Receptor
PDB id Resolution Class Description Source Keywords
1BFD 1.6 Å EC: 4.1.1.7 BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA PSEUDOMONAS PUTIDA LYASE CARBON-CARBON DECARBOXYLASE MANDELATE CATABOLISM TDIPHOSPHATE
Ref.: THE CRYSTAL STRUCTURE OF BENZOYLFORMATE DECARBOXYLA A RESOLUTION: DIVERSITY OF CATALYTIC RESIDUES IN TH DIPHOSPHATE-DEPENDENT ENZYMES. BIOCHEMISTRY V. 37 9918 1998
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CA A:529;
A:532;
Part of Protein;
Part of Protein;
none;
none;
submit data
40.078 Ca [Ca+2...
MG A:531;
Part of Protein;
none;
submit data
24.305 Mg [Mg+2...
TPP A:530;
Valid;
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
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 1 families.
1 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
6 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 3FSJ Kd = 5.49 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
8 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
10 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
11 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
12 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
13 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
15 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
17 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
18 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
70% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
6 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 3FSJ Kd = 5.49 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
8 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
10 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
11 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
12 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
13 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
15 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
17 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
18 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
50% Homology Family (19)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1BFD - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
2 4GM1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
3 2FWN - TDP C12 H18 N4 O7 P2 S Cc1c(sc[n+....
4 1PO7 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
5 3F6B - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
6 4JD5 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
7 3FSJ Kd = 5.49 mM D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
8 4GP9 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
9 4GM4 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
10 1YNO - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
11 3F6E - 8PA C20 H26 N5 O8 P2 S Cc1c(sc([n....
12 4GM0 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
13 4MPR - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
14 1Q6Z - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
15 4GG1 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
16 3FZN - D7K C20 H28 N4 O11 P3 S Cc1c(sc([n....
17 4GPE - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
18 4MQ5 - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
19 1PI3 - TZD C12 H18 N4 O8 P2 S Cc1ncc(c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TPP; Similar ligands found: 36
No: Ligand ECFP6 Tc MDL keys Tc
1 TPP 1 1
2 TDP 0.84 0.985714
3 TPS 0.816901 0.957143
4 TMV 0.769231 0.958333
5 2TP 0.725 0.932432
6 VNP 0.721519 0.958904
7 VIB 0.621622 0.75
8 PYI 0.581395 0.887324
9 TDW 0.566667 0.972222
10 HTL 0.566667 0.958904
11 N1T 0.556818 0.985714
12 FTP 0.551724 0.835616
13 THV 0.548387 0.958904
14 TPW 0.546512 0.9
15 WWF 0.542553 0.933333
16 TD6 0.540816 0.921053
17 THY 0.536842 0.945946
18 TDL 0.53125 0.897436
19 THW 0.530612 0.958904
20 TD8 0.53 0.921053
21 TD9 0.53 0.921053
22 TDK 0.525773 0.921053
23 D7K 0.490566 0.909091
24 S1T 0.489362 0.887324
25 R1T 0.489362 0.887324
26 TPU 0.483146 0.842105
27 T5X 0.476636 0.897436
28 T6F 0.476636 0.897436
29 1U0 0.474227 0.84
30 8PA 0.459459 0.945946
31 TZD 0.451613 0.883117
32 TDM 0.443299 0.894737
33 THD 0.411765 0.839506
34 MP5 0.407895 0.676056
35 TD7 0.40566 0.85
36 DPX 0.4 0.734177
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3FSJ; Ligand: D7K; Similar sites found: 48
This union binding pocket(no: 1) in the query (biounit: 3fsj.bio1) has 33 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc)
1 1T9D P22 0.0000001966 0.68986
2 1OZH HE3 0.00000002525 0.62304
3 1V5F TPP 0.0000005783 0.57666
4 1V5F FAD 0.0000005783 0.57666
5 2Q28 TPP 0.00000001407 0.56127
6 2UZ1 TPP 0.0000008018 0.5608
7 4RJK TDL 0.000002771 0.50156
8 4RJK TPP 0.000001761 0.49734
9 3IAE D7K 0.000005089 0.49723
10 1ZPD DPX 0.000002873 0.49643
11 2NXW TPP 0.000008509 0.4936
12 2NXW TPP 0.000008509 0.4936
13 4RJK TPP 0.000002329 0.49342
14 2VBF TPP 0.000003885 0.49177
15 4RJK TPP 0.000003449 0.48793
16 1QPB TPP 0.00001167 0.48001
17 1QPB TPP 0.00001167 0.48001
18 1QPB PYM 0.000009157 0.47929
19 1QPB PYM 0.000009157 0.47929
20 2VK4 TPP 0.000005207 0.47223
21 2VK4 TPP 0.000005238 0.47223
22 1T9D PYD 0.001603 0.46501
23 2IHT TPP 0.00000983 0.46206
24 1UPA TPP 0.00001086 0.46093
25 2IHU TP9 0.0000234 0.46
26 4KGD TDP 0.0000000007027 0.45794
27 4KGD FAD 0.0000000007522 0.45418
28 1YBH P22 0.00000006918 0.44686
29 1YBH P22 0.00000006918 0.44686
30 2X7J TPP 0.0005566 0.44528
31 3EYA TDP 0.00005091 0.43971
32 3EYA TDP 0.00006749 0.43555
33 2C31 ADP 0.002511 0.4336
34 2C31 TZD 0.0026 0.4336
35 2C42 PYR 0.0005042 0.4217
36 2C42 TPP 0.0005042 0.4217
37 1OLS TDP 0.002094 0.41903
38 2OH5 CTP 0.03169 0.4148
39 2OH5 CTP 0.03169 0.4148
40 2OH5 CTP 0.03169 0.4148
41 3EYA TDP 0.0002313 0.41331
42 3AHC TPP 0.001048 0.41228
43 1WAP TRP 0.01343 0.41186
44 2FJK 13P 0.02535 0.4089
45 2V3U DSN 0.03902 0.40445
46 1QS0 TDP 0.0002002 0.40292
47 2XBL M7P 0.02229 0.40132
48 3B9Q MLI 0.03888 0.40051
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