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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 (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 6EFG - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (8)
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 6EFG - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
7 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (14)
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 2WVG - TPU C11 H18 N6 O7 P2 Cc1c(nnn1C....
9 3OE1 - TDL C15 H23 N4 O10 P2 S Cc1c(sc([n....
10 2WVA - PYR C3 H4 O3 CC(=O)C(=O....
11 1ZPD - DPX C11 H20 N4 O8 P2 S Cc1ncc(c(n....
12 6EFG - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
13 2VK4 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 2VJY - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 47
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 AUJ 0.55914 0.921053
13 N1T 0.556818 0.985714
14 FTP 0.551724 0.835616
15 THV 0.548387 0.958904
16 TPW 0.546512 0.9
17 WWF 0.542553 0.933333
18 TD6 0.540816 0.921053
19 THY 0.536842 0.945946
20 TOG 0.536082 0.921053
21 TDL 0.53125 0.897436
22 THW 0.530612 0.958904
23 TD8 0.53 0.921053
24 TD9 0.53 0.921053
25 TDK 0.525773 0.921053
26 D7K 0.490566 0.909091
27 S1T 0.489362 0.887324
28 R1T 0.489362 0.887324
29 TPU 0.483146 0.842105
30 5SR 0.479167 0.945205
31 T6F 0.476636 0.897436
32 T5X 0.476636 0.897436
33 1U0 0.474227 0.84
34 8PA 0.459459 0.945946
35 8FL 0.457447 0.894737
36 8EO 0.457447 0.92
37 TZD 0.451613 0.883117
38 O2T 0.45098 0.909091
39 TDM 0.443299 0.894737
40 8EL 0.442105 0.894737
41 G8G 0.44086 0.805195
42 TDN 0.415842 0.871795
43 THD 0.411765 0.839506
44 8N9 0.411765 0.839506
45 MP5 0.407895 0.676056
46 TD7 0.40566 0.85
47 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 with APoc: 137
This union binding pocket(no: 1) in the query (biounit: 2vk4.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
1 2WPF WPF 1.41414
2 2WPF FAD 1.41414
3 3OTH TYD 1.45631
4 4UP4 NDG 1.49626
5 5MB4 NAG 1.49626
6 5MB4 NDG 1.49626
7 4UP4 GAL NAG 1.49626
8 1VRP ADP 1.5748
9 1VRP IOM 1.5748
10 5ND5 TPP 1.59858
11 6FXR UDP 1.59858
12 2R5N TPP 1.64425
13 2R5N R5P 1.64425
14 2R5N RP5 1.64425
15 1QS0 TDP 1.7199
16 4TQK NAG 1.72414
17 2OG2 MLI 1.94986
18 3CQO FUC 2.04778
19 2J4D MHF 2.28571
20 3ZQE DXC 2.29508
21 3B9Q MLI 2.31788
22 3B6R ADP 2.3622
23 1TKB N1T 2.48668
24 3KLL MAL 2.48668
25 1ITZ TPP 2.6643
26 3W9F I3P 2.69231
27 5C9P FUC 2.88714
28 2OZL TPP 3.0137
29 5FJJ MAN 3.01954
30 1G8S MET 3.04348
31 1EJ4 M7G 3.15789
32 1ZUW DGL 3.19716
33 6C0B MLI 3.20513
34 5ESO ISC 3.37478
35 5ESO TDP 3.37478
36 5ZI9 FLC 3.46154
37 3P13 RIP 3.47222
38 3EXH TPP 3.64742
39 2O66 FLC 3.7037
40 3CTL S6P 3.8961
41 3T6E UQ9 3.93258
42 5WHU SIA GAL GLC 4.02685
43 6EV2 BGC 4.05405
44 2YIC TPP 4.08526
45 3AJM 4IP 4.22535
46 4WBD CIT 4.25139
47 5W3Y ACO 4.26136
48 1R9J TPP 4.26288
49 5X2N ALA 4.39331
50 3LL5 IP8 4.41767
51 2O1S TDP 4.4405
52 5NM7 GLY 4.51128
53 4D86 ADP 4.57831
54 1KSK URA 4.70085
55 1KNY APC 4.74308
56 6F5W KG1 4.87805
57 1GPM CIT 4.95238
58 4PYA 2X3 4.96894
59 1UMD TDP COI 5.24691
60 2VZ6 FEF 5.43131
61 5ABU GTG 5.43478
62 5URY PAM 5.47945
63 5XLS URA 5.51724
64 5B48 TDN 5.57377
65 2IYA UDP 5.66038
66 1IZC PYR 5.8997
67 1U4J MAN 5.9322
68 3HWW AKG 6.11511
69 5B0I BOG 6.12245
70 3K6V CIT 6.21469
71 2C42 PYR 6.2167
72 2C42 TPP 6.2167
73 3DVA TPW 6.30841
74 3KIF GDL 6.60377
75 5W6Y TRP 6.64557
76 1OLS TDP 6.75
77 2RI1 GLP 6.80851
78 1Z6K OAA 6.82594
79 3I7S PYR 6.84932
80 5GLN XYP XYP XYP 6.97674
81 5TSH ADP 7.81528
82 1PFK ADP 8.125
83 1ZX5 LFR 8.33333
84 4PPF FLC 8.57143
85 4JEJ 1GP 8.60656
86 1RP7 TZD 8.70337
87 4KXV TDP DX5 8.70337
88 2J9D ADP 9.2437
89 6FYQ PLP 9.71074
90 2BO4 FLC 10.5793
91 5EXE 5SR 11.1465
92 4E03 ADP 11.165
93 2X7J TPP 14.9201
94 3AI7 TPP 15.2753
95 2DC1 CIT 15.678
96 1M0S CIT 15.9817
97 5B47 PYR 16.7763
98 5B47 TPP 16.7763
99 3HY2 ATP 17.2727
100 1O8B ABF 17.3516
101 5BXV MGP 18.1818
102 3CYI ATP 19.0909
103 4D5G FAD 21.6696
104 4D5G TPP 21.6696
105 1W85 TDP 22.449
106 6E8I PTR 26.6272
107 1EJH M7G 31.25
108 4RJK TPP 32.6821
109 4RJK TDL 32.6821
110 4RJK PYR 32.6821
111 1V5F TPP 33.3925
112 1V5F FAD 33.3925
113 3IAE D7K 34.7368
114 3EYA TDP 34.9727
115 2UZ1 TPP 35.3464
116 4KGD FAD 35.7016
117 4KGD TDP 35.7016
118 2IHU TP9 36.8237
119 1T9D P22 36.9449
120 5WKC TP9 36.9449
121 1T9D FAD 36.9449
122 1T9D 1MM 36.9449
123 1T9D P25 36.9449
124 5WKC AUJ 36.9449
125 1T9D PYD 36.9449
126 1YBH P22 37.1226
127 2IHT TPP 37.1728
128 1UPA TPP 37.1728
129 6DEN G8A 37.4778
130 6DEN FAD 37.4778
131 6DEN TP9 37.4778
132 2C31 TZD 37.6761
133 2C31 ADP 37.6761
134 3FSJ D7K 37.6894
135 1OZH HE3 37.833
136 2Q28 TPP 38.1206
137 2NXW TPP 41.9183
Pocket No.: 2; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found with APoc: 48
This union binding pocket(no: 2) in the query (biounit: 2vk4.bio1) has 27 residues
No: Leader PDB Ligand Sequence Similarity
1 1U6R IOM 1.31579
2 1USI PHE 1.44509
3 1O9P MLA 1.69082
4 5A1S FLC 1.78571
5 2CFC KPC 2
6 2ZPA ADP 2.13144
7 2DVZ GLU 2.2293
8 2P3V SRT 2.34375
9 2Q1A 2KT 2.38908
10 3VM7 GLC 2.43902
11 2CI5 HCS 2.46479
12 2ZFZ ARG 2.53165
13 1HSR BHO 2.61628
14 4ARU TLA 2.90557
15 1DNP MHF 2.9724
16 4WOE 3S5 3.01954
17 6B5K TYD 3.04054
18 5XH2 NPO 3.05344
19 3VKC FPQ 3.4965
20 3EZ2 ADP 3.76884
21 6FOG OXL 4.01786
22 5XDR ADP 4.26288
23 1RJW ETF 4.42478
24 5B19 TLA 4.74138
25 5OCQ CIT 4.91228
26 1JI0 ATP 5
27 2UVO NAG 5.26316
28 1GY8 UDP 5.28967
29 1G6H ADP 5.44747
30 3G4Q MCH 5.47945
31 5N26 CPT 5.49451
32 2QV7 ADP 5.63798
33 4DD8 BAT 5.76923
34 1A8S PPI 6.22711
35 2B3B BGC 6.75
36 2B3B GLC 6.75
37 3ITJ CIT 6.80473
38 1SW0 PGA 7.1048
39 3HRD NIO 8.18182
40 1D8C GLV 9.05861
41 2ZL4 ALA ALA ALA ALA 9.18367
42 1XVB BHL BHL 10
43 1B09 PC 10.1942
44 6AC9 ANP 11.1901
45 2GGX NPJ 13.125
46 4FCW ADP 13.8264
47 4U00 ADP 14.3443
48 1ONI BEZ 15.2174
Pocket No.: 3; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found with APoc: 17
This union binding pocket(no: 3) in the query (biounit: 2vk4.bio2) has 36 residues
No: Leader PDB Ligand Sequence Similarity
1 4IP7 FLC 1.84162
2 4JUI EGR 2.55319
3 1I0B PEL 2.71084
4 4V36 LYN 2.98507
5 1VBH PEP 3.01954
6 5EYW PGA 3.21285
7 5EXA 5SO 3.47826
8 2X7I CIT 3.57143
9 2D3Y DU 3.65297
10 5KXE 6Y2 3.7037
11 6FAA ADP 3.73002
12 5WHU SIA 4.02685
13 5GP0 GPP 4.69799
14 2BWJ AMP 6.03015
15 3KO0 TFP 9.90099
16 1XVB 3BR 10
17 4YMZ 13P 17.1315
Pocket No.: 4; Query (leader) PDB : 2VK4; Ligand: TPP; Similar sites found with APoc: 9
This union binding pocket(no: 4) in the query (biounit: 2vk4.bio2) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 3AHC TPP 3.01954
2 4CZ1 VNJ 3.34928
3 4U8P FDA 3.50877
4 4U8P UDP 3.50877
5 2VNI A2P 3.67647
6 2VNI FAD 3.67647
7 3NOJ PYR 4.20168
8 3AI8 HNQ 4.29688
9 2CYB TYR 4.33437
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