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Receptor
PDB id Resolution Class Description Source Keywords
4MPN 1.75 Å EC: 2.7.11.2 CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 COMPLEX WITH INHIBITOR PS10 HOMO SAPIENS GHKL PROTEIN KINASE PYRUVATE DEHYDROGENASE COMPLEX MITOCHOPROTEIN KINASES IMPAIRED GLUCOSE OXIDATION HEPATIC STEATO2 DIABETES CANCER BERGERAT NUCLEOTIDE-BINDING FOLD PROTEKINASE TRANSFERASE
Ref.: STRUCTURE-GUIDED DEVELOPMENT OF SPECIFIC PYRUVATE DEHYDROGENASE KINASE INHIBITORS TARGETING THE ATP-B POCKET. J.BIOL.CHEM. V. 289 4432 2014
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TLA A:502;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
PV0 A:501;
Valid;
none;
Kd = 239 nM
323.321 C14 H13 N O6 S c1cc(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5J6A 2.05 Å EC: 2.7.11.2 CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 COMPLEX WITH INHIBITOR PS46 HOMO SAPIENS GHKL PROTEIN KINASE PYRUVATE DEHYDROGENASE COMPLEX MITOCHOPROTEIN KINASES IMPAIRED GLUCOSE OXIDATION HEPATIC STEATO2 DIABETES CANCER BERGERAT NUCLEOTIDE-BINDING FOLD PROTEKINASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DEVELOPMENT OF DIHYDROXYPHENYL SULFONYLISOINDOLINE DERIVATIVES AS LIVER-TARGETING PYRUVATE DEHYDROGENA INHIBITORS. J. MED. CHEM. V. 60 1142 2017
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 2BU8 - TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
2 1JM6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
4 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
5 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
6 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
7 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
8 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
9 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
10 5J6A ic50 = 58 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
11 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
12 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
14 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
16 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
70% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2BU8 - TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
2 1JM6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
4 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
5 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
6 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
7 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
8 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
9 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
10 5J6A ic50 = 58 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
11 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
12 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
14 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
16 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
17 2Q8H Ki = 1 mM TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
18 2Q8G ic50 = 0.087 uM AZX C19 H18 Cl F3 N2 O5 S C[C@@](C(=....
19 3D2R Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 2ZKJ Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 2ZDY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 2E0A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
50% Homology Family (22)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2BU8 - TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
2 1JM6 - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
3 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
4 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
5 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
6 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
7 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
8 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
9 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
10 5J6A ic50 = 58 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
11 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
12 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
14 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
16 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
17 2Q8H Ki = 1 mM TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
18 2Q8G ic50 = 0.087 uM AZX C19 H18 Cl F3 N2 O5 S C[C@@](C(=....
19 3D2R Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
20 2ZKJ Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
21 2ZDY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 2E0A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PV0; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 PV0 1 1
2 PV2 0.561404 0.967742
3 PV8 0.559322 0.983871
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5J6A; Ligand: P46; Similar sites found with APoc: 273
This union binding pocket(no: 1) in the query (biounit: 5j6a.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
1 4RJD TFP None
2 5N8V KZZ None
3 4WG0 CHD None
4 2FDW D3G 1.25
5 4UBS DIF 1.27226
6 6B21 C9V 1.5
7 1EWF PC1 1.5
8 1V59 NAD 1.5
9 2FN1 SAL 1.5
10 5LA1 XYP 1.5
11 2EXK XYS XYS 1.5
12 1SJD NPG 1.63043
13 4I90 CHT 1.65016
14 2O1V ADP 1.75
15 1E4I NFG 1.75
16 4MRP GSH 1.75
17 4DO1 ANN 1.75
18 6D28 NEC 1.8315
19 1YYE 196 1.86567
20 4DE3 DN8 1.90114
21 1NF8 BOG 1.93237
22 4V3I ASP LEU THR ARG PRO 1.94553
23 3O01 DXC 1.94805
24 1TMX HGX 2.04778
25 4HY1 19X 2.05128
26 1S16 ANP 2.05128
27 2GFD RDA 2.11864
28 3B6C SDN 2.13675
29 1GNI OLA 2.25
30 5JOX EDG 2.25
31 1BGV GLU 2.25
32 3X01 AMP 2.29008
33 4RW3 PLM 2.31788
34 4RW3 TDA 2.31788
35 1GEG GLC 2.34375
36 3F8C HT1 2.38095
37 1ZDQ MSM 2.38095
38 1UNQ 4IP 2.4
39 2FGQ MLT 2.40964
40 4WGF HX2 2.43902
41 4MNS 2AX 2.51572
42 2IOR ADP 2.55319
43 5M37 9SZ 2.6087
44 4OB6 S2T 2.6393
45 5EE7 5MV 2.65487
46 3K60 ADP 2.69058
47 3G5K BB2 2.73224
48 5URY PAM 2.73973
49 5IM3 DTP 2.75
50 3CV2 COA 2.75
51 4ARE FLC 2.75
52 2W8Q SIN 2.75
53 4AZI OAN 2.75
54 5A4W QCT 2.83019
55 4IMO PWZ 2.84091
56 5IUY BOG 2.86976
57 3RWP ABQ 2.89389
58 1JGS SAL 2.89855
59 1U3R 338 2.90456
60 3TDC 0EU 3
61 5Y3N 8MF 3
62 4IVG ANP 3
63 4IPE ANP 3
64 1ZPD CIT 3
65 2WH8 II2 3
66 4B7P 9UN 3.04348
67 2YI0 YI0 3.05677
68 6CB2 OLC 3.07167
69 3VV5 SLZ 3.07692
70 3PMA SCR 3.0888
71 3EHG ATP 3.125
72 1QZR ANP 3.25
73 1QZR CDX 3.25
74 2JHP GUN 3.25
75 5TG5 JW8 3.26531
76 3H4L ANP 3.26975
77 5EY0 GTP 3.28467
78 2OWZ CIT 3.31325
79 1R6N 434 3.31754
80 3I6B KDO 3.33333
81 6BR9 6OU 3.34262
82 6BR9 PGV 3.34262
83 5NTP 98E 3.36134
84 3MG9 GHP 3MY 3FG GHP GHP OMY 3FG 3.40136
85 3NB0 G6P 3.5
86 5VRH OLB 3.5
87 1XVB 3BR 3.52941
88 1YRE COA 3.5533
89 2HHP FLC 3.75
90 1KAH HIS 3.75
91 1J78 OLA 3.75
92 3TL1 JRO 3.77358
93 5F5R ANP 3.78151
94 3R9V DXC 3.84615
95 4G86 BNT 3.87324
96 5OF9 ANP 4
97 1VEM GLC GLC 4
98 5WL1 D3D 4.0404
99 5WL1 CUY 4.0404
100 5IJJ I6P 4.16667
101 1UUY PPI 4.19162
102 4LZB URA 4.20168
103 1HSL HIS 4.20168
104 5GLT BGC GAL NAG GAL 4.22535
105 5IN3 G1P 4.25
106 5C9J DAO 4.27046
107 6BR8 6OU 4.36508
108 6BR8 PGV 4.36508
109 2CNT COA 4.375
110 1BGQ RDC 4.44444
111 5XQL C2E 4.46735
112 5JSP DQY 4.47761
113 2GBB CIT 4.48718
114 3R9C ECL 4.5
115 2HFN FMN 4.57516
116 3L9R L9R 4.59364
117 4XCL AGS 4.6332
118 4NB5 2JT 4.67836
119 5OCA 9QZ 4.7619
120 4DW4 U5P 4.79042
121 4ZGM 32M 4.91803
122 1TIQ COA 5
123 2Q4G CIT 5
124 4A59 AMP 5
125 4BTB PRO PRO PRO PRO PRO PRO PRO PRO PRO 5.02092
126 3QRC SCR 5.09554
127 4O4Z N2O 5.19481
128 3GZ9 D32 5.20446
129 5DCH 1YO 5.20833
130 2WPX ACO 5.30973
131 4W9N TCL 5.30973
132 5HCN DAO 5.36398
133 5MBC FMN 5.38244
134 1TV5 N8E 5.5
135 2YLD CMO 5.51181
136 5C1M OLC 5.6
137 5C1M CLR 5.6
138 2PEH LYS ARG LYS SER ARG TRP ASP GLU THR PRO 5.71429
139 5AZC PGT 5.75
140 5U0L 8YP 5.75
141 4WQ2 3SU 5.78035
142 5LX9 OLB 5.86319
143 6D5V FVY 5.98802
144 4IA6 EIC 6
145 4HZ0 1AV 6.10329
146 1SQL GUN 6.16438
147 5V4R MGT 6.17284
148 1NU4 MLA 6.18557
149 4IBF 1D5 6.20155
150 4NTO 1PW 6.28019
151 1XMY ROL 6.28141
152 1YRO UDP 6.29371
153 3W54 RNB 6.38298
154 2RH1 CLR 6.5
155 6MPT C30 6.5
156 3AQT RCO 6.53061
157 4F4S EFO 6.57895
158 3KP6 SAL 6.62252
159 4ZVI 4S4 6.6313
160 5EW9 5VC 6.64207
161 1S14 NOV 6.70103
162 2FCU AKG 6.70927
163 5LWY OLB 6.72269
164 2PRG BRL 6.81818
165 2VWA PTY 6.93069
166 5WSY 7UC 6.93642
167 5OLK DTP 7
168 3GFZ FMN 7
169 1M2Z BOG 7.00389
170 4YSX E23 7.05128
171 1KIJ NOV 7.17949
172 3RMK BML 7.25
173 5FH7 5XL 7.25806
174 3EHH ADP 7.33945
175 5V3Y 5V8 7.34266
176 1UCD U5P 7.36842
177 2QQC AG2 7.54717
178 1MT1 AG2 7.69231
179 1N13 AG2 7.69231
180 1ZED PNP 7.75
181 1B63 ANP 7.80781
182 2QQD AG2 7.83133
183 6BMS POV 7.91789
184 1YC4 43P 7.95455
185 5UGW GSH 8
186 4JMU 1ML 8.03571
187 5B4B LP5 8.06452
188 4V1F BQ1 8.13953
189 5EOO CIT 8.30189
190 5LXT GTP 8.39161
191 3B12 FAH 8.55263
192 4MBY BGC SIA GAL 8.63309
193 5NM7 GLY 8.64662
194 3EYK EYK 8.72093
195 2BCG GER 9.2233
196 5CHR 4NC 9.48905
197 5DXE EST 9.57854
198 5WGD EST 9.57854
199 5WGQ EST 9.57854
200 2QA8 GEN 9.68992
201 2QZO KN1 9.68992
202 4XPL ACO 9.81595
203 2BHW NEX 9.91379
204 5HYR EST 10.0775
205 4GCZ ADP 10.1299
206 2D7I UDP 10.25
207 1T0S BML 10.303
208 3L1N PLM 10.3093
209 5AAV GW5 10.3175
210 3PMD 11A 10.4575
211 2QE4 JJ3 10.4839
212 6DIO CIT 10.5
213 1N8V BDD 10.7143
214 6MVU K4V 10.75
215 2XCM ADP 10.8696
216 3CHT 4NB 11.0119
217 4I67 G G G RPC 11.4943
218 4URL XAM 11.5
219 2D5Z L35 11.6438
220 2HKJ RDC 11.75
221 6D61 4AA 11.7949
222 5UC4 83S 11.8182
223 1KZN CBN 12.1951
224 4V2O CLQ 12.1951
225 1ZXM ANP 12.25
226 6BLD DXJ 12.25
227 1X0P FAD 12.5874
228 2D3Y DU 12.7854
229 4RYV ZEA 12.9032
230 2IYG FMN 13.7097
231 1YRX FMN 14.0496
232 4BAE RWX 14.1463
233 4B6C B5U 14.2857
234 5W7B MYR 14.8936
235 5IDM ANP 15.0838
236 4GGL CJC 15.3488
237 5B25 4QJ 15.3846
238 4UA3 COA 15.4639
239 4EMV 0R9 16.3717
240 4ZSI GLP 16.3743
241 1Y9Q MED 16.6667
242 6GMN F4E 16.6667
243 3TTZ 07N 17.6768
244 4HBM 0Y7 18.3333
245 1TH8 ADP 18.6207
246 4P8O 883 18.7166
247 5I8F ML1 18.7879
248 1TID ATP 19.1176
249 4PL9 ADP 19.1257
250 1ID0 ANP 19.7368
251 4OGQ 7PH 20.5882
252 4OGQ 1O2 20.5882
253 5TVI O8N 20.6522
254 4URN NOV 20.8889
255 3D36 ADP 20.9016
256 2WOR 2AN 22
257 5ZCO CHD 22.0339
258 5W97 CHD 22.0339
259 5Z84 CHD 22.0339
260 5Z84 PGV 22.0339
261 2DYS PGV 22.0339
262 5ZCO PGV 22.0339
263 2C2A ADP 22.093
264 4OAS 2SW 22.9167
265 4BIX ADP 23.4899
266 1I58 ACP 28.0423
267 1I58 ADP 28.0423
268 3OLL EST 31.5789
269 3KPE TM3 37.2549
270 1GKZ ADP 45.1031
271 4TV1 36M 46.1538
272 4TUZ 36J 46.1538
273 3UUD EST 46.1538
Pocket No.: 2; Query (leader) PDB : 5J6A; Ligand: P46; 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: 5j6a.bio1) has 32 residues
No: Leader PDB Ligand Sequence Similarity
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