Receptor
PDB id Resolution Class Description Source Keywords
2VBG 1.8 Å EC: 4.-.-.- THE COMPLEX STRUCTURE OF THE BRANCHED-CHAIN KETO ACID DECARBOXYLASE (KDCA) FROM LACTOCOCCUS LACTIS WITH 2R-1- H YDROXYETHYL-DEAZATHDP 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 A:1548;
B:1548;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
24.305 Mg [Mg+2...
R1T A:1549;
B:1549;
 Valid;
Valid;
 none;
none;
 submit data
467.371 C15 H23 N3 O8 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: R1T; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 R1T 1 1
2 S1T 1 1
3 1U0 0.792683 0.941176
4 TPW 0.574713 0.984375
5 TDW 0.542553 0.888889
6 WWF 0.520408 0.853333
7 TD6 0.504854 0.842105
8 THV 0.494949 0.876712
9 TPP 0.489362 0.887324
10 THY 0.485149 0.864865
11 HTL 0.479592 0.876712
12 TD8 0.46729 0.842105
13 TD9 0.46729 0.842105
14 THW 0.466667 0.876712
15 TDL 0.466019 0.820513
16 AUJ 0.460784 0.842105
17 TOG 0.457143 0.842105
18 V4E 0.454545 0.887324
19 TDK 0.447619 0.842105
20 TPU 0.446809 0.810811
21 8PA 0.443478 0.864865
22 T6F 0.433628 0.820513
23 T5X 0.433628 0.820513
24 TZD 0.43299 0.805195
25 5SR 0.431373 0.837838
26 PYI 0.428571 0.828571
27 TDM 0.425743 0.84
28 8FL 0.424242 0.815789
29 8EL 0.424242 0.815789
30 8N9 0.423077 0.7875
31 THD 0.423077 0.7875
32 D7K 0.421053 0.831169
33 TDN 0.413462 0.818182
34 8EO 0.41 0.815789
35 TDP 0.405941 0.873239
Similar Ligands (3D)
Ligand no: 1; Ligand: R1T; Similar ligands found: 8
No: Ligand Similarity coefficient
1 TPP PYR 0.9309
2 TDP COI 0.9166
3 G8G 0.9121
4 8EF 0.8815
5 TD7 0.8797
6 HE3 0.8795
7 TP9 0.8691
8 1TP 0.8639
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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