Receptor
PDB id Resolution Class Description Source Keywords
4MP7 1.8 Å EC: 2.7.1.99 CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 COMPLEX WITH INHIBITOR PA7 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.: 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
PFT A:501;
Valid;
none;
Kd = 1827 nM
255.269 C15 H13 N O3 c1ccc...
TLA A:502;
Invalid;
none;
submit data
150.087 C4 H6 O6 [C@@H...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5J6A 2.05 Å EC: 2.7.1.99 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 (18)
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 6LIO Kd = 64.4 nM EH3 C30 H34 Cl N3 O9 S CS(=O)(=O)....
4 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
5 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
6 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
7 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
8 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
9 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
10 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
11 5J6A Kd = 22 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
12 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
14 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
16 6LIL - EGX C22 H19 N3 O2 c1ccc2c(c1....
17 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
18 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
70% Homology Family (24)
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 6LIO Kd = 64.4 nM EH3 C30 H34 Cl N3 O9 S CS(=O)(=O)....
4 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
5 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
6 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
7 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
8 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
9 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
10 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
11 5J6A Kd = 22 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
12 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
14 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
16 6LIL - EGX C22 H19 N3 O2 c1ccc2c(c1....
17 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
18 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
19 2Q8H Ki = 1 mM TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
20 2Q8G ic50 = 0.087 uM AZX C19 H18 Cl F3 N2 O5 S C[C@@](C(=....
21 3D2R Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 2ZKJ Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 2ZDY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 2E0A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
50% Homology Family (24)
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 6LIO Kd = 64.4 nM EH3 C30 H34 Cl N3 O9 S CS(=O)(=O)....
4 2BU6 - TF2 C19 H21 F3 N2 O4 S CC[N@@](c1....
5 4MPN Kd = 239 nM PV0 C14 H13 N O6 S c1cc(c(cc1....
6 5M4M Ki = 1.02 uM 7FW C31 H26 N4 O4 CN(Cc1ccc2....
7 2BU7 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
8 5J71 - P35 C19 H23 N3 O4 S c1cc2c(cc1....
9 4MP2 Kd = 3570 nM PV1 C15 H12 Br N O3 c1ccc2c(c1....
10 4MPE Kd = 426 nM PV8 C14 H13 N O5 S c1cc2c(cc1....
11 5J6A Kd = 22 nM P46 C23 H27 N5 O6 S c1cc2cn(cc....
12 4V26 - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
13 5M4P - TF3 C20 H25 Cl N2 O2 CC(C)c1ccc....
14 2BU5 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
15 2BU2 - TF1 C18 H20 F3 N3 O3 C[C@H]1CN(....
16 6LIL - EGX C22 H19 N3 O2 c1ccc2c(c1....
17 4MP7 Kd = 1827 nM PFT C15 H13 N O3 c1ccc2c(c1....
18 4MPC Kd = 711 nM PV2 C14 H13 N O4 S c1ccc2c(c1....
19 2Q8H Ki = 1 mM TF4 C2 H2 Cl2 O2 C(C(=O)O)(....
20 2Q8G ic50 = 0.087 uM AZX C19 H18 Cl F3 N2 O5 S C[C@@](C(=....
21 3D2R Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
22 2ZKJ Kd = 3.3 uM ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
23 2ZDY - ADP C10 H15 N5 O10 P2 c1nc(c2c(n....
24 2E0A - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PFT; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PFT 1 1
2 PV1 0.526316 0.916667
3 VHD 0.5 0.93617
4 83S 0.47619 0.875
5 XJG 0.46875 0.857143
6 L81 0.462687 0.767857
Similar Ligands (3D)
Ligand no: 1; Ligand: PFT; Similar ligands found: 164
No: Ligand Similarity coefficient
1 PV2 0.9518
2 BGK 0.9389
3 PV8 0.9388
4 9ME 0.9387
5 TCT 0.9357
6 DBE 0.9347
7 7ZO 0.9334
8 WCU 0.9257
9 LVY 0.9251
10 CHV 0.9245
11 SVG 0.9245
12 27M 0.9244
13 4EU 0.9240
14 9JT 0.9225
15 PV0 0.9191
16 9MK 0.9184
17 7XX 0.9172
18 5F4 0.9153
19 S46 0.9139
20 BXZ 0.9114
21 Q8D 0.9097
22 CUQ 0.9092
23 DCN 0.9068
24 BZM 0.9067
25 CUH 0.9066
26 9JH 0.9043
27 4RV 0.9039
28 9W7 0.9027
29 4AU 0.9023
30 Q8G 0.9016
31 4KN 0.9013
32 JE7 0.9009
33 LR2 0.9008
34 FT1 0.9004
35 9RK 0.8993
36 A8K 0.8978
37 2OH 0.8978
38 FT3 0.8970
39 F4U 0.8965
40 KUP 0.8961
41 J84 0.8959
42 43J 0.8948
43 H48 0.8944
44 QTJ 0.8943
45 IPJ 0.8940
46 KXN 0.8939
47 FT2 0.8936
48 5R9 0.8934
49 TPM 0.8933
50 C4F 0.8927
51 LZJ 0.8922
52 TCL 0.8910
53 5C1 0.8907
54 PZX 0.8906
55 2OX 0.8903
56 0X2 0.8901
57 4L2 0.8899
58 JF5 0.8886
59 VIB 0.8885
60 7FX 0.8881
61 A18 0.8875
62 CBE 0.8872
63 FB4 0.8868
64 QTD 0.8867
65 ZW2 0.8865
66 4YE 0.8864
67 SJR 0.8855
68 CUT 0.8852
69 SNJ 0.8847
70 FX5 0.8847
71 1FL 0.8843
72 AX8 0.8838
73 DZ1 0.8832
74 YUG 0.8822
75 F41 0.8820
76 QTS 0.8815
77 62P 0.8813
78 XYS XYS 0.8812
79 Q11 0.8808
80 1SF 0.8801
81 ESJ 0.8795
82 JVD 0.8793
83 MW5 0.8783
84 XDI 0.8782
85 EV2 0.8780
86 5R8 0.8779
87 FL9 0.8778
88 IXE 0.8774
89 WVV 0.8766
90 S45 0.8764
91 OJD 0.8763
92 AJ4 0.8761
93 TCC 0.8759
94 XDH 0.8753
95 5F7 0.8753
96 WDW 0.8750
97 9HK 0.8746
98 5RU 0.8734
99 47V 0.8728
100 8OE 0.8726
101 L23 0.8720
102 8OB 0.8719
103 QTV 0.8714
104 NAR 0.8712
105 CMP 0.8711
106 JOB 0.8711
107 EMU 0.8711
108 51P 0.8705
109 WL3 0.8692
110 40N 0.8685
111 CC6 0.8680
112 6WS 0.8677
113 MQR 0.8676
114 5WK 0.8671
115 RK4 0.8668
116 A7Q 0.8665
117 Q9P 0.8664
118 HH6 0.8662
119 0OY 0.8661
120 4L6 0.8660
121 EAT 0.8657
122 MRI 0.8653
123 28E 0.8653
124 J3B 0.8648
125 H7S 0.8640
126 JD7 0.8639
127 FM2 0.8639
128 0OP 0.8637
129 2L1 0.8635
130 AX4 0.8624
131 MEX 0.8624
132 5NR 0.8615
133 EFT 0.8609
134 RKY 0.8607
135 LFK 0.8604
136 5TO 0.8602
137 7VF 0.8601
138 D25 0.8600
139 4NR 0.8593
140 1HR 0.8593
141 43F 0.8590
142 TOP 0.8590
143 3IP 0.8590
144 536 0.8584
145 3CA 0.8580
146 AUE 0.8578
147 MJ5 0.8574
148 7PS 0.8571
149 AP6 0.8571
150 SP1 0.8566
151 16J 0.8565
152 B4L 0.8563
153 0QV 0.8561
154 FPL 0.8560
155 R75 0.8559
156 KW7 0.8549
157 6XC 0.8541
158 JOT 0.8541
159 X29 0.8541
160 D8X 0.8538
161 DP4 0.8535
162 IQW 0.8532
163 IPL 0.8532
164 EJ5 0.8518
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: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 5j6a.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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 37 residues
No: Leader PDB Ligand Sequence Similarity
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