Receptor
PDB id Resolution Class Description Source Keywords
6PCD 1.37 Å EC: 2.3.1.16 CRYSTAL STRUCTURE OF BETA-KETOADIPYL-COA THIOLASE MUTANT (C9 IN COMPLEX OCTANOYL COENZYME A PSEUDOMONAS PUTIDA (STRAIN ATCC 47054 6125 / NCIMB 11950 / KT2440) AROMATIC POLLUTANT CATABOLISM DEGRADATIVE ENZYMES TRANSFER
Ref.: STRUCTURAL BASIS FOR DIFFERENTIATION BETWEEN TWO CL THIOLASE: DEGRADATIVE VS BIOSYNTHETIC THIOLASE. J STRUCT BIOL X V. 4 00018 2020
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL C:502;
C:501;
D:503;
A:503;
B:502;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
92.094 C3 H8 O3 C(C(C...
OYA A:502;
B:501;
D:502;
 Valid;
Valid;
Valid;
 none;
none;
none;
 submit data
128.212 C8 H16 O CCCCC...
COA A:501;
D:501;
 Valid;
Valid;
 none;
none;
 submit data
767.534 C21 H36 N7 O16 P3 S CC(C)...
CL C:503;
B:503;
A:504;
D:504;
B:504;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
 submit data
35.453 Cl [Cl-]
K C:505;
C:504;
B:505;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
39.098 K [K+]
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6PCD 1.37 Å EC: 2.3.1.16 CRYSTAL STRUCTURE OF BETA-KETOADIPYL-COA THIOLASE MUTANT (C9 IN COMPLEX OCTANOYL COENZYME A PSEUDOMONAS PUTIDA (STRAIN ATCC 47054 6125 / NCIMB 11950 / KT2440) AROMATIC POLLUTANT CATABOLISM DEGRADATIVE ENZYMES TRANSFER
Ref.: STRUCTURAL BASIS FOR DIFFERENTIATION BETWEEN TWO CL THIOLASE: DEGRADATIVE VS BIOSYNTHETIC THIOLASE. J STRUCT BIOL X V. 4 00018 2020
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6PCD - OYA C8 H16 O CCCCCCCC=O
2 6PCC - O8Y C6 H12 O CCCCCC=O
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6PCD - OYA C8 H16 O CCCCCCCC=O
2 6PCC - O8Y C6 H12 O CCCCCC=O
50% Homology Family (26)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4UBT - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
2 4UBV - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
3 2VU0 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
4 1M1O - CAA C25 H40 N7 O18 P3 S CC(=O)CC(=....
5 1QFL - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
6 1M3Z - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
7 1DM3 - ACO C23 H38 N7 O17 P3 S CC(=O)SCCN....
8 2WKV Kd = 128 uM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
9 1NL7 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
10 2VTZ Kd = 307 uM COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
11 1OU6 - 168 C18 H32 N2 O7 CC(=O)OCCN....
12 2VU1 - OPI C16 H30 N2 O6 CC(C)(C)C(....
13 1DLV - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
14 7CW5 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
15 6L2C - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
16 4XL4 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
17 6BJB - 1VU C24 H40 N7 O17 P3 S CCC(=O)SCC....
18 2IBY - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
19 2IBU - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
20 2IBW - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
21 1WL4 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
22 5BZ4 - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
23 6BJA - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
24 6PCD - OYA C8 H16 O CCCCCCCC=O
25 6PCC - O8Y C6 H12 O CCCCCC=O
26 4O9C - COA C21 H36 N7 O16 P3 S CC(C)(CO[P....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: OYA; Similar ligands found: 22
No: Ligand ECFP6 Tc MDL keys Tc
1 OYA 1 1
2 UNA 0.954545 1
3 8YP 0.954545 1
4 OCD 0.954545 1
5 O8Y 0.695652 0.857143
6 PTL 0.565217 0.714286
7 B7M 0.545455 0.75
8 1EY 0.5 0.6875
9 OCT 0.47619 0.733333
10 R16 0.454545 0.733333
11 TWT 0.454545 0.733333
12 LFA 0.454545 0.733333
13 D10 0.454545 0.733333
14 8K6 0.454545 0.733333
15 D12 0.454545 0.733333
16 C14 0.454545 0.733333
17 DD9 0.454545 0.733333
18 MYS 0.454545 0.733333
19 TRD 0.454545 0.733333
20 UND 0.454545 0.733333
21 3X1 0.428571 0.65
22 HP6 0.409091 0.666667
Ligand no: 2; Ligand: COA; Similar ligands found: 243
No: Ligand ECFP6 Tc MDL keys Tc
1 COA 1 1
2 0T1 0.894737 0.976744
3 DCA 0.893805 0.954023
4 COS 0.887931 0.977012
5 ETB 0.877193 0.920455
6 30N 0.871795 0.913979
7 CAO 0.871795 0.965909
8 AMX 0.871795 0.988235
9 SCO 0.864407 0.976744
10 CMX 0.864407 0.976744
11 ACO 0.857143 0.965909
12 FCX 0.857143 0.94382
13 FAM 0.857143 0.954545
14 HAX 0.85 0.954545
15 FYN 0.842975 1
16 3KK 0.842975 0.977012
17 OXK 0.836066 0.977012
18 KGP 0.836066 0.885417
19 SOP 0.836066 0.977012
20 YZS 0.836066 0.885417
21 COK 0.836066 0.977012
22 MCD 0.836066 0.954545
23 CA6 0.836066 0.885417
24 1VU 0.829268 0.965909
25 CMC 0.829268 0.977012
26 CO6 0.829268 0.977012
27 NMX 0.829268 0.903226
28 CAJ 0.822581 0.954545
29 2MC 0.822581 0.934066
30 SCD 0.822581 0.976744
31 2CP 0.81746 0.965909
32 3HC 0.816 0.988372
33 KGJ 0.816 0.893617
34 A1S 0.816 0.977012
35 MLC 0.816 0.977012
36 BCO 0.816 0.977012
37 IVC 0.816 0.988372
38 1HE 0.816 0.955056
39 COD 0.810345 0.988235
40 CAA 0.809524 0.988372
41 MCA 0.809524 0.965909
42 SO5 0.809524 0.876289
43 YE1 0.809524 0.965517
44 COO 0.809524 0.977012
45 LCV 0.809524 0.876289
46 YXS 0.80315 0.885417
47 MC4 0.80315 0.923913
48 YXR 0.80315 0.885417
49 SCA 0.80315 0.977012
50 KGA 0.796875 0.884211
51 HGG 0.796875 0.977012
52 BYC 0.796875 0.977012
53 3CP 0.796875 0.977012
54 COW 0.796875 0.965909
55 CA8 0.796875 0.885417
56 1GZ 0.796875 0.965909
57 KFV 0.796875 0.894737
58 IRC 0.796875 0.988372
59 COF 0.796875 0.955056
60 2KQ 0.796875 0.955056
61 4CA 0.790698 0.965909
62 FAQ 0.790698 0.977012
63 BCA 0.790698 0.965909
64 HXC 0.784615 0.955056
65 GRA 0.784615 0.977012
66 1CV 0.781955 0.977012
67 TGC 0.778626 0.965909
68 1CZ 0.772727 0.965909
69 S0N 0.772727 0.954545
70 CO8 0.772727 0.955056
71 2NE 0.772727 0.955056
72 CIC 0.772727 0.977012
73 MYA 0.766917 0.955056
74 0FQ 0.766917 0.977012
75 DCC 0.766917 0.955056
76 5F9 0.766917 0.955056
77 UCC 0.766917 0.955056
78 MFK 0.766917 0.955056
79 ST9 0.766917 0.955056
80 4CO 0.766917 0.965909
81 01A 0.761194 0.934066
82 0ET 0.761194 0.955056
83 CS8 0.755556 0.944444
84 WCA 0.755556 0.955056
85 NHW 0.75 0.955056
86 HDC 0.75 0.955056
87 NHM 0.75 0.955056
88 4KX 0.75 0.944444
89 UOQ 0.75 0.955056
90 HFQ 0.744526 0.955056
91 MRS 0.744526 0.955056
92 MRR 0.744526 0.955056
93 J5H 0.73913 0.977012
94 YNC 0.73913 0.965909
95 DAK 0.73913 0.944444
96 COA FLC 0.736 0.965116
97 8Z2 0.733813 0.944444
98 NHQ 0.723404 0.988372
99 F8G 0.715278 0.913979
100 1HA 0.713287 0.955056
101 01K 0.708333 0.977012
102 COT 0.703448 0.977012
103 CCQ 0.695652 0.934066
104 CA3 0.693878 0.977012
105 7L1 0.692308 0.965909
106 RMW 0.682119 0.955056
107 CA5 0.671053 0.934066
108 93P 0.666667 0.965909
109 UCA 0.666667 0.955056
110 CO7 0.664234 0.977012
111 N9V 0.647887 0.922222
112 93M 0.64557 0.965909
113 OXT 0.634146 0.913979
114 4BN 0.607143 0.913979
115 5TW 0.607143 0.913979
116 BUA COA 0.605634 0.943182
117 PAP 0.603604 0.811765
118 JBT 0.598837 0.894737
119 BSJ 0.592814 0.944444
120 6NA COA 0.585034 0.922222
121 HMG 0.581081 0.943182
122 MYR COA 0.573333 0.922222
123 EO3 COA 0.573333 0.922222
124 DAO COA 0.573333 0.922222
125 DCR COA 0.573333 0.922222
126 X90 COA 0.573333 0.922222
127 DKA COA 0.573333 0.922222
128 PLM COA 0.573333 0.922222
129 A3P 0.54955 0.8
130 PPS 0.547009 0.752688
131 ASP ASP ASP ILE NH2 CMC 0.536585 0.932584
132 0WD 0.521739 0.788889
133 SFC 0.490683 0.955056
134 RFC 0.490683 0.955056
135 ACE SER ASP ALY THR NH2 COA 0.483333 0.932584
136 3AM 0.482143 0.788235
137 PTJ 0.48062 0.872093
138 MET VAL ASN ALA CMC 0.480447 0.932584
139 4PS 0.477477 0.682353
140 5AD NJS 0.47619 0.913043
141 A22 0.468254 0.813953
142 A2D 0.465517 0.802326
143 PUA 0.462585 0.820225
144 PAJ 0.460938 0.883721
145 HQG 0.460317 0.813953
146 ATR 0.459016 0.8
147 AGS 0.459016 0.806818
148 3OD 0.458015 0.825581
149 ADP 0.453782 0.823529
150 9BG 0.451389 0.788889
151 A2R 0.448819 0.813953
152 8LE 0.448 0.848837
153 ACE MET LEU GLY PRO NH2 COA 0.447917 0.932584
154 UBG 0.447853 0.844444
155 BA3 0.445378 0.802326
156 OAD 0.442748 0.825581
157 NA7 0.442748 0.858824
158 ATP 0.442623 0.823529
159 HEJ 0.442623 0.823529
160 AP5 0.441667 0.802326
161 B4P 0.441667 0.802326
162 5FA 0.439024 0.823529
163 2A5 0.439024 0.847059
164 APR 0.439024 0.802326
165 AR6 0.439024 0.802326
166 AQP 0.439024 0.823529
167 AT4 0.438017 0.816092
168 AN2 0.438017 0.813953
169 48N 0.435714 0.808989
170 JNT 0.435115 0.847059
171 M33 0.434426 0.813953
172 QA7 0.434109 0.848837
173 8LQ 0.434109 0.837209
174 9X8 0.431818 0.806818
175 SRP 0.429688 0.837209
176 ANP 0.428571 0.804598
177 ADQ 0.427481 0.804598
178 YLB 0.426573 0.908046
179 YLP 0.425532 0.886364
180 5AL 0.425197 0.813953
181 7D3 0.425 0.793103
182 AD9 0.424 0.804598
183 APU 0.423611 0.786517
184 CA0 0.422764 0.804598
185 7D4 0.422764 0.793103
186 25L 0.422222 0.813953
187 ATF 0.421875 0.795455
188 F2R 0.421769 0.865169
189 NJP 0.421769 0.806818
190 A2P 0.421488 0.788235
191 8QN 0.419847 0.813953
192 PNS 0.419643 0.682353
193 ACP 0.419355 0.825581
194 KG4 0.419355 0.804598
195 8LH 0.418605 0.837209
196 J4G 0.41791 0.848837
197 NDP 0.417808 0.788889
198 ACQ 0.417323 0.825581
199 A1R 0.416667 0.882353
200 ATP A 0.416058 0.770115
201 ATP A A A 0.416058 0.770115
202 AMP 0.415254 0.8
203 A 0.415254 0.8
204 1ZZ 0.414815 0.842697
205 TXA 0.414815 0.816092
206 FYA 0.414815 0.813953
207 NB8 0.414815 0.808989
208 00A 0.413534 0.758242
209 DLL 0.413534 0.793103
210 AHX 0.413534 0.829545
211 PAX 0.412903 0.793478
212 DQV 0.411348 0.813953
213 OMR 0.409722 0.853933
214 9ZD 0.409091 0.818182
215 25A 0.409091 0.802326
216 9ZA 0.409091 0.818182
217 OOB 0.409091 0.793103
218 NPW 0.408163 0.822222
219 6YZ 0.407692 0.825581
220 WAQ 0.407407 0.860465
221 TAT 0.40625 0.816092
222 T99 0.40625 0.816092
223 4AD 0.406015 0.827586
224 AMO 0.406015 0.837209
225 A3R 0.406015 0.882353
226 B5Y 0.405797 0.786517
227 FA5 0.405797 0.816092
228 KMQ 0.405797 0.795455
229 TXP 0.405405 0.829545
230 45A 0.404959 0.781609
231 ABM 0.404959 0.781609
232 PRX 0.404762 0.825581
233 ME8 0.404412 0.842697
234 BIS 0.404412 0.818182
235 AFH 0.404255 0.78022
236 J7V 0.403846 0.778947
237 LQJ 0.402878 0.781609
238 NAI 0.402778 0.777778
239 ODP 0.402685 0.78022
240 DAL AMP 0.401515 0.793103
241 SRA 0.4 0.784091
242 ADX 0.4 0.752688
243 AU1 0.4 0.804598
Similar Ligands (3D)
Ligand no: 1; Ligand: OYA; Similar ligands found: 105
No: Ligand Similarity coefficient
1 OC9 1.0000
2 AE3 1.0000
3 NSD 0.9825
4 AG2 0.9688
5 HE4 0.9664
6 ODI 0.9649
7 HPL 0.9629
8 BHL BHL 0.9626
9 BHL 0.9626
10 16D 0.9619
11 011 0.9603
12 OCA 0.9593
13 DIA 0.9579
14 SPD 0.9571
15 PG0 0.9453
16 KQY 0.9405
17 LYS 0.9380
18 3OL 0.9378
19 5XA 0.9378
20 N6C 0.9354
21 HPN 0.9349
22 MLZ 0.9321
23 ACA 0.9315
24 6XA 0.9309
25 MHN 0.9298
26 NWH 0.9285
27 NF3 0.9283
28 ENV 0.9267
29 GVA 0.9262
30 ONH 0.9254
31 8AC 0.9236
32 TEG 0.9235
33 N8C 0.9230
34 PML 0.9221
35 SHV 0.9215
36 KNA 0.9200
37 DKA 0.9200
38 CLT 0.9200
39 3OM 0.9194
40 M1T 0.9173
41 7XA 0.9166
42 NTU 0.9152
43 NMH 0.9152
44 DAR 0.9142
45 BHH 0.9135
46 ENW 0.9123
47 FXY 0.9118
48 PJL 0.9118
49 0L1 0.9090
50 SS9 0.9072
51 ARG 0.9058
52 37Z 0.9051
53 7BC 0.9050
54 HNE 0.9042
55 HOC 0.9023
56 DE1 0.9000
57 64Z 0.8968
58 6NA 0.8963
59 650 0.8960
60 266 0.8948
61 1H1 0.8944
62 8SZ 0.8943
63 GRQ 0.8936
64 7UC 0.8933
65 SLZ 0.8925
66 EXY 0.8920
67 NOT 0.8917
68 3YP 0.8916
69 MEQ 0.8910
70 AJ3 0.8905
71 4DI 0.8900
72 JX7 0.8861
73 HE2 0.8855
74 9J6 0.8832
75 CIR 0.8828
76 7OD 0.8826
77 MLY 0.8825
78 OHJ 0.8822
79 DLT 0.8811
80 UN1 0.8808
81 GGB 0.8808
82 GLY GLY GLY 0.8808
83 LYN 0.8797
84 DZA 0.8794
85 LPA 0.8789
86 DLY 0.8771
87 7C3 0.8766
88 B3M 0.8738
89 NPI 0.8731
90 YIV 0.8725
91 XOG 0.8715
92 ILO 0.8712
93 DHH 0.8678
94 HTX 0.8665
95 2FM 0.8656
96 K6V 0.8652
97 1N5 0.8650
98 HGA 0.8647
99 NNH 0.8643
100 6HN 0.8642
101 GGG 0.8636
102 HPO 0.8631
103 1KA 0.8607
104 58X 0.8590
105 U4G 0.8581
Ligand no: 2; Ligand: COA; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6PCD; Ligand: OYA; 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: 6pcd.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6PCD; Ligand: COA; 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: 6pcd.bio1) has 29 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6PCD; Ligand: OYA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 6pcd.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 6PCD; Ligand: OYA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 6pcd.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 6PCD; Ligand: COA; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 6pcd.bio1) has 31 residues
No: Leader PDB Ligand Sequence Similarity
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