17 5C1M CLR 0.763359
18 2I0G I0G 0.77821
19 3OKI OKI 1.28755
20 2HFN FMN 1.30719
21 5FS0 5JC 1.4218
22 4WGF HX2 1.46341
23 4NAT ADP 1.875
24 2BCG GER 1.9084
25 3X01 AMP 1.9084
26 2P4Y C03 1.9084
27 3FUR Z12 1.9084
28 3KDU NKS 1.9084
29 3G9E RO7 1.9084
30 6BMS POV 1.9084
31 1H82 FAD 1.9084
32 6BMS PLM 1.9084
33 2HFP NSI 1.9084
34 1H82 GZZ 1.9084
35 5OKL PAM 1.9084
36 4UP5 94W 2.0202
37 5URY PAM 2.05479
38 4EKQ NPO 2.13904
39 1I0B PEL 2.29008
40 2WH8 II2 2.29008
41 1SR7 MOF 2.3166
42 4OAR 2S0 2.32558
43 4V3I ASP LEU THR ARG PRO 2.33463
44 2AX9 BHM 2.34375
45 1YOK P6L 2.34375
46 2YLD CMO 2.3622
47 3WYJ H78 2.37154
48 1L0I PSR 2.5641
49 5NM7 GLY 2.63158
50 4URN NOV 2.66667
51 6BR9 PGV 2.67176
52 2HHP FLC 2.67176
53 6BR9 6OU 2.67176
54 2RH1 CLR 2.67176
55 4ORM 2V6 2.67176
56 4ORM FMN 2.67176
57 4ORM ORO 2.67176
58 2Q8G AZX 2.67176
59 5X20 AOT 2.67176
60 3NY4 SMX 2.67176
61 3RWP ABQ 2.67176
62 5HYR EST 2.71318
63 4MGA 27L 2.7451
64 4MGD 27N 2.7451
65 4TUZ 36J 2.7451
66 5AAV GW5 2.77778
67 4TV1 36M 2.78884
68 2QE4 JJ3 2.82258
69 5X3R 7Y3 2.92683
70 2BHW NEX 3.01724
71 2BHW XAT 3.01724
72 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 3.04348
73 5LX9 OLB 3.05344
74 2GWH PCI 3.05344
75 4OMJ 2TX 3.05344
76 1XQP 8HG 3.125
77 4MNS 2AX 3.14465
78 5A4W QCT 3.30189
79 4XU6 TDA 3.33333
80 5W7B MYR 3.43511
81 5B4B LP5 3.43511
82 2XN5 FUN 3.43511
83 4X8D AVI 3.43511
84 4UMJ BFQ 3.43511
85 3R9V DXC 3.43511
86 2XN3 ID8 3.43511
87 3G5N PB2 3.43511
88 1XX4 BAM 3.44828
89 5HCN DAO 3.44828
90 5OFW 9TW 3.58744
91 3E85 BSU 3.79747
92 4YC9 4C1 3.80435
93 5E58 CPZ 3.81679
94 1GNI OLA 3.81679
95 4DE3 DN8 3.81679
96 3SQP 3J8 3.81679
97 5XJN 88L 3.81679
98 1YUC EPH 3.92157
99 5KBE IPH 3.93013
100 5L7G LYS SER LEU LEU GLN GLN LEU LEU THR GLU 3.93443
101 4F4S EFO 3.94737
102 3KP6 SAL 3.97351
103 5UC9 MYR 3.9823
104 2XRH NIO 4
105 5VRH OLB 4.02299
106 4QWT ACD 4.02299
107 6D28 NEC 4.0293
108 2IYG FMN 4.03226
109 6GL8 F3Q 4.06977
110 5N53 8NB 4.10256
111 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 4.1841
112 4G86 BNT 4.19847
113 5EW9 5VC 4.19847
114 5OLK DTP 4.19847
115 1M5B BN1 4.19847
116 2Q2Y ADP 4.19847
117 2Q2Y MKR 4.19847
118 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 4.19847
119 1Z6T ADP 4.19847
120 5KAU RHQ 4.24242
121 4LSJ LSJ 4.26357
122 1M2Z BOG 4.28016
123 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 4.30464
124 5LGA 6VH 4.33333
125 5E7V M7E 4.33333
126 5M37 9SZ 4.34783
127 4DOO DAO 4.39024
128 1N8V BDD 4.46429
129 5XJ7 87O 4.47761
130 4RYV ZEA 4.51613
131 3E8T UQ8 4.54545
132 2OYH GLY HIS ARG PRO 4.54545
133 1TV5 N8E 4.58015
134 1XMY ROL 4.58015
135 4LY9 1YY 4.58015
136 4LY9 S6P 4.58015
137 3GZ9 D32 4.58015
138 3G58 988 4.58015
139 3NB0 G6P 4.58015
140 5U0L 8YP 4.58015
141 3L9R L9R 4.58015
142 3UG4 AHR 4.58015
143 1XM4 PIL 4.58015
144 6C1R EFD 4.58015
145 1XMU ROF 4.58015
146 3L9R L9Q 4.58015
147 3RDE OYP 4.58015
148 4Y9J UCC 4.58015
149 5EEH P9P 4.58015
150 4O1Z MXM 4.58015
151 5KOR GDP 4.58015
152 1XW6 GSH 4.58716
153 2Z9I GLY ALA THR VAL 4.62963
154 4KBS PX2 4.65116
155 3F8C HT1 4.7619
156 5X13 HC4 4.78723
157 3AQT RCO 4.89796
158 6CB2 OLC 4.96183
159 3B9Z CO2 4.96183
160 4MRP GSH 4.96183
161 2HZL PYR 4.96183
162 1ZPD CIT 4.96183
163 3KAL HGS 4.96183
164 5CX6 CDP 4.96183
165 5NI5 8YB 4.96183
166 6ESN BWE 4.96183
167 2BW7 APC 5.02283
168 5NTW 98N 5.05837
169 4JE7 BB2 5.07614
170 5CHR 4NC 5.10949
171 5MTE BB2 5.10949
172 3B6C SDN 5.12821
173 3GAC ENO 5.12821
174 3KXC PLM 5.15464
175 1R6N 434 5.21327
176 3LN0 52B 5.34351
177 3O01 DXC 5.34351
178 5V3Y 5V8 5.34351
179 4DXJ 0M9 5.34351
180 4Q86 AMP 5.34351
181 4ZW3 4S9 5.34351
182 5IKR ID8 5.34351
183 4B9E FAH 5.34351
184 2P1C GG3 5.34351
185 5WKR NAR 5.38117
186 5UC4 83S 5.45455
187 5NTP 98E 5.46218
188 1X0P FAD 5.59441
189 5IXK 6EW 5.70175
190 1FX8 BOG 5.72519
191 3TDC 0EU 5.72519
192 6B21 C9V 5.72519
193 2IHU TP9 5.72519
194 3MBG FAD 5.7554
195 3WUR O4B 5.84795
196 1D5Z ACE ALC ARG ALA ODA SER LEU NH2 5.85774
197 2F2G HMH 5.88235
198 2Q4X HMH 5.88235
199 4LWU 20U 5.88235
200 1QSM ACO 5.92105
201 4UCC ZKW 6.00858
202 1YC4 43P 6.06061
203 5IM3 DTP 6.10687
204 6DIO CIT 6.10687
205 4WX0 HXD 6.10687
206 2XXP DSL 6.10687
207 2V95 HCY 6.10687
208 1DTL BEP 6.21118
209 1Y4Z PCI 6.22222
210 2W3L DRO 6.25
211 4P6X HCY 6.27451
212 1NF8 BOG 6.28019
213 3O55 FAD 6.4
214 3HP9 CF1 6.48855
215 3VRV YSD 6.48855
216 2OBD PCW 6.48855
217 6BMM OLB 6.48855
218 1DB1 VDX 6.48855
219 1EWF PC1 6.48855
220 4OKD GLC GLC GLC 6.48855
221 1M13 HYF 6.64557
222 1NRL SRL 6.64557
223 1N83 CLR 6.66667
224 5EK3 5PK 6.87023
225 2Q4G CIT 6.87023
226 2ZCQ B65 6.87023
227 3JUQ AKD 7.02703
228 3JUQ AJD 7.02703
229 1LEK GLU GLN TYR LYS PHE TYR SER VAL 7.07071
230 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 7.07071
231 1FO0 ILE ASN PHE ASP PHE ASN THR ILE 7.07071
232 4OIV XX9 7.07965
233 3E3U NVC 7.1066
234 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 7.25191
235 5MBC FMN 7.25191
236 2FV5 541 7.27969
237 3IIS PID 7.28477
238 5DCH 1YO 7.29167
239 3PVT 3HC 7.33591
240 6CHP F0Y 7.45342
241 1XZ3 ICF 7.47126
242 5LWY OLB 7.47664
243 3GF2 SAL 7.53425
244 3B99 U51 7.63359
245 3WFD AXO 7.63359
246 5Z3I ADE 7.63359
247 3FAL REA 7.85124
248 2VWA PTY 7.92079
249 3G08 FEE 8.01527
250 2JHP GUN 8.01527
251 3RUG DB6 8.01527
252 3SCM LGN 8.01527
253 3T6E UQ9 8.01527
254 5LOF 70R 8.01527
255 4ZBR DIF 8.01527
256 4ZBR NPS 8.01527
257 1JAY F42 8.01887
258 1LOJ URI 8.04598
259 3SFI 3SF 8.05085
260 1Q1Y BB2 8.37696
261 4OGQ 7PH 8.37989
262 4OGQ 1O2 8.37989
263 1LOX RS7 8.39695
264 4IGH 1EA 8.39695
265 4IGH ORO 8.39695
266 4IGH FMN 8.39695
267 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 8.40336
268 5Y02 HBX 8.41121
269 5Y02 MXN 8.41121
270 5I8F ML1 8.48485
271 1SBR VIB 8.5
272 2PFC PLM 8.74317
273 5X80 SAL 8.75
274 6F6E PLM 8.77863
275 5OSW DIU 8.77863
276 5OSW AE4 8.77863
277 5OLZ T4E 8.77863
278 5M36 9SZ 9.17031
279 5CSD ACD 9.43396
280 5TDU PCR 9.54198
281 4F7E 0SH 9.54198
282 3RMK BML 9.54198
283 5N9T 8QQ 9.92366
284 4XCP PLM 10
285 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 10.2041
286 2UW1 GVM 10.3053
287 3RLF MAL 10.3053
288 4I67 G G G RPC 10.3448
289 4DR9 BB2 10.4167
290 4X6F 3XU 10.4762
291 1XVB BHL 10.687
292 1XVB 3BR 10.687
293 5IF4 6AK 10.6918
294 6FS0 E4W 10.6918
295 6BVM EBV 10.7784
296 6BVK EAV 10.7784
297 6BVJ EAS 10.7784
298 6BVI EC4 10.7784
299 6BVL EBY 10.7784
300 3L1N PLM 10.8247
301 3KO0 TFP 10.8911
302 1MID LAP 10.989
303 4WO4 JLS 11
304 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 11
305 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 11
306 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 11
307 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 11
308 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 11
309 3QKD HI0 11.0497
310 6BR8 PGV 11.0687
311 6BR8 6OU 11.0687
312 5DUF G7A 11.0687
313 5C9J DAO 11.1111
314 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 11.1111
315 5WL1 CUY 11.1111
316 5WL1 D3D 11.1111
317 5U98 1KX 11.1111
318 3HUJ AGH 11.1111
319 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 11.1111
320 5U98 VAL THR THR ASP ILE GLN VAL LYS VAL 11.1111
321 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 11.2245
322 4MA7 P2Z 11.2676
323 1ZEI CRS 11.3208
324 3N7S 3N7 11.4583
325 4V1F BQ1 11.6279
326 4O4Z N2O 11.6883
327 5IUY BOG 11.8321
328 4QVX 3CQ 11.976
329 2WOR 2AN 12
330 4RLT FSE 12.0253
331 3PF7 MLA 12.2137
332 3AI3 SOE 12.2137
333 3F3E LEU 12.2137
334 5FPN KYD 12.5954
335 3QUZ QUV 13.278
336 1RSG FAD 13.3588
337 4FHT DHB 13.3758
338 5AZC PGT 13.7405
339 3KFC 61X 13.834
340 5V03 658 14.094
341 4HBM 0Y7 14.1667
342 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 14.2857
343 3ZPG 5GP 14.5038
344 5IVX ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 14.5299
345 2FKW RG1 15.0943
346 1HBK MYR 15.7303
347 2CB8 MYA 16.092
348 4WT2 3UD 16.1905
349 4OAS 2SW 16.6667
350 4URX FK1 16.7568
351 6BJO DUY 16.8
352 3BJC WAN 17.1756
353 4YSX E23 17.3077
354 3ZLR X0B 17.7215
355 5FH7 5XL 17.7419
356 1ZED PNP 17.9389
357 4YV5 SVR 18.0328
358 5Z84 CHD 18.3673
359 5ZCO CHD 18.3673
360 5W97 CHD 18.3673
361 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 18.3673
362 2DYR PGV 18.3673
363 5ZCO PEK 18.3673
364 5Z84 PGV 18.3673
365 5ZCO PGV 18.3673
366 5V4R MGT 18.5185
367 4ZGM 32M 18.8525
368 3D9F N6C 20.6107
369 2Y69 CHD 22.2222
370 2QQD AG2 22.6415
371 5OCA 9QZ 23.0159
372 1RV1 IMZ 23.5294
373 4OB6 S2T 24.4275
374 1N13 AG2 25
375 3KPE TM3 25.641
376 5MWE TCE 27.1605
377 3EE4 MYR 37.4046
Pocket No.: 2; Query (leader) PDB : 5K53; Ligand: STE; Similar sites found with APoc: 47
This union binding pocket(no: 2) in the query (biounit: 5k53.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 2ALG DAO None
2 1LNX URI None
3 5C1M 4VO 0.763359
4 3T03 3T0 1.9084
5 5GWE GWM 1.9084
6 2J07 FAD 2.29008
7 2J07 HDF 2.29008
8 1YYE 196 2.67176
9 3T3Z 9PL 3.05344
10 3RI1 3RH 3.51438
11 2FP2 TSA 3.61446
12 3ZGE ASP 3.81679
13 3V66 D3A 3.81679
14 3G5K BB2 3.82514
15 3TJH SER PRO LEU ASP SER LEU TRP TRP ILE 3.9823
16 1RTW MP5 4.09091
17 5ZKC 3C0 4.19847
18 1YMT DR9 4.19847
19 3IX9 MTX 4.21053
20 2JC9 ADN 4.58015
21 1SJD NPG 4.58015
22 4UZI IMD 4.58015
23 2YLN CYS 4.59364
24 5U9J GER 4.73373
25 5KAX RHQ 4.81928
26 6A56 LAT 4.87805
27 1NQ7 HIS LYS ILE LEU HIS ARG LEU LEU GLN GLU 4.91803
28 5KD8 TNR 4.96183
29 2E2R 2OH 5.34351
30 4MOP 2H5 5.34351
31 3BPX SAL 6.10687
32 4I90 CHT 6.10687
33 3H0A D30 6.14035
34 6GMN F4E 6.18557
35 4CA5 3EF 6.48855
36 1ZT1 PHE GLU ALA ASN GLY ASN LEU ILE 7
37 1MO9 FAD 7.25191
38 1MO9 KPC 7.25191
39 4BNU 9KQ 8.39695
40 2GJ5 VD3 9.87654
41 1E4I NFG 9.92366
42 1ZOY UQ1 10.7143
43 6D5V FVY 10.7784
44 1HBK COA 15.7303
45 2QQC AG2 24.5283
46 4RW3 TDA 27.4809
47 2D5X L35 32.8767
APoc FAQ
Feedback