Receptor
PDB id Resolution Class Description Source Keywords
2FWN 1.4 Å EC: 4.1.1.7 PHOSPHORYLATION OF AN ACTIVE SITE SERINE IN A THDP- DEPENDENT ENZYME BY PHOSPHONATE INACTIVATION PSEUDOMONAS PUTIDA LYASE CARBON-CARBON DECARBOXYLASE PHOPHONATED MANDELATE CATABOLISM THIAMINE DIPHOSPHATE HIGH RESOLUTION
Ref.: MECHANISM-BASED INACTIVATION OF BENZOYLFORMATE DECARBOXYLASE, A THIAMIN DIPHOSPHATE-DEPENDENT ENZYME J.AM.CHEM.SOC. V. 129 4120 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:532;
A:533;
A:534;
 Part of Protein;
Part of Protein;
Part of Protein;
 none;
none;
none;
 submit data
40.078 Ca [Ca+2...
MG A:531;
 Part of Protein;
 none;
 submit data
24.305 Mg [Mg+2...
TDP A:530;
 Valid;
 none;
 submit data
424.306 C12 H18 N4 O7 P2 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3FSJ 1.37 Å EC: 4.1.1.7 CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH THE INHIBITOR MBP PSEUDOMONAS PUTIDA THIAMIN ADDUCT AROMATIC HYDROCARBONS CATABOLISM CALCIUM DECARBOXYLASE LYASE MAGNESIUM MANDELATE PATHWAY METAL BINDING THIAMINE PYROPHOSPHATE METAL-BINDING
Ref.: SNAPSHOT OF A REACTION INTERMEDIATE: ANALYSIS OF BENZOYLFORMATE DECARBOXYLASE IN COMPLEX WITH A BENZOYLPHOSPHONATE INHIBITOR. BIOCHEMISTRY V. 48 3247 2009
Members (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
2 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
4 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
6 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
11 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
12 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
13 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
14 3FSJ Kd = 0.113 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
15 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
17 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
18 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
2 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
4 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
6 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
11 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
12 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
13 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
14 3FSJ Kd = 0.113 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
15 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
17 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
18 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
20 6QSI - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
2 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
4 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
6 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
8 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
10 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
11 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
12 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
13 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
14 3FSJ Kd = 0.113 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
15 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
17 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
18 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
20 6QSI - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TDP; Similar ligands found: 34
No: Ligand ECFP6 Tc MDL keys Tc
1 TDP 1 1
2 TPP 0.84 0.985714
3 V4E 0.797468 0.985714
4 TPS 0.77027 0.942857
5 TMV 0.75 0.944444
6 VNP 0.703704 0.945205
7 N1T 0.674699 1
8 NDQ 0.647059 0.896104
9 2TP 0.609195 0.918919
10 VIB 0.605263 0.760563
11 5SR 0.582418 0.958333
12 FTP 0.574713 0.847222
13 O2T 0.546392 0.896104
14 PYI 0.483871 0.873239
15 HTL 0.474227 0.945205
16 TDW 0.474227 0.958333
17 AUJ 0.47 0.907895
18 THV 0.46 0.945205
19 TD6 0.457143 0.907895
20 WWF 0.455446 0.92
21 TOG 0.451923 0.907895
22 TPW 0.451613 0.885714
23 THY 0.45098 0.932432
24 TD9 0.448598 0.907895
25 TD8 0.448598 0.907895
26 THW 0.447619 0.945205
27 TDL 0.446602 0.884615
28 TDK 0.442308 0.907895
29 D7K 0.415929 0.896104
30 TPU 0.410526 0.828947
31 S1T 0.405941 0.873239
32 R1T 0.405941 0.873239
33 T6F 0.403509 0.884615
34 T5X 0.403509 0.884615
Similar Ligands (3D)
Ligand no: 1; Ligand: TDP; Similar ligands found: 14
No: Ligand Similarity coefficient
1 TZD 0.9840
2 TP9 0.9719
3 8EO 0.9703
4 8EL 0.9688
5 8EF 0.9680
6 DPX 0.9588
7 8FL 0.9547
8 HTD 0.9474
9 G8G 0.9423
10 TDM 0.9227
11 1U0 0.8889
12 THD 0.8812
13 8N9 0.8650
14 TDN 0.8521
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3FSJ; Ligand: D7K; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3fsj.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3FSJ; Ligand: D7K; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3fsj.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 3FSJ; Ligand: D7K; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 3fsj.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 3FSJ; Ligand: D7K; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 3fsj.bio1) has 33 residues
No: Leader PDB Ligand Sequence Similarity
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