Receptor
PDB id Resolution Class Description Source Keywords
5D2J 1.72 Å EC: 4.1.1.77 4-OXALOCROTONATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA G7 - WITH MAGNESIUM AND ADIPATE PSEUDOMONAS PUTIDA NAPHTHALENE DEGRADATION LYASE
Ref.: CRYSTAL STRUCTURES OF APO AND LIGANDED 4-OXALOCROTO DECARBOXYLASE UNCOVER A STRUCTURAL BASIS FOR THE METAL-ASSISTED DECARBOXYLATION OF A VINYLOGOUS BETA ACID. BIOCHEMISTRY V. 55 2632 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
EDO A:304;
B:302;
A:305;
B:303;
B:304;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
ACT B:306;
B:305;
 Invalid;
Invalid;
 none;
none;
 submit data
59.044 C2 H3 O2 CC(=O...
MG A:302;
B:301;
A:301;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
24.305 Mg [Mg+2...
0L1 A:303;
 Valid;
 none;
 submit data
146.141 C6 H10 O4 C(CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5D2H 1.94 Å EC: 4.1.1.77 4-OXALOCROTONATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA G7 - WITH MAGNESIUM AND ALPHA-KETOGLUTARATE PSEUDOMONAS PUTIDA NAPHTHALENE DEGRADATION LYASE
Ref.: CRYSTAL STRUCTURES OF APO AND LIGANDED 4-OXALOCROTO DECARBOXYLASE UNCOVER A STRUCTURAL BASIS FOR THE METAL-ASSISTED DECARBOXYLATION OF A VINYLOGOUS BETA ACID. BIOCHEMISTRY V. 55 2632 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
2 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
3 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
2 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
3 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2EB5 - OXL C2 O4 C(=O)(C(=O....
2 5D2K - OOG C6 H8 O5 C(CC(=O)C(....
3 5D2H - AKG C5 H6 O5 C(CC(=O)O)....
4 5D2J - 0L1 C6 H10 O4 C(CCC(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 0L1; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 0L1 1 1
2 PML 0.764706 0.947368
3 AZ1 0.722222 0.9
4 SHO 0.65 0.761905
5 GUA 0.647059 0.944444
6 6NA 0.619048 0.608696
7 SIN 0.5625 0.833333
8 12H 0.541667 0.695652
9 9J6 0.538462 0.68
10 BRC 0.52 0.608696
11 NPI 0.464286 0.692308
12 OOG 0.458333 0.85
13 KTC 0.433333 0.615385
14 RED 0.419355 0.625
15 MLA 0.411765 0.619048
16 SSN 0.409091 0.722222
17 5PV 0.40625 0.666667
Similar Ligands (3D)
Ligand no: 1; Ligand: 0L1; Similar ligands found: 298
No: Ligand Similarity coefficient
1 AKG 0.9680
2 ENW 0.9621
3 OGA 0.9615
4 UN1 0.9572
5 DGL 0.9549
6 GLU 0.9541
7 AG2 0.9535
8 N6C 0.9534
9 2IT 0.9528
10 GVA 0.9503
11 7UC 0.9498
12 DGN 0.9484
13 CCU 0.9483
14 011 0.9458
15 S8V 0.9447
16 KQY 0.9439
17 LUQ 0.9439
18 650 0.9426
19 9YT 0.9423
20 HPN 0.9422
21 4TB 0.9421
22 SHV 0.9407
23 2HG 0.9392
24 DZA 0.9383
25 1HS 0.9372
26 OCA 0.9370
27 GLN 0.9368
28 2FM 0.9367
29 URO 0.9361
30 MHN 0.9357
31 S2G 0.9354
32 ACA 0.9353
33 O45 0.9324
34 KPC 0.9322
35 LVD 0.9301
36 11C 0.9295
37 SLZ 0.9279
38 URP 0.9274
39 AHN 0.9268
40 AE3 0.9258
41 DHI 0.9258
42 NM2 0.9256
43 3S5 0.9256
44 HIS 0.9250
45 ONH 0.9247
46 LYN 0.9246
47 3LR 0.9244
48 3YP 0.9239
49 M1T 0.9236
50 ENV 0.9234
51 7BC 0.9232
52 MHO 0.9226
53 LYS 0.9220
54 DLY 0.9220
55 CCD 0.9205
56 R9M 0.9202
57 9ON 0.9195
58 MF3 0.9195
59 AT3 0.9194
60 M3P 0.9190
61 ORN 0.9186
62 2JJ 0.9185
63 JX7 0.9181
64 KNA 0.9180
65 Q9Z 0.9180
66 IP8 0.9175
67 CLT 0.9175
68 7C3 0.9175
69 FOM 0.9173
70 8GL 0.9170
71 KMH 0.9170
72 OCT 0.9166
73 ZGL 0.9166
74 7OD 0.9164
75 HHI 0.9163
76 DAL DAL 0.9156
77 MLZ 0.9152
78 6XA 0.9150
79 KPA 0.9149
80 RUJ 0.9137
81 B3M 0.9136
82 BHH 0.9131
83 OEG 0.9123
84 ARG 0.9115
85 HPV 0.9113
86 OC9 0.9111
87 13P 0.9110
88 DIR 0.9103
89 9J3 0.9103
90 3PG 0.9099
91 5OY 0.9098
92 PG0 0.9091
93 OYA 0.9090
94 IXW 0.9086
95 152 0.9086
96 HE4 0.9084
97 SYM 0.9083
98 ONL 0.9082
99 ALA ALA 0.9081
100 NSD 0.9080
101 GGL 0.9079
102 PPY 0.9079
103 PBA 0.9076
104 HCI 0.9076
105 GPJ 0.9074
106 TEG 0.9073
107 PGH 0.9073
108 NNH 0.9069
109 IAR 0.9065
110 HGA 0.9061
111 16D 0.9061
112 TYR 0.9060
113 G3P 0.9056
114 CIR 0.9054
115 PHE 0.9052
116 NLE 0.9048
117 CCE 0.9047
118 1BN 0.9041
119 HTX 0.9039
120 4HP 0.9039
121 7XA 0.9038
122 CHH 0.9038
123 ILO 0.9036
124 0VT 0.9032
125 BHU 0.9031
126 OKG 0.9031
127 DHH 0.9026
128 HMS 0.9025
129 TCA 0.9024
130 DXP 0.9023
131 6HN 0.9018
132 CXP 0.9016
133 GLY GLY 0.9014
134 3OL 0.9011
135 HC4 0.9011
136 DAR 0.9008
137 QFJ 0.9007
138 BHL 0.9004
139 BHL BHL 0.9004
140 GGB 0.9003
141 G3H 0.8999
142 J0Z 0.8996
143 SME 0.8993
144 PO6 0.8992
145 SEP 0.8985
146 4LR 0.8982
147 GPF 0.8979
148 MLY 0.8977
149 HPL 0.8977
150 N9J 0.8976
151 GRQ 0.8970
152 GLY GLY GLY 0.8968
153 I38 0.8967
154 5XB 0.8961
155 XIZ 0.8960
156 PC 0.8958
157 FK8 0.8958
158 DHM 0.8956
159 MSL 0.8952
160 ODI 0.8952
161 2FT 0.8946
162 BNF 0.8945
163 P81 0.8940
164 SSC 0.8934
165 MZT 0.8933
166 8SZ 0.8932
167 NMH 0.8929
168 NWH 0.8928
169 TIH 0.8926
170 HG3 0.8920
171 MED 0.8919
172 AL0 0.8919
173 NF3 0.8918
174 MET 0.8917
175 O8Y 0.8917
176 E4P 0.8914
177 49F 0.8914
178 NM3 0.8913
179 NTU 0.8913
180 5XA 0.8908
181 KMT 0.8908
182 M6H 0.8905
183 2D8 0.8902
184 PRO GLY 0.8899
185 OSE 0.8895
186 RTK 0.8891
187 F98 0.8890
188 SPD 0.8887
189 LPA 0.8885
190 MEQ 0.8884
191 HBU 0.8879
192 NFA 0.8878
193 DXG 0.8878
194 SSB 0.8878
195 NSB 0.8877
196 M45 0.8876
197 4TP 0.8874
198 64Z 0.8872
199 EGV 0.8872
200 VKC 0.8872
201 P80 0.8869
202 3OM 0.8863
203 AFS 0.8863
204 58X 0.8854
205 LTL 0.8851
206 3HG 0.8846
207 5DL 0.8844
208 HL5 0.8843
209 DIA 0.8839
210 DAV 0.8836
211 CUW 0.8833
212 MES 0.8832
213 NYL 0.8832
214 DEZ 0.8831
215 GP9 0.8820
216 IVL 0.8819
217 DER 0.8819
218 AZM 0.8818
219 DLT 0.8813
220 9SE 0.8810
221 API 0.8809
222 NMM 0.8808
223 XRX 0.8802
224 9GB 0.8795
225 2BX 0.8794
226 3QO 0.8792
227 1X4 0.8791
228 5LD 0.8786
229 XOG 0.8786
230 KDG 0.8777
231 1PS 0.8776
232 LY0 0.8775
233 B3U 0.8773
234 129 0.8767
235 SD4 0.8765
236 F90 0.8765
237 2NP 0.8765
238 GVM 0.8763
239 HPP 0.8761
240 PBN 0.8759
241 PG3 0.8758
242 ZZU 0.8752
243 1GP 0.8750
244 Q06 0.8747
245 HPO 0.8744
246 PDC 0.8744
247 HAR 0.8739
248 TZP 0.8738
249 X1R 0.8738
250 492 0.8737
251 YIP 0.8730
252 NLP 0.8730
253 ENO 0.8724
254 3PO 0.8724
255 LX1 0.8722
256 ABH 0.8721
257 TZM 0.8719
258 2CO 0.8712
259 EXY 0.8707
260 GCO 0.8706
261 AHC 0.8699
262 M3L 0.8697
263 GOJ 0.8695
264 PSE 0.8693
265 6CL 0.8692
266 1SH 0.8692
267 GLR 0.8685
268 PPT 0.8684
269 264 0.8684
270 SNO 0.8684
271 HIC 0.8683
272 GB5 0.8682
273 3H2 0.8681
274 268 0.8679
275 S7A 0.8671
276 XYH 0.8668
277 MSE 0.8667
278 MPJ 0.8661
279 HL4 0.8656
280 E79 0.8653
281 BL0 0.8647
282 RP3 0.8647
283 266 0.8644
284 M44 0.8643
285 5RP 0.8640
286 NOT 0.8631
287 P58 0.8608
288 11X 0.8606
289 MPH 0.8604
290 CS2 0.8603
291 CYX 0.8600
292 YIE 0.8598
293 S0W 0.8596
294 8EW 0.8589
295 6ZX 0.8569
296 JFM 0.8567
297 6J5 0.8551
298 RA7 0.8536
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5D2H; 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: 1) in the query (biounit: 5d2h.bio1) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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