Receptor
PDB id Resolution Class Description Source Keywords
2Q5L 1.85 Å EC: 4.1.1.43 X-RAY STRUCTURE OF PHENYLPYRUVATE DECARBOXYLASE IN COMPLEX W HYDROXYETHYL)-3-DEAZA-THDP AZOSPIRILLUM BRASILENSE THIAMINE DIPHOSPHATE ASYMMETRIC DIMER OF DIMERS OPEN ACTIVLOOP COVALENT INTERMEDIATE ANALOGUE LYASE
Ref.: MOLECULAR MECHANISM OF ALLOSTERIC SUBSTRATE ACTIVAT THIAMINE DIPHOSPHATE-DEPENDENT DECARBOXYLASE. J.BIOL.CHEM. V. 282 35269 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
CL A:3004;
B:3003;
Invalid;
Invalid;
none;
none;
submit data
35.453 Cl [Cl-]
GOL A:4001;
B:4000;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
MG A:3002;
B:3001;
Part of Protein;
Part of Protein;
none;
none;
submit data
24.305 Mg [Mg+2...
R1T A:2004;
B:2003;
Valid;
Valid;
none;
none;
submit data
467.371 C15 H23 N3 O8 P2 S Cc1c(...
S1T A:2002;
B:2001;
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
2NXW 1.5 Å EC: 4.1.1.43 CRYSTAL STRUCTURE OF PHENYLPYRUVATE DECARBOXYLASE OF AZOSPIR BRASILENSE AZOSPIRILLUM BRASILENSE THIAMINE PYROPHOSPHATE ASYMMETRIC DIMER OF DIMERS OPEN ACTLOOPS LYASE
Ref.: THE CRYSTAL STRUCTURE OF PHENYLPYRUVATE DECARBOXYLA AZOSPIRILLUM BRASILENSE AT 1.5 A RESOLUTION. IMPLIC FOR ITS CATALYTIC AND REGULATORY MECHANISM. FEBS J. V. 274 2363 2007
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Q5Q - KPV C11 H12 O3 c1ccc(cc1)....
2 2NXW - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 2Q5O - PPY C9 H8 O3 c1ccc(cc1)....
4 2Q5L - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Q5Q - KPV C11 H12 O3 c1ccc(cc1)....
2 2NXW - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 2Q5O - PPY C9 H8 O3 c1ccc(cc1)....
4 2Q5L - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 2Q5Q - KPV C11 H12 O3 c1ccc(cc1)....
2 2NXW - TPP C12 H19 N4 O7 P2 S Cc1c(sc[n+....
3 2Q5O - PPY C9 H8 O3 c1ccc(cc1)....
4 2Q5L - R1T C15 H23 N3 O8 P2 S Cc1c(sc(c1....
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
Ligand no: 2; Ligand: S1T; 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
Ligand no: 2; Ligand: S1T; Similar ligands found: 6
No: Ligand Similarity coefficient
1 G8G 0.9114
2 TDP COI 0.8919
3 TPP PYR 0.8775
4 8EF 0.8684
5 TP9 0.8590
6 TD7 0.8564
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NXW; Ligand: TPP; Similar sites found with APoc: 8
This union binding pocket(no: 1) in the query (biounit: 2nxw.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1T9D P25 38.0531
2 1T9D FAD 38.0531
3 1T9D 1MM 38.0531
4 1T9D PYD 38.0531
5 1T9D P25 38.0531
6 1T9D PYD 38.0531
7 1T9D 1MM 38.0531
8 1T9D FAD 38.0531
Pocket No.: 2; Query (leader) PDB : 2NXW; Ligand: TPP; 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: 2nxw.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2NXW; Ligand: TPP; Similar sites found with APoc: 8
This union binding pocket(no: 3) in the query (biounit: 2nxw.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1T9D 1MM 38.0531
2 1T9D FAD 38.0531
3 1T9D P25 38.0531
4 1T9D PYD 38.0531
5 1T9D FAD 38.0531
6 1T9D PYD 38.0531
7 1T9D 1MM 38.0531
8 1T9D P25 38.0531
Pocket No.: 4; Query (leader) PDB : 2NXW; Ligand: TPP; 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: 2nxw.bio1) has 35 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2NXW; Ligand: TPP; Similar sites found with APoc: 29
This union binding pocket(no: 5) in the query (biounit: 2nxw.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1UPA TPP 19.7208
2 5WKC TP9 38.0531
3 5WKC TP9 38.0531
4 5WKC TP9 38.0531
5 5WKC AUJ 38.0531
6 1T9D PYD 38.0531
7 1T9D PYD 38.0531
8 1T9D 1MM 38.0531
9 1T9D PYD 38.0531
10 1T9D P25 38.0531
11 1T9D FAD 38.0531
12 1T9D FAD 38.0531
13 1T9D PYD 38.0531
14 1T9D P25 38.0531
15 1T9D 1MM 38.0531
16 1T9D P22 38.0531
17 1T9D P22 38.0531
18 1YBH P22 38.5841
19 6QSI TPP 38.6364
20 6QSI TPP 38.6364
21 1OZH HE3 38.9381
22 1OZH HE3 38.9381
23 4RJK TPP 39.115
24 4RJK TDL 39.115
25 2VK4 TPP 41.9183
26 2VK4 TPP 41.9183
27 2VK4 TPP 41.9183
28 2VK4 TPP 41.9183
29 1QPB TPP 42.0959
Pocket No.: 6; Query (leader) PDB : 2NXW; Ligand: TPP; Similar sites found with APoc: 29
This union binding pocket(no: 6) in the query (biounit: 2nxw.bio2) has 35 residues
No: Leader PDB Ligand Sequence Similarity
1 1UPA TPP 19.7208
2 5WKC TP9 38.0531
3 5WKC TP9 38.0531
4 5WKC TP9 38.0531
5 1T9D PYD 38.0531
6 5WKC AUJ 38.0531
7 1T9D PYD 38.0531
8 1T9D FAD 38.0531
9 1T9D P25 38.0531
10 1T9D PYD 38.0531
11 1T9D 1MM 38.0531
12 1T9D FAD 38.0531
13 1T9D PYD 38.0531
14 1T9D P25 38.0531
15 1T9D 1MM 38.0531
16 1T9D P22 38.0531
17 1T9D P22 38.0531
18 1YBH P22 38.5841
19 6QSI TPP 38.6364
20 6QSI TPP 38.6364
21 1OZH HE3 38.9381
22 1OZH HE3 38.9381
23 4RJK TPP 39.115
24 4RJK TDL 39.115
25 2VK4 TPP 41.9183
26 2VK4 TPP 41.9183
27 2VK4 TPP 41.9183
28 2VK4 TPP 41.9183
29 1QPB TPP 42.0959
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