Receptor
PDB id Resolution Class Description Source Keywords
2PLK 2.14 Å EC: 4.1.1.18 CRYSTAL STRUCTURE OF LYSINE/ORNITHINE DECARBOXYLASE COMPLEXE CADAVERINE FROM VIBRIO VULNIFICUS VIBRIO VULNIFICUS TYPE IV DECARBOXYLASE BETA/ALPHA BARREL BETA BARREL LYASE
Ref.: PHYLOGENETIC DIVERSITY AND THE STRUCTURAL BASIS OF SPECIFICITY IN THE BETA/ALPHA-BARREL FOLD BASIC AMI DECARBOXYLASES. J.BIOL.CHEM. V. 282 27115 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
P3D A:501;
B:501;
Valid;
Valid;
none;
none;
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331.305 C13 H22 N3 O5 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2PLK 2.14 Å EC: 4.1.1.18 CRYSTAL STRUCTURE OF LYSINE/ORNITHINE DECARBOXYLASE COMPLEXE CADAVERINE FROM VIBRIO VULNIFICUS VIBRIO VULNIFICUS TYPE IV DECARBOXYLASE BETA/ALPHA BARREL BETA BARREL LYASE
Ref.: PHYLOGENETIC DIVERSITY AND THE STRUCTURAL BASIS OF SPECIFICITY IN THE BETA/ALPHA-BARREL FOLD BASIC AMI DECARBOXYLASES. J.BIOL.CHEM. V. 282 27115 2007
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2PLK - P3D C13 H22 N3 O5 P Cc1c(c(c(c....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 2PLK - P3D C13 H22 N3 O5 P Cc1c(c(c(c....
50% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2PLK - P3D C13 H22 N3 O5 P Cc1c(c(c(c....
2 5GJO Kd = 21 uM PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: P3D; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 P3D 1 1
2 EXT 0.681818 0.85
3 PLP PUT 0.638889 0.932203
4 Z98 0.621622 0.857143
5 PLP ABU 0.578947 0.761905
6 EPC 0.571429 0.783333
7 PLP 0.571429 0.704918
8 0JO 0.569444 0.738462
9 P89 0.567901 0.791045
10 F0G 0.561644 0.758065
11 4LM 0.547945 0.723077
12 MPM 0.540541 0.774194
13 PZP 0.538462 0.79661
14 KOU 0.533333 0.793651
15 FEV 0.533333 0.712121
16 EVM 0.526316 0.78125
17 HCP 0.526316 0.852459
18 6DF 0.506329 0.770492
19 PL6 0.506329 0.806452
20 PL5 0.506024 0.854839
21 FEJ 0.5 0.723077
22 GLY PLP 0.5 0.714286
23 EQJ 0.488372 0.888889
24 5DK 0.488372 0.888889
25 PUS 0.488095 0.732394
26 LUK 0.471264 0.712329
27 LUH 0.471264 0.712329
28 P70 0.470588 0.761905
29 AN7 0.466667 0.68254
30 FOO 0.460526 0.746032
31 O1G 0.449438 0.695652
32 Q0P 0.445652 0.757576
33 PMP 0.442857 0.85
34 PLT 0.43617 0.731343
35 PLR 0.432836 0.716667
36 PFM 0.428571 0.765625
37 PE1 0.425287 0.875
38 SER PLP 0.421687 0.746032
39 PLP ALO 0.416667 0.703125
40 ORX 0.413793 0.875
41 PLP 999 0.411765 0.703125
42 PXP 0.408451 0.754098
43 L7N 0.406977 0.653846
44 P0P 0.402778 0.704918
Similar Ligands (3D)
Ligand no: 1; Ligand: P3D; Similar ligands found: 5
No: Ligand Similarity coefficient
1 PL2 0.9113
2 PSZ 0.9105
3 PLP AOA 0.8897
4 2B9 0.8838
5 EBR 0.8820
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PLK; Ligand: P3D; Similar sites found with APoc: 12
This union binding pocket(no: 1) in the query (biounit: 2plk.bio1) has 23 residues
No: Leader PDB Ligand Sequence Similarity
1 1NJJ ORX 45.5847
2 1NJJ ORX 45.5847
3 1NJJ ORX 45.5847
4 1NJJ ORX 45.5847
5 2NVA PL2 45.6989
6 2NVA PL2 45.6989
7 2NVA PL2 45.6989
8 2NVA PL2 45.6989
9 2NVA PL2 45.6989
10 2NVA PL2 45.6989
11 2NVA PL2 45.6989
12 2OO0 PLP 46.5394
Pocket No.: 2; Query (leader) PDB : 2PLK; Ligand: P3D; Similar sites found with APoc: 10
This union binding pocket(no: 2) in the query (biounit: 2plk.bio1) has 22 residues
No: Leader PDB Ligand Sequence Similarity
1 1NJJ ORX 45.5847
2 1NJJ ORX 45.5847
3 1NJJ ORX 45.5847
4 1NJJ ORX 45.5847
5 2NVA PL2 45.6989
6 2NVA PL2 45.6989
7 2NVA PL2 45.6989
8 2NVA PL2 45.6989
9 2OO0 PLP 46.5394
10 2OO0 PLP 46.5394
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