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Receptor
PDB id Resolution Class Description Source Keywords
5K52 2.4 Å EC: 4.1.99.5 CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM SP. KNUA012 LIMNOTHRIX SP. KNUA012 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. V. 477 395 2016 COMMUN.
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
OCD A:500;
C:500;
Valid;
Valid;
none;
none;
submit data
268.478 C18 H36 O CCCCC...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5K52 2.4 Å EC: 4.1.99.5 CRYSTAL STRUCTURES OF ALDEHYDE DEFORMYLATING OXYGENASE FROM SP. KNUA012 LIMNOTHRIX SP. KNUA012 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. V. 477 395 2016 COMMUN.
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 5K52 - OCD C18 H36 O CCCCCCCCCC....
70% Homology Family (12)
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 4QUW - PL3 C16 H34 O CCCCCCCCCC....
10 4RC5 - PL3 C16 H34 O CCCCCCCCCC....
11 4RC8 - STE C18 H36 O2 CCCCCCCCCC....
12 5K52 - OCD C18 H36 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: OCD; Similar ligands found: 23
No: Ligand ECFP6 Tc MDL keys Tc
1 8YP 1 1
2 OCD 1 1
3 UNA 1 1
4 OYA 0.954545 1
5 B7M 0.575758 0.75
6 PTL 0.541667 0.714286
7 1EY 0.529412 0.6875
8 R16 0.5 0.733333
9 D12 0.5 0.733333
10 TRD 0.5 0.733333
11 UND 0.5 0.733333
12 DD9 0.5 0.733333
13 MYS 0.5 0.733333
14 C14 0.5 0.733333
15 8K6 0.5 0.733333
16 TWT 0.5 0.733333
17 LFA 0.5 0.733333
18 D10 0.5 0.733333
19 3X1 0.457143 0.65
20 OCT 0.454545 0.733333
21 ELA 0.421053 0.636364
22 OLA 0.421053 0.636364
23 NER 0.421053 0.636364
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5K52; Ligand: OCD; Similar sites found with APoc: 326
This union binding pocket(no: 1) in the query (biounit: 5k52.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 5X13 HC4 None
2 1B4B ARG None
3 4FHT DHB None
4 4WG0 CHD None
5 5ET3 60C None
6 2ALG DAO None
7 1UO5 PIH None
8 5FH7 5XL None
9 6BOC RIM None
10 1S8G DAO None
11 6BKL RIM None
12 2Z9I GLY ALA THR VAL 0.754717
13 3E3U NVC 1.01523
14 3O01 DXC 1.13208
15 1YYE 196 1.13208
16 1M2Z BOG 1.16732
17 5U9J GER 1.18343
18 5URY PAM 1.36986
19 4KBS PX2 1.39535
20 4DXJ 0M9 1.50943
21 3VRV YSD 1.50943
22 4XVX P33 FDA 1.50943
23 3PF7 MLA 1.88679
24 4LY9 1YY 1.88679
25 4LY9 S6P 1.88679
26 6BMS PLM 1.88679
27 5CSD ACD 1.88679
28 6BMS POV 1.88679
29 6F5W KG1 1.88679
30 2HFN FMN 1.96078
31 4UP5 94W 2.0202
32 5VRH OLB 2.10728
33 6F6E PLM 2.26415
34 3X01 AMP 2.26415
35 3B9Z CO2 2.26415
36 5C1M CLR 2.26415
37 5LWY OLB 2.26415
38 4X8D AVI 2.26415
39 4IGH 1EA 2.26415
40 4IGH FMN 2.26415
41 4IGH ORO 2.26415
42 1XZ3 ICF 2.29885
43 1GNI OLA 2.64151
44 6B21 C9V 2.64151
45 3W54 RNB 2.64151
46 3HP9 CF1 2.64151
47 3RWP ABQ 2.64151
48 2PX6 DH9 2.64151
49 1DB1 VDX 2.7027
50 3GF2 SAL 2.73973
51 2BCG GER 2.91262
52 3WUR O4B 2.92398
53 1ZPD CIT 2.99296
54 2BHW NEX 3.01724
55 3E70 GDP 3.01887
56 3W5N RAM 3.01887
57 5IKR ID8 3.01887
58 3G9E RO7 3.01887
59 2RH1 CLR 3.01887
60 5EK3 5PK 3.01887
61 2P4Y C03 3.01887
62 5MBC FMN 3.01887
63 5V3Y 5V8 3.01887
64 1IID NHM 3.01887
65 1XQP 8HG 3.125
66 3F8C HT1 3.1746
67 1PU7 39A 3.21101
68 4ZGM 32M 3.27869
69 4XU6 TDA 3.33333
70 1HBK MYR 3.37079
71 1HBK COA 3.37079
72 5OSW DIU 3.39623
73 1I0B PEL 3.39623
74 2HHP FLC 3.39623
75 3LN0 52B 3.39623
76 3ZPG 5GP 3.39623
77 4RQL SNE 3.39623
78 4MOP 2H5 3.39623
79 3F3E LEU 3.39623
80 4WGF HX2 3.41463
81 4V3I ASP LEU THR ARG PRO 3.50195
82 5W7B MYR 3.5461
83 4JE7 BB2 3.5533
84 3KFC 61X 3.55731
85 5AAV GW5 3.57143
86 1G27 BB1 3.57143
87 2F2G HMH 3.61991
88 2Q4X HMH 3.61991
89 2UW1 GVM 3.77358
90 3SQP 3J8 3.77358
91 5AZC PGT 3.77358
92 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 3.77358
93 1EWF PC1 3.77358
94 5L8N 6RQ 3.77358
95 3E85 BSU 3.79747
96 4YC9 4C1 3.80435
97 4RHP PEF 3.82979
98 3QKD HI0 3.8674
99 2I0G I0G 3.89105
100 1UI0 URA 3.90244
101 5UGW GSH 4
102 5NM7 GLY 4.15094
103 3GFZ FMN 4.15094
104 6MVU K4V 4.15094
105 1T0S BML 4.15094
106 6C1R EFD 4.15094
107 4UZI IMD 4.15094
108 1N83 CLR 4.15094
109 4ZUL UN1 4.15094
110 4QVX 3CQ 4.19162
111 4Q0A GLY HIS LYS ILE LEU HIS ARG LEU LEU GLN 4.30464
112 3EE4 MYR 4.33437
113 5N8V KZZ 4.34783
114 3NB0 G6P 4.5283
115 1TV5 N8E 4.5283
116 1XMY ROL 4.5283
117 4OMJ 2TX 4.5283
118 1XM4 PIL 4.5283
119 5LOF 70R 4.5283
120 1XMU ROF 4.5283
121 5CX6 CDP 4.5283
122 3T3Z 9PL 4.5283
123 5KOR GDP 4.5283
124 2OZ5 7XY 4.5283
125 1XW6 GSH 4.58716
126 5F74 AMP 4.59184
127 2J8C SPO 4.61538
128 2J8C U10 4.61538
129 5LGA 6VH 4.66667
130 2AX9 BHM 4.6875
131 3B6C SDN 4.70085
132 1R6N 434 4.73934
133 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 4.7619
134 5XS3 VAL ARG SER ARG ARG CYS LEU ARG LEU 4.7619
135 5KAX RHQ 4.81928
136 3AQT RCO 4.89796
137 6CB2 OLC 4.90566
138 3GZ9 D32 4.90566
139 1SR7 MOF 4.90566
140 3RS8 ALA TRP LEU PHE GLU ALA 4.90566
141 3KDU NKS 4.90566
142 5KD8 TNR 4.90566
143 1J78 OLA 4.90566
144 5B25 4QJ 4.90566
145 5OFW 9TW 4.93274
146 2VWA PTY 4.9505
147 3KO0 TFP 4.9505
148 2BW7 APC 5.02283
149 3KXC PLM 5.06329
150 5M37 9SZ 5.21739
151 5M36 9SZ 5.24017
152 5KBE IPH 5.24017
153 3TDC 0EU 5.28302
154 1ZED PNP 5.28302
155 2QES ADE 5.36398
156 6BMM OLB 5.46075
157 5XJ7 87O 5.47264
158 2YLD CMO 5.51181
159 5N53 8NB 5.64103
160 4G86 BNT 5.66038
161 4MRP GSH 5.66038
162 3WYJ H78 5.66038
163 3B99 U51 5.66038
164 1XX4 BAM 5.74713
165 1Y4Z PCI 5.77778
166 1NF8 BOG 5.7971
167 2J8R MSL 5.81395
168 3IPQ 965 6.00707
169 5OLK DTP 6.03774
170 5ZQ4 AMP 6.03774
171 1OFZ FUL 6.03774
172 1OFZ FUC 6.03774
173 1MT1 AG2 6.19469
174 6BJO DUY 6.4
175 4OB6 S2T 6.41509
176 3TL1 JRO 6.41509
177 4DE3 DN8 6.46388
178 5TVI MYR 6.52174
179 4F4S EFO 6.57895
180 5NTW 98N 6.61479
181 5YEE LAB 6.61765
182 3KP6 SAL 6.62252
183 2EVL GAL SPH EIC 6.69856
184 6GMN F4E 6.73077
185 3KU0 ADE 6.77291
186 3G58 988 6.79245
187 1RSG FAD 6.79245
188 2XN5 FUN 6.79245
189 3AI3 SOE 6.84411
190 2Q4G CIT 6.97674
191 6GSG RCO 7.16981
192 2GJ5 VD3 7.40741
193 5IXK 6EW 7.45614
194 4HBM 0Y7 7.5
195 4MNS 2AX 7.54717
196 4XCP PLM 7.54717
197 2WH8 II2 7.74818
198 6EVN PRO PRO GLY PRO ALA GLY PRO PRO GLY 7.84314
199 2GWH PCI 7.92453
200 5OKL PAM 7.92453
201 3IIS PID 7.94702
202 5UC9 MYR 7.9646
203 5A4W QCT 8.01887
204 4F7E 0SH 8.16327
205 3L9R L9R 8.16327
206 3L9R L9Q 8.16327
207 4LWU 20U 8.23529
208 6FS0 E4W 8.25688
209 6BR9 PGV 8.30189
210 6BR9 6OU 8.30189
211 3BPX SAL 8.30189
212 5DCH 1YO 8.33333
213 5Y02 HBX 8.41121
214 5Y02 MXN 8.41121
215 3RMK BML 8.43373
216 1SBR VIB 8.5
217 4WT2 3UD 8.57143
218 4UCC ZKW 8.58369
219 5EW9 5VC 8.67924
220 5B4B LP5 8.67924
221 6BR8 PGV 8.73016
222 6BR8 6OU 8.73016
223 5X80 SAL 8.75
224 5NTP 98E 8.82353
225 5Z3I ADE 9.0566
226 3G5K BB2 9.28962
227 4OAS 2SW 9.375
228 4MGA 27L 9.41177
229 4MGD 27N 9.41177
230 4RLT FSE 9.49367
231 4X6F 3XU 9.52381
232 4TV1 36M 9.56175
233 6DIO CIT 9.81132
234 1MID LAP 9.89011
235 1OGA GLY ILE LEU GLY PHE VAL PHE THR LEU 10
236 3QFJ LEU LEU PHE GLY PHE PRO VAL TYR VAL 10
237 5JHD GLY ILE LEU GLY PHE VAL PHE THR LEU 10
238 5C0C ARG GLN PHE GLY PRO ASP TRP ILE VAL ALA 10
239 5LX9 OLB 10.0977
240 5C9J DAO 10.101
241 6BJ3 ILE PRO LEU THR GLU GLU ALA GLU LEU 10.101
242 5WL1 CUY 10.101
243 5T70 THR SER ASN LEU GLN GLU GLN ILE GLY TRP 10.101
244 5U98 1KX 10.101
245 5IUY BOG 10.1887
246 5IM3 DTP 10.1887
247 5ISZ GLY ILE LEU GLY PHE VAL PHE THR LEU 10.2041
248 4YSX E23 10.2564
249 1X0P FAD 10.4895
250 3GXO MQA 10.5691
251 1RV1 IMZ 10.5882
252 1N13 AG2 10.6195
253 6CAY ERG 10.6509
254 5X3R 7Y3 10.7317
255 3L1N PLM 10.8247
256 2FP2 TSA 10.8434
257 5KAU RHQ 10.9091
258 4WO4 JLS 10.9434
259 3HUJ AGH 10.9434
260 4O4Z N2O 11.039
261 5OCA 9QZ 11.0599
262 5FUS DAO 11.3208
263 2PFC PLM 12.0219
264 3WFD AXO 12.3288
265 5V4R MGT 12.3457
266 5CHR 4NC 12.4088
267 1DTL BEP 12.4224
268 4DR9 BB2 12.5
269 5TDU PCR 12.6214
270 2CB8 MYA 12.6437
271 2Y69 CHD 12.6984
272 2NV2 GLN 12.7451
273 3FAL LO2 12.8099
274 3FAL REA 12.8099
275 1XXA ARG 12.8205
276 4UMJ BFQ 12.8302
277 1LOX RS7 12.8302
278 3NY4 SMX 13.2075
279 1XVB BHL 13.5849
280 1XVB 3BR 13.5849
281 4V1F BQ1 13.9535
282 3RUU 37G 14.4105
283 5ICK FEZ 14.4105
284 3CHT 4NB 14.5833
285 4OIV XX9 14.6018
286 4CVZ TYR GLU LEU ASP GLU LYS PHE ASP ARG LEU 15.0943
287 1NU4 MLA 15.4639
288 3N7S 3N7 15.6522
289 4MA7 P2Z 15.7895
290 1RTW MP5 15.9091
291 1BII ARG GLY PRO GLY ARG ALA PHE VAL THR ILE 16.8067
292 3PVT 3HC 16.9884
293 5Z84 CHD 17.0213
294 5ZCO CHD 17.0213
295 5W97 CHD 17.0213
296 2DYS PGV 17.0213
297 5ZCO PGV 17.0213
298 5Z84 PGV 17.0213
299 3D9F N6C 17.3585
300 2WOR 2AN 18
301 4RYV ZEA 18.7097
302 2ZFZ ARG 18.9873
303 2XRH NIO 19
304 5V03 658 19.6078
305 3G08 FEE 20.202
306 3RUG DB6 20.202
307 3QUZ QUV 20.202
308 1MHC FME TYR PHE ILE ASN ILE LEU THR LEU 20.202
309 3SCM LGN 20.202
310 1LEK GLU GLN TYR LYS PHE TYR SER VAL 20.202
311 5MTE BB2 21.1679
312 6BVJ EAS 22.1557
313 6D5V FVY 22.1557
314 6BVM EBV 23.9521
315 6BVK EAV 23.9521
316 6BVL EBY 23.9521
317 6BVI EC4 23.9521
318 6D5H FV7 23.9521
319 5MWE TCE 25.9259
320 5EEH P9P 26.0377
321 4URX FK1 27.027
322 4OGQ 1O2 29.7297
323 4OGQ 7PH 29.7297
324 4OGQ 2WD 29.7297
325 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 33.3333
326 3KPE TM3 33.3333
Pocket No.: 2; Query (leader) PDB : 5K52; Ligand: OCD; Similar sites found with APoc: 35
This union binding pocket(no: 2) in the query (biounit: 5k52.bio3) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 6BOC EU7 None
2 4NAT ADP None
3 3LE7 ADE None
4 4DXJ IPE 1.50943
5 1TO9 HMH 1.53846
6 1LQY BB2 2.17391
7 2E2R 2OH 2.45902
8 3ZLR X0B 2.53165
9 3R9V DXC 2.64151
10 4HDK 13X 3.01887
11 5NXX 3Q7 3.39623
12 3L0E G58 3.55731
13 5IJJ I6P 3.64583
14 2HZL PYR 4.15094
15 5MZI FYK 4.15094
16 2JHP GUN 4.15094
17 3UG4 AHR 4.5283
18 2YIV YIV 4.5283
19 1YUC EPH 4.70588
20 3FS1 ALA ALA LEU ALA ALA LEU LEU ALA ALA 4.78261
21 1KJM ALA GLN PHE SER ALA SER ALA SER ARG 5
22 2IYG FMN 5.64516
23 5FS0 5JC 5.6872
24 2BYC FMN 6.56934
25 3SFI 3SF 8.05085
26 3GYT DL4 8.19672
27 3RLF MAL 9.0566
28 2QE4 JJ3 9.67742
29 6GH1 ARG LEU PRO ALA LYS ALA PRO LEU LEU 10
30 5WL1 D3D 10.101
31 5L2R MLA 10.1887
32 2GBB CIT 10.2564
33 2QQD AG2 10.7143
34 1H82 GZZ 12.0755
35 1G51 AMP 13.2075
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