Receptor
PDB id Resolution Class Description Source Keywords
2PLK 2.14 Å EC: 4.1.1.17 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: 4.1.1.17 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 2 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
Ligand no: 1; Ligand: P3D; Similar ligands found: 31
No: Ligand ECFP6 Tc MDL keys Tc
1 P3D 1 1
2 LLP 0.689189 0.903226
3 EXT 0.681818 0.85
4 PLP PUT 0.638889 0.830508
5 Z98 0.621622 0.857143
6 PLP ABU 0.578947 0.761905
7 EPC 0.571429 0.783333
8 PLP 0.571429 0.704918
9 0JO 0.569444 0.738462
10 P89 0.567901 0.791045
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 HCP 0.526316 0.852459
16 PL6 0.506329 0.806452
17 6DF 0.506329 0.770492
18 PL5 0.506024 0.854839
19 5DK 0.488372 0.888889
20 PUS 0.488095 0.732394
21 AN7 0.466667 0.68254
22 FOO 0.460526 0.746032
23 O1G 0.449438 0.695652
24 PMP 0.442857 0.85
25 PLT 0.43617 0.731343
26 PLR 0.432836 0.716667
27 PFM 0.428571 0.765625
28 PE1 0.425287 0.875
29 ORX 0.413793 0.875
30 PXP 0.408451 0.754098
31 P0P 0.402778 0.704918
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2PLK; Ligand: P3D; Similar sites found: 39
This union binding pocket(no: 1) in the query (biounit: 2plk.bio1) has 23 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3UPY FOM 0.02492 0.4059 1.19332
2 3G6M CFF 0.01413 0.41589 1.47783
3 2P3V SRT 0.01132 0.42197 1.95312
4 1ME8 RVP 0.016 0.4004 2.14797
5 4V15 PLP 0.0003569 0.48023 2.37467
6 1EIX BMQ 0.009372 0.4016 2.44898
7 4EWN 0VR 0.01051 0.40283 2.7668
8 1QDS PGA 0.0007941 0.46911 2.78884
9 1GVF PGH 0.02602 0.40299 2.7972
10 3WQD PLP 999 0.005591 0.41159 2.82051
11 5GVR LMR 0.00278 0.4105 2.99145
12 4YMZ 13P 0.001306 0.46405 3.18725
13 4NAE 1GP 0.0005224 0.48824 3.55556
14 5EYW PGA 0.002201 0.45272 3.61446
15 2Y88 2ER 0.002493 0.43522 3.68852
16 1LYX PGA 0.001655 0.40522 4.03226
17 3B0P FMN 0.00787 0.40855 4.28571
18 2BTM PGA 0.001124 0.4673 4.7619
19 3OVR 5SP 0.0003502 0.44467 4.82456
20 1WHT BZS 0.01314 0.41845 5.07812
21 1DBT U5P 0.001753 0.42997 5.43933
22 3EXS 5RP 0.001292 0.45881 5.48926
23 5TCI MLI 0.003064 0.45829 5.7971
24 3GLC R5P 0.004602 0.42741 6.1017
25 1M5W DXP 0.005091 0.43956 6.58436
26 3TAO PGH 0.0008351 0.40716 6.74157
27 3PNQ 2HA 0.01697 0.40968 7.0028
28 1SW0 PGA 0.002517 0.43989 8.87097
29 3N2O AG2 0.02979 0.40061 9.06921
30 2YPI PGA 0.002427 0.44546 10.1215
31 1X1Z BMP 0.02559 0.40084 11.1111
32 5TVA AMP 0.01262 0.41048 11.6667
33 5TV6 PML 0.0291 0.40047 11.6667
34 2FLI DX5 0.001103 0.43088 11.8182
35 5CSS G3P 0.000474 0.48605 12.3894
36 1GXS DKA 0.01796 0.41374 15.1899
37 1Q6O LG6 0.0006428 0.42312 26.8519
38 1TUF AZ1 0.000000005395 0.61232 37.7088
39 2NVA PL2 0.00000000000879 0.70095 45.6989
Pocket No.: 2; Query (leader) PDB : 2PLK; Ligand: P3D; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 2plk.bio1) has 22 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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