Receptor
PDB id Resolution Class Description Source Keywords
2VBF 1.6 Å EC: 4.-.-.- THE HOLOSTRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS LACTOCOCCUS LACTIS KDCA FLAVOPROTEIN THDP-DEPENDENT ENZYMES THIAMINE PYROPHOSPHATE LYASE
Ref.: CRYSTAL STRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS PROVIDES INSIGHTS INTO THE STRUCTURAL BASIS FOR THE CHEMO- AND ENANTIOSELECTIVE CARBOLIGATION REACTION ACTA CRYSTALLOGR.,SECT.D V. 63 1217 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MG B:1548;
B:1550;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
TPP B:1549;
B:1551;
Valid;
Valid;
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
2VBF 1.6 Å EC: 4.-.-.- THE HOLOSTRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS LACTOCOCCUS LACTIS KDCA FLAVOPROTEIN THDP-DEPENDENT ENZYMES THIAMINE PYROPHOSPHATE LYASE
Ref.: CRYSTAL STRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS PROVIDES INSIGHTS INTO THE STRUCTURAL BASIS FOR THE CHEMO- AND ENANTIOSELECTIVE CARBOLIGATION REACTION ACTA CRYSTALLOGR.,SECT.D V. 63 1217 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 38 families.
1 2VBG - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
2 2VBF - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 35 families.
1 2VBG - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
2 2VBF - 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 : 2VBF; Ligand: TPP; Similar sites found: 104
This union binding pocket(no: 1) in the query (biounit: 2vbf.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2J4D MHF 0.01251 0.43167 1.14286
2 3ZDS OMD 0.0367 0.40475 1.84758
3 3ZDS HQ9 0.04151 0.40265 1.84758
4 3ZDS M8O 0.03557 0.40156 1.84758
5 5TPC GAL SIA NGA GAL SIA 0.02319 0.41628 1.88235
6 4XH0 ADP 0.03971 0.40255 1.98511
7 1TZJ A3B 0.0422 0.40228 2.07101
8 1TKB N1T 0.0001738 0.42919 2.10526
9 2ACV UDP 0.007072 0.42513 2.15983
10 2DE4 BPS 0.01699 0.41038 2.19178
11 1ITZ TPP 0.0001047 0.47812 2.22222
12 2IYA UDP 0.008811 0.41329 2.35849
13 1NW4 IMH 0.02879 0.40636 2.53623
14 4X1T UDP 0.01597 0.40463 2.69608
15 2OG2 MLI 0.007506 0.41545 2.78552
16 1R9J TPP 0.00007818 0.48339 2.80702
17 2X7I CIT 0.03043 0.40135 2.92208
18 2QV7 ADP 0.01575 0.40491 2.96736
19 2R5N R5P 0.00009252 0.44139 2.98246
20 2R5N RP5 0.00009559 0.43654 2.98246
21 2R5N TPP 0.0001277 0.43654 2.98246
22 1XNG ATP 0.01183 0.40416 2.98507
23 1KSK URA 0.007359 0.45213 2.99145
24 5ND5 TPP 0.0001148 0.47644 3.03468
25 1G8S MET 0.03639 0.40486 3.04348
26 5FJJ MAN 0.003385 0.44994 3.15789
27 4JEJ 1GP 0.01202 0.41781 3.27869
28 3B9Q MLI 0.0172 0.40545 3.31126
29 5T8U LPA 0.0254 0.40172 3.33333
30 2YIC TPP 0.0007044 0.43032 3.34101
31 5FBK TCR 0.02911 0.41015 3.34507
32 4Y7U 491 0.01742 0.42268 3.4632
33 2O1S TDP 0.00002327 0.53783 3.50877
34 1SW0 PGA 0.02705 0.40037 3.62903
35 2AWN ADP 0.04099 0.40272 3.67454
36 5M0T AKG 0.03116 0.40425 3.7415
37 1BW9 PPY 0.01956 0.40381 3.93258
38 4E3Q PMP 0.01931 0.41139 4.01691
39 5XDR ADP 0.01795 0.40921 4.05797
40 3B5J 12D 0.01416 0.42685 4.11523
41 1OYF MHN 0.02742 0.40985 4.13223
42 1QDS PGA 0.0274 0.40367 4.38247
43 2C42 PYR 0.0000003478 0.55528 4.5614
44 2C42 TPP 0.0000003478 0.54568 4.5614
45 1JI0 ATP 0.02115 0.41757 4.58333
46 4UP4 GAL NAG 0.01192 0.42332 4.98753
47 3AI7 TPP 0.000003452 0.52939 5.08772
48 4WZ6 ATP 0.02436 0.41636 5.17241
49 1RZU ADP 0.02165 0.40517 5.36082
50 3EXH TPP 0.0001338 0.48236 5.49738
51 5VE5 GSH 0.0281 0.40691 5.57029
52 2X7J TPP 0.0000000142 0.62508 5.61404
53 3W9F I3P 0.008549 0.4656 5.76923
54 1UMD TDP COI 0.0001322 0.4659 5.8642
55 4PB2 5UD 0.02705 0.41187 5.89623
56 3KC1 2T6 0.00862 0.41037 5.93472
57 5B48 TDN 0.000000161 0.55805 6.31579
58 4ZXA H8N 0.02814 0.40688 6.54762
59 2O66 FLC 0.03415 0.40709 6.66667
60 1I06 TZL 0.04201 0.40159 6.66667
61 2EPN NGT 0.02719 0.41018 6.84211
62 3P13 RIP 0.01644 0.41077 6.94444
63 2OZL TPP 0.00006532 0.49581 7.12329
64 4PPF FLC 0.03711 0.41318 7.42857
65 1WW5 SGA BGC 0.02094 0.41897 7.5
66 5EXE 5SR 0.000001094 0.52734 7.64331
67 3HWW AKG 0.00001531 0.54636 7.73381
68 1RP7 TZD 0.00006997 0.473 8.07018
69 5ESO TDP 0.000000003538 0.58504 8.24561
70 5ESO ISC 0.000000003538 0.58504 8.24561
71 3BRE C2E 0.01768 0.42099 8.93855
72 4REI 3MV 0.03427 0.4071 9.27152
73 2YAJ 4HP 0.009202 0.42353 10.4651
74 1YQT ADP 0.03774 0.40554 10.5948
75 1V3S ATP 0.008205 0.40812 12.069
76 3DVA TPW 0.000307 0.45122 12.3077
77 1W85 TDP 0.0003009 0.46714 12.3457
78 3NHB ADP 0.04501 0.40156 13.0719
79 3OTH TYD 0.01896 0.4011 13.1068
80 2ALG DAO 0.02221 0.41745 14.1304
81 1YRO UDP 0.03211 0.40548 14.6341
82 5E5U MLI 0.04671 0.40491 15.0754
83 3HY2 ATP 0.0316 0.40425 17.4757
84 2C31 TZD 0.000000495 0.60062 21.1268
85 2C31 ADP 0.000000489 0.59991 21.1268
86 1YBH P22 0.00000006998 0.68488 34.9123
87 2Q28 TPP 0.000008888 0.51292 35.8156
88 4RJK TDL 0.000000001715 0.63145 35.9019
89 4RJK TPP 0.00000000534 0.62861 35.9019
90 1UPA TPP 0.00000001502 0.6241 36.8237
91 2IHT TPP 0.00000003337 0.57435 36.8237
92 1V5F FAD 0.00005044 0.50893 37.0175
93 1T9D P22 0.00000005192 0.71408 37.193
94 1T9D PYD 0.00000006226 0.67723 37.193
95 1T9D P25 0.000000001844 0.41535 37.193
96 1T9D FAD 0.000000001928 0.4152 37.193
97 1T9D 1MM 0.000000002035 0.41248 37.193
98 2IHU TP9 0.000000007978 0.56675 37.3473
99 3IAE D7K 0.0000000001138 0.66333 38.9474
100 2UZ1 TPP 0.000000000133 0.70643 39.4316
101 3EYA TDP 0.000000001325 0.66639 39.7086
102 3FSJ D7K 0.000003885 0.49177 41.2879
103 1OZH HE3 0.0000001792 0.44109 43.1095
104 2NXW TPP 0.00000000008789 0.65743 44.6018
Pocket No.: 2; Query (leader) PDB : 2VBF; Ligand: TPP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2vbf.bio1) has 30 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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