Receptor
PDB id Resolution Class Description Source Keywords
2VK4 1.95 Å EC: 4.1.1.1 CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS KLUYVEROMYCES LACTIS METAL-BINDING DECARBOXYLASE DIMER OF DIMERS SUBSTRATE ACTIVATION THIAMINE DIPHOSPHATE TDP TPP LYASE MAGNESIUM FLAVOPROTEIN THIAMINE PYROPHOSPHATE ASYMMETRIC ACTIVE SITES
Ref.: ALLOSTERIC ACTIVATION OF PYRUVATE DECARBOXYLASES. A NEVER-ENDING STORY? TO BE PUBLISHED
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG A:601;
B:601;
C:601;
D:601;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
24.305 Mg [Mg+2...
TPP A:600;
B:600;
C:600;
D:600;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
425.314 C12 H19 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2VK4 1.95 Å EC: 4.1.1.1 CRYSTAL STRUCTURE OF PYRUVATE DECARBOXYLASE FROM KLUYVEROMYCES LACTIS KLUYVEROMYCES LACTIS METAL-BINDING DECARBOXYLASE DIMER OF DIMERS SUBSTRATE ACTIVATION THIAMINE DIPHOSPHATE TDP TPP LYASE MAGNESIUM FLAVOPROTEIN THIAMINE PYROPHOSPHATE ASYMMETRIC ACTIVE SITES
Ref.: ALLOSTERIC ACTIVATION OF PYRUVATE DECARBOXYLASES. A NEVER-ENDING STORY? TO BE PUBLISHED
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
7 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2VK8 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 1PYD - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
3 1QPB Kd = 44 mM PYM C3 H5 N O2 CC(=O)C(=O....
4 2VK1 - TPP PYR n/a n/a
5 1PVD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
6 2VBG - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
7 2VBF - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
9 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
11 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
12 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
13 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 41
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 V4E 0.891892 1
3 TDP 0.84 0.985714
4 TPS 0.816901 0.957143
5 TMV 0.769231 0.958333
6 2TP 0.725 0.932432
7 VNP 0.721519 0.958904
8 VIB 0.621622 0.75
9 PYI 0.581395 0.887324
10 TDW 0.566667 0.972222
11 HTL 0.566667 0.958904
12 N1T 0.556818 0.985714
13 FTP 0.551724 0.835616
14 THV 0.548387 0.958904
15 TPW 0.546512 0.9
16 WWF 0.542553 0.933333
17 TD6 0.540816 0.921053
18 THY 0.536842 0.945946
19 TOG 0.536082 0.921053
20 TDL 0.53125 0.897436
21 THW 0.530612 0.958904
22 TD9 0.53 0.921053
23 TD8 0.53 0.921053
24 TDK 0.525773 0.921053
25 D7K 0.490566 0.909091
26 S1T 0.489362 0.887324
27 R1T 0.489362 0.887324
28 TPU 0.483146 0.842105
29 5SR 0.479167 0.945205
30 T5X 0.476636 0.897436
31 T6F 0.476636 0.897436
32 1U0 0.474227 0.84
33 8PA 0.459459 0.945946
34 TZD 0.451613 0.883117
35 O2T 0.45098 0.909091
36 TDM 0.443299 0.894737
37 TDN 0.415842 0.871795
38 THD 0.411765 0.839506
39 MP5 0.407895 0.676056
40 TD7 0.40566 0.85
41 DPX 0.4 0.734177
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 2vk4.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found: 84
This union binding pocket(no: 2) in the query (biounit: 2vk4.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1U6R IOM 0.02292 0.41854 1.31579
2 3OTH TYD 0.01422 0.40298 1.45631
3 5ND5 TPP 0.0001967 0.44593 1.59858
4 2R5N TPP 0.0005613 0.40516 1.64425
5 2R5N R5P 0.000583 0.4045 1.64425
6 2R5N RP5 0.0004681 0.40335 1.64425
7 1QS0 TDP 0.0007025 0.40932 1.7199
8 2OG2 MLI 0.003323 0.42966 1.94986
9 2DVZ GLU 0.02203 0.40457 2.2293
10 3B9Q MLI 0.007483 0.42497 2.31788
11 2Q1A 2KT 0.03629 0.40668 2.38908
12 3VM7 GLC 0.02481 0.4126 2.43902
13 2CI5 HCS 0.03484 0.4011 2.46479
14 1HSR BHO 0.02114 0.42104 2.61628
15 1ITZ TPP 0.000192 0.46199 2.6643
16 3W9F I3P 0.008204 0.46043 2.69231
17 1DNP MHF 0.0231 0.41463 2.9724
18 2OZL TPP 0.00008144 0.45238 3.0137
19 5FJJ MAN 0.002387 0.45581 3.01954
20 1G8S MET 0.01731 0.41917 3.04348
21 1EJ4 M7G 0.03841 0.40365 3.15789
22 5ESO ISC 0.00000001278 0.63819 3.37478
23 5ESO TDP 0.00000001278 0.63819 3.37478
24 3P13 RIP 0.01739 0.40407 3.47222
25 3VKC FPQ 0.005041 0.40989 3.4965
26 3EXH TPP 0.0001195 0.47917 3.64742
27 2O66 FLC 0.01906 0.41843 3.7037
28 3CTL S6P 0.008446 0.40338 3.8961
29 2YIC TPP 0.001189 0.41406 4.08526
30 1R9J TPP 0.0001399 0.46763 4.26288
31 5XDR ADP 0.02227 0.40064 4.26288
32 2CYB TYR 0.009257 0.43361 4.33437
33 2O1S TDP 0.00002529 0.53043 4.4405
34 5B19 TLA 0.02303 0.40751 4.74138
35 1JI0 ATP 0.01463 0.42207 5
36 1UMD TDP COI 0.0001909 0.45432 5.24691
37 1GY8 UDP 0.01934 0.40741 5.28967
38 1G6H ADP 0.02572 0.40792 5.44747
39 5B48 TDN 0.00000007043 0.55527 5.57377
40 2QV7 ADP 0.01377 0.40363 5.63798
41 2IYA UDP 0.006864 0.41406 5.66038
42 3HWW AKG 0.00008956 0.42444 6.11511
43 2C42 PYR 0.00000006984 0.59959 6.2167
44 2C42 TPP 0.00000006984 0.59959 6.2167
45 1A8S PPI 0.02377 0.4087 6.22711
46 3DVA TPW 0.0004248 0.4406 6.30841
47 2B3B BGC 0.01895 0.41187 6.75
48 2B3B GLC 0.01955 0.41117 6.75
49 1ZX5 LFR 0.02477 0.40905 8.33333
50 4PPF FLC 0.02437 0.41917 8.57143
51 1RP7 TZD 0.0001843 0.44908 8.70337
52 1D8C GLV 0.04857 0.40178 9.05861
53 2ZL4 ALA ALA ALA ALA 0.02083 0.41592 9.18367
54 1XVB BHL BHL 0.03018 0.40088 10
55 5EXE 5SR 0.000001164 0.55036 11.1465
56 2X7J TPP 0.00000002303 0.6091 14.9201
57 3AI7 TPP 0.00002431 0.48967 15.2753
58 3HY2 ATP 0.02239 0.40814 17.2727
59 1O8B ABF 0.03204 0.40012 17.3516
60 5BXV MGP 0.02858 0.41199 18.1818
61 3CYI ATP 0.04149 0.40003 19.0909
62 1W85 TDP 0.0003396 0.45985 22.449
63 1EJH M7G 0.02598 0.40978 31.25
64 4RJK TPP 0.000000002577 0.6262 32.6821
65 4RJK TDL 0.000000003315 0.60325 32.6821
66 1V5F FAD 0.00001771 0.54088 33.3925
67 1V5F TPP 0.04924 0.43662 33.3925
68 3IAE D7K 0.0000000002975 0.62798 34.7368
69 3EYA TDP 0.0000000003794 0.67954 34.9727
70 2UZ1 TPP 0.0000000001551 0.69488 35.3464
71 2IHU TP9 0.00000001501 0.54162 36.8237
72 1T9D P22 0.0000000474 0.70881 36.9449
73 1T9D PYD 0.00000006435 0.66924 36.9449
74 1T9D FAD 0.000000003037 0.40097 36.9449
75 1T9D P25 0.000000003011 0.40093 36.9449
76 1YBH P22 0.00000005911 0.68126 37.1226
77 1UPA TPP 0.00000001333 0.61849 37.1728
78 2IHT TPP 0.00000003157 0.6037 37.1728
79 2C31 TZD 0.0000006076 0.61253 37.6761
80 2C31 ADP 0.000000599 0.61188 37.6761
81 3FSJ D7K 0.000005238 0.47223 37.6894
82 1OZH HE3 0.000000191 0.62004 37.833
83 2Q28 TPP 0.00001289 0.50057 38.1206
84 2NXW TPP 0.00000000008818 0.63649 41.9183
Pocket No.: 3; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found: 11
This union binding pocket(no: 3) in the query (biounit: 2vk4.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2WPF WPF 0.03534 0.40781 1.41414
2 4JUI EGR 0.03563 0.40165 2.55319
3 1I0B PEL 0.02741 0.40353 2.71084
4 2X7I CIT 0.02309 0.40354 3.57143
5 1RE8 BD2 0.008707 0.40803 4
6 2J5V PCA 0.03276 0.40111 4.63215
7 1KNY APC 0.01928 0.40016 4.74308
8 2VZ6 FEF 0.01686 0.40655 5.43131
9 3I7S PYR 0.01424 0.40987 6.84932
10 1XVB 3BR 0.02429 0.40244 10
11 4YMZ 13P 0.03089 0.40094 17.1315
Pocket No.: 4; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2vk4.bio2) has 24 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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