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 62 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 59 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 (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 (2D)
Ligand no: 1; Ligand: TPP; Similar ligands found: 48
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 NDQ 0.769231 0.909091
6 TMV 0.769231 0.958333
7 2TP 0.725 0.932432
8 VNP 0.721519 0.958904
9 VIB 0.621622 0.75
10 PYI 0.581395 0.887324
11 HTL 0.566667 0.958904
12 TDW 0.566667 0.972222
13 AUJ 0.55914 0.921053
14 N1T 0.556818 0.985714
15 FTP 0.551724 0.835616
16 THV 0.548387 0.958904
17 TPW 0.546512 0.9
18 WWF 0.542553 0.933333
19 TD6 0.540816 0.921053
20 THY 0.536842 0.945946
21 TOG 0.536082 0.921053
22 TDL 0.53125 0.897436
23 THW 0.530612 0.958904
24 TD9 0.53 0.921053
25 TD8 0.53 0.921053
26 TDK 0.525773 0.921053
27 D7K 0.490566 0.909091
28 R1T 0.489362 0.887324
29 S1T 0.489362 0.887324
30 TPU 0.483146 0.842105
31 5SR 0.479167 0.945205
32 T6F 0.476636 0.897436
33 T5X 0.476636 0.897436
34 1U0 0.474227 0.84
35 8PA 0.459459 0.945946
36 8EO 0.457447 0.92
37 8FL 0.457447 0.894737
38 TZD 0.451613 0.883117
39 O2T 0.45098 0.909091
40 TDM 0.443299 0.894737
41 8EL 0.442105 0.894737
42 G8G 0.44086 0.805195
43 TDN 0.415842 0.871795
44 THD 0.411765 0.839506
45 8N9 0.411765 0.839506
46 MP5 0.407895 0.676056
47 TD7 0.40566 0.85
48 DPX 0.4 0.734177
Similar Ligands (3D)
Ligand no: 1; Ligand: TPP; Similar ligands found: 4
No: Ligand Similarity coefficient
1 8EF 0.9955
2 TP9 0.9752
3 HTD 0.9623
4 HE3 0.9027
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2VBF; Ligand: TPP; Similar sites found with APoc: 14
This union binding pocket(no: 1) in the query (biounit: 2vbf.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5WKC TP9 37.193
2 5WKC TP9 37.193
3 5WKC TP9 37.193
4 1T9D P22 37.193
5 5WKC AUJ 37.193
6 1T9D P22 37.193
7 1T9D FAD 37.193
8 1T9D PYD 37.193
9 1T9D P25 37.193
10 1T9D 1MM 37.193
11 1T9D 1MM 37.193
12 1T9D FAD 37.193
13 1T9D PYD 37.193
14 1T9D P25 37.193
Pocket No.: 2; Query (leader) PDB : 2VBF; Ligand: TPP; Similar sites found with APoc: 14
This union binding pocket(no: 2) in the query (biounit: 2vbf.bio1) has 30 residues
No: Leader PDB Ligand Sequence Similarity
1 5WKC TP9 37.193
2 5WKC TP9 37.193
3 5WKC TP9 37.193
4 1T9D P22 37.193
5 5WKC AUJ 37.193
6 1T9D 1MM 37.193
7 1T9D P25 37.193
8 1T9D FAD 37.193
9 1T9D PYD 37.193
10 1T9D FAD 37.193
11 1T9D 1MM 37.193
12 1T9D P25 37.193
13 1T9D PYD 37.193
14 1T9D P22 37.193
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