Receptor
PDB id Resolution Class Description Source Keywords
4MP2 1.75 Å EC: 2.7.1.99 CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 COMPLEX WITH INHIBITOR PA1 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
PV1 A:501;
 Valid;
 none;
 Kd = 3570 nM
334.165 C15 H12 Br 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: PV1; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PV1 1 1
2 VHD 0.576271 0.862745
3 PFT 0.526316 0.916667
4 83S 0.5 0.807692
5 XJG 0.492308 0.792453
6 L81 0.463768 0.716667
Similar Ligands (3D)
Ligand no: 1; Ligand: PV1; Similar ligands found: 84
No: Ligand Similarity coefficient
1 PV2 0.9242
2 9ME 0.9179
3 TCT 0.9142
4 DBE 0.9106
5 9W7 0.9106
6 PV8 0.9094
7 5V3 0.9094
8 9RK 0.9078
9 0QX 0.9076
10 FL9 0.9044
11 CHV 0.9020
12 F91 0.9019
13 PV0 0.9009
14 BGK 0.8996
15 Q8D 0.8978
16 FVY 0.8974
17 DCN 0.8969
18 QRP 0.8949
19 AX8 0.8931
20 27M 0.8908
21 LVY 0.8907
22 BXZ 0.8906
23 KXN 0.8900
24 Q8G 0.8894
25 5R9 0.8893
26 CUQ 0.8892
27 XDI 0.8891
28 VIB 0.8885
29 S46 0.8878
30 9MK 0.8876
31 OA5 0.8872
32 7XX 0.8867
33 PNW 0.8859
34 KU3 0.8849
35 4KN 0.8847
36 A8K 0.8844
37 TCL 0.8813
38 94M 0.8812
39 5F4 0.8812
40 TCW 0.8801
41 C4F 0.8797
42 QTS 0.8778
43 KUP 0.8775
44 XYS XYS 0.8767
45 4EU 0.8761
46 SVG 0.8755
47 4L6 0.8750
48 28E 0.8749
49 FT1 0.8727
50 BZM 0.8724
51 YUG 0.8720
52 BXB 0.8720
53 J84 0.8717
54 2OH 0.8716
55 LZJ 0.8711
56 9JH 0.8700
57 4RV 0.8696
58 FT2 0.8693
59 4YE 0.8691
60 9FN 0.8689
61 CUH 0.8683
62 IGP 0.8683
63 4L2 0.8682
64 FT3 0.8679
65 CUT 0.8679
66 CMP 0.8667
67 S45 0.8665
68 X29 0.8660
69 FB4 0.8645
70 FM2 0.8633
71 FIP 0.8627
72 TCC 0.8626
73 RK4 0.8621
74 EFT 0.8620
75 5RU 0.8620
76 9JT 0.8611
77 62P 0.8596
78 EEY 0.8589
79 LR2 0.8585
80 ZW2 0.8568
81 3QI 0.8558
82 CD9 0.8535
83 BC3 0.8528
84 6JO 0.8519
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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