Receptor
PDB id Resolution Class Description Source Keywords
4KVR 1.88 Å EC: 4.1.99.5 CRYSTAL STRUCTURE OF PROCHLOROCOCCUS MARINUS ALDEHYDE-DEFORM OXYGENASE (MUTANT V41Y) PROCHLOROCOCCUS MARINUS PROPANE PRODUCTION ALDEHYDE-DEFORMYLATING OXYGENASE OXIDOR
Ref.: PRODUCTION OF PROPANE AND OTHER SHORT-CHAIN ALKANES STRUCTURE-BASED ENGINEERING OF LIGAND SPECIFICITY I ALDEHYDE-DEFORMYLATING OXYGENASE. CHEMBIOCHEM V. 14 1204 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
FE A:303;
A:302;
Part of Protein;
Part of Protein;
none;
none;
submit data
55.845 Fe [Fe+3...
6NA A:301;
Valid;
none;
submit data
116.158 C6 H12 O2 CCCCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4PGK 2.17 Å EC: 4.1.99.5 INSIGHTS INTO SUBSTRATE AND METAL BINDING FROM THE CRYSTAL S OF CYANOBACTERIAL ALDEHYDE DEFORMYLATING OXYGENASE WITH SUBB OUND PROCHLOROCOCCUS MARINUS NON-HEME DI-IRON PROTEIN HYDROCARBON PRODUCTION ALPHA-HELIOXIDOREDUCTASE
Ref.: INSIGHTS INTO SUBSTRATE AND METAL BINDING FROM THE STRUCTURE OF CYANOBACTERIAL ALDEHYDE DEFORMYLATING WITH SUBSTRATE BOUND. ACS CHEM.BIOL. V. 9 2584 2014
Members (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 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)....
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 (2D)
Ligand no: 1; Ligand: 6NA; Similar ligands found: 38
No: Ligand ECFP6 Tc MDL keys Tc
1 6NA 1 1
2 SHV 0.782609 0.95
3 OCA 0.75 0.904762
4 PLM 0.72 0.904762
5 DCR 0.72 0.904762
6 11A 0.72 0.904762
7 EW8 0.72 0.904762
8 F15 0.72 0.904762
9 DKA 0.72 0.904762
10 X90 0.72 0.904762
11 STE 0.72 0.904762
12 DAO 0.72 0.904762
13 F23 0.72 0.904762
14 MYR 0.72 0.904762
15 TDA 0.72 0.904762
16 KNA 0.72 0.904762
17 LEA 0.681818 0.894737
18 0L1 0.619048 0.608696
19 KTC 0.580645 0.791667
20 BUA 0.545455 0.736842
21 OOA 0.533333 0.75
22 NER 0.529412 0.863636
23 ELA 0.529412 0.863636
24 PAM 0.529412 0.863636
25 VCA 0.529412 0.863636
26 OLA 0.529412 0.863636
27 MYZ 0.5 0.818182
28 ODD 0.486486 0.826087
29 9J6 0.483871 0.653846
30 EIC 0.461538 0.826087
31 EOD 0.461538 0.633333
32 M12 0.454545 0.782609
33 3LA 0.428571 0.72
34 D0G 0.416667 0.863636
35 BMJ 0.416667 0.863636
36 BNV 0.416667 0.863636
37 ITY 0.410256 0.76
38 ACD 0.410256 0.826087
Similar Ligands (3D)
Ligand no: 1; Ligand: 6NA; Similar ligands found: 357
No: Ligand Similarity coefficient
1 HTX 0.9944
2 SHO 0.9866
3 VKC 0.9740
4 DAV 0.9710
5 DQY 0.9620
6 3OM 0.9601
7 ACA 0.9590
8 NLE 0.9576
9 HPN 0.9566
10 GLU 0.9559
11 FUM 0.9555
12 GUA 0.9553
13 ABU 0.9550
14 SIN 0.9544
15 16D 0.9540
16 AG2 0.9511
17 4MV 0.9497
18 HSE 0.9482
19 ORN 0.9469
20 MAE 0.9457
21 N6C 0.9451
22 OKG 0.9440
23 LEU 0.9429
24 BHH 0.9429
25 MET 0.9424
26 SHF 0.9420
27 GLN 0.9419
28 SSN 0.9418
29 KQY 0.9414
30 49F 0.9412
31 HDA 0.9411
32 5XA 0.9400
33 HP6 0.9400
34 3OL 0.9398
35 HE2 0.9394
36 A8C 0.9393
37 0VT 0.9392
38 BUB 0.9392
39 O8Y 0.9389
40 MED 0.9387
41 YIV 0.9387
42 PG0 0.9385
43 HE4 0.9383
44 2CO 0.9381
45 9X7 0.9373
46 LMR 0.9372
47 AKG 0.9371
48 KMT 0.9369
49 URO 0.9369
50 98J 0.9361
51 HCS 0.9354
52 NVA 0.9346
53 1SH 0.9335
54 MHN 0.9329
55 GLY GLY 0.9329
56 OEG 0.9328
57 S2G 0.9327
58 1KA 0.9319
59 OCT 0.9318
60 PG3 0.9312
61 BHL 0.9311
62 BHL BHL 0.9311
63 DGL 0.9308
64 9X6 0.9308
65 OPE 0.9295
66 BP9 0.9290
67 HSM 0.9288
68 HX2 0.9287
69 69O 0.9281
70 MUC 0.9278
71 IXW 0.9272
72 CMS 0.9271
73 650 0.9250
74 7BC 0.9247
75 FBJ 0.9244
76 MLT 0.9241
77 H95 0.9237
78 DAS 0.9236
79 OGA 0.9231
80 NMG 0.9225
81 2HG 0.9222
82 4SD 0.9221
83 URP 0.9217
84 7C3 0.9215
85 ASP 0.9211
86 CYS 0.9208
87 258 0.9206
88 266 0.9204
89 DGN 0.9203
90 G3P 0.9201
91 2RH 0.9199
92 9J3 0.9199
93 GOJ 0.9199
94 PE9 0.9196
95 2IT 0.9188
96 1SP 0.9185
97 HYP 0.9183
98 OAA 0.9180
99 3SS 0.9179
100 HBA 0.9173
101 LYN 0.9171
102 PUT 0.9168
103 ONL 0.9166
104 13P 0.9165
105 PEA 0.9165
106 PGA 0.9160
107 IHG 0.9160
108 MSE 0.9159
109 NTU 0.9152
110 S8V 0.9151
111 6JN 0.9138
112 ZBT 0.9137
113 COI 0.9135
114 LYS 0.9133
115 BXO 0.9131
116 HIS 0.9130
117 X1S 0.9128
118 ITU 0.9128
119 JYD 0.9125
120 ASN 0.9124
121 HY1 0.9123
122 HL5 0.9121
123 ILE 0.9121
124 ZGL 0.9118
125 4HA 0.9115
126 AML 0.9112
127 4FA 0.9110
128 ONH 0.9107
129 AL0 0.9105
130 CSS 0.9097
131 DLY 0.9094
132 NYL 0.9094
133 9YL 0.9091
134 UGC 0.9090
135 TEO 0.9089
136 MPJ 0.9088
137 KMH 0.9087
138 IZC 0.9086
139 PRA 0.9084
140 PEL 0.9084
141 4VP 0.9083
142 FQI 0.9083
143 GLY ALA 0.9081
144 GPJ 0.9078
145 PAH 0.9077
146 2KT 0.9075
147 DE5 0.9073
148 4LR 0.9073
149 DYA 0.9072
150 8EW 0.9069
151 GPF 0.9066
152 BNF 0.9066
153 3HG 0.9066
154 HSO 0.9061
155 7WG 0.9058
156 UY7 0.9058
157 SEP 0.9057
158 G3H 0.9041
159 PHB 0.9038
160 CCD 0.9037
161 SD4 0.9036
162 9ON 0.9036
163 CEE 0.9036
164 RB5 0.9035
165 PGH 0.9033
166 271 0.9032
167 ETX 0.9031
168 AC6 0.9030
169 VAH 0.9028
170 LTL 0.9024
171 CXF 0.9023
172 NF3 0.9019
173 AT3 0.9015
174 XBT 0.9015
175 GGL 0.9013
176 SSB 0.9012
177 OK7 0.9012
178 PAC 0.9011
179 SER 0.9010
180 40E 0.9010
181 1GP 0.9010
182 TZL 0.9008
183 23W 0.9006
184 7CL 0.9004
185 1DU 0.9003
186 TIU 0.9001
187 XLS 0.9001
188 ACH 0.9000
189 54D 0.9000
190 6XA 0.8993
191 YRL 0.8993
192 ROR 0.8992
193 AE3 0.8992
194 R9M 0.8991
195 268 0.8990
196 MEQ 0.8989
197 XYL 0.8988
198 XRG 0.8988
199 A20 0.8987
200 SPA 0.8987
201 MEV 0.8984
202 C2B 0.8984
203 3S5 0.8979
204 LLQ 0.8979
205 AEF 0.8977
206 CCE 0.8975
207 FAN 0.8974
208 LNO 0.8974
209 ISZ 0.8973
210 FW5 0.8969
211 NIZ 0.8969
212 THE 0.8968
213 XUL 0.8966
214 FBA 0.8965
215 OC9 0.8963
216 OYA 0.8963
217 IP8 0.8961
218 DHR 0.8958
219 BHO 0.8954
220 3PP 0.8953
221 NSD 0.8952
222 PSE 0.8951
223 GP9 0.8949
224 NM3 0.8949
225 RTK 0.8948
226 HZP 0.8942
227 TZE 0.8940
228 EHM 0.8935
229 DPF 0.8933
230 QY9 0.8933
231 FEH 0.8926
232 MHO 0.8924
233 1SA 0.8922
234 CHH 0.8920
235 MD0 0.8919
236 14J 0.8919
237 I1E 0.8917
238 QDK 0.8908
239 5BR 0.8907
240 264 0.8907
241 B3M 0.8903
242 PPR 0.8903
243 H8N 0.8902
244 DTL 0.8901
245 SME 0.8899
246 HYA 0.8893
247 4JM 0.8891
248 RBL 0.8885
249 NLP 0.8885
250 EOU 0.8882
251 PEP 0.8875
252 JZ7 0.8874
253 DAL DAL 0.8874
254 N4B 0.8872
255 XAP 0.8869
256 SPV 0.8867
257 5FX 0.8865
258 717 0.8863
259 PLU 0.8862
260 GJZ 0.8862
261 K6V 0.8861
262 SGL 0.8861
263 RBJ 0.8854
264 CFI 0.8851
265 SKJ 0.8849
266 COM 0.8849
267 PHU 0.8843
268 CCU 0.8840
269 PO6 0.8838
270 I38 0.8838
271 ALA ALA 0.8837
272 AHN 0.8836
273 FK8 0.8836
274 NM2 0.8828
275 LT1 0.8827
276 ITN 0.8825
277 129 0.8821
278 FOM 0.8819
279 3SL 0.8816
280 PZM 0.8814
281 MPH 0.8805
282 MZW 0.8805
283 NBN 0.8803
284 NXA 0.8801
285 TPA 0.8800
286 PKU 0.8799
287 2EH 0.8796
288 M4T 0.8792
289 3PG 0.8790
290 2AS 0.8789
291 K34 0.8789
292 DHI 0.8789
293 O45 0.8788
294 1CO 0.8785
295 TAR 0.8781
296 152 0.8779
297 TAU 0.8777
298 7UC 0.8772
299 3YP 0.8771
300 2FT 0.8769
301 GZ3 0.8767
302 I4B 0.8767
303 UYA 0.8763
304 0V5 0.8758
305 3LR 0.8757
306 9SB 0.8757
307 TYL 0.8757
308 R67 0.8753
309 5XC 0.8745
310 CYX 0.8741
311 Q9Z 0.8735
312 DCL 0.8729
313 7OD 0.8724
314 DZA 0.8719
315 HCI 0.8711
316 GVM 0.8710
317 PC 0.8709
318 LDP 0.8706
319 UN1 0.8705
320 M45 0.8703
321 XIZ 0.8701
322 LUQ 0.8700
323 DPJ 0.8695
324 LER 0.8695
325 M6W 0.8690
326 ENW 0.8688
327 JFJ 0.8684
328 SYM 0.8681
329 HDH 0.8677
330 5XB 0.8670
331 CUW 0.8664
332 PEQ 0.8662
333 HPV 0.8642
334 OSE 0.8642
335 HG3 0.8638
336 RNT 0.8635
337 1DV 0.8635
338 ICF 0.8634
339 9GB 0.8623
340 FOC 0.8619
341 8GL 0.8616
342 OOG 0.8615
343 HGA 0.8612
344 URS 0.8610
345 AHB 0.8603
346 TIH 0.8602
347 DE2 0.8601
348 11C 0.8593
349 PBA 0.8592
350 Q07 0.8581
351 RB0 0.8581
352 DHM 0.8569
353 MAH 0.8569
354 MZT 0.8554
355 M3H 0.8553
356 4HP 0.8553
357 2BG 0.8538
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4PGK; Ligand: Y69; Similar sites found with APoc: 2
This union binding pocket(no: 1) in the query (biounit: 4pgk.bio1) has 40 residues
No: Leader PDB Ligand Sequence Similarity
1 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.68852
2 6LM1 D10 5.32787
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