Receptor
PDB id Resolution Class Description Source Keywords
2NV9 1.95 Å EC: 4.1.1.19 THE X-RAY CRYSTAL STRUCTURE OF THE PARAMECIUM BURSARIA CHLOR ARGININE DECARBOXYLASE PARAMECIUM BURSARIA CHLORELLA VIRUS 1 ARGININE DECARBOXYLASE PLP TIM BARREL EUKARYOTIC-LIKE ODC
Ref.: X-RAY STRUCTURE OF PARAMECIUM BURSARIA CHLORELLA VI ARGININE DECARBOXYLASE: INSIGHT INTO THE STRUCTURAL FOR SUBSTRATE SPECIFICITY. BIOCHEMISTRY V. 46 2831 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PLP A:2001;
B:2002;
C:2003;
D:2004;
E:2005;
F:2006;
G:2007;
H:2008;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
247.142 C8 H10 N O6 P Cc1c(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2NVA 1.8 Å EC: 4.1.1.19 THE X-RAY CRYSTAL STRUCTURE OF THE PARAMECIUM BURSARIA CHLORELLA VIRUS ARGININE DECARBOXYLASE BOUND TO AGMATINE PARAMECIUM BURSARIA CHLORELLA VIRUS 1 ARGININE DECARBOXYLASE PLP TIM BARREL EUKARYOTIC ODC- LIKE LYASE
Ref.: X-RAY STRUCTURE OF PARAMECIUM BURSARIA CHLORELLA VIRUS ARGININE DECARBOXYLASE: INSIGHT INTO THE STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY. BIOCHEMISTRY V. 46 2831 2007
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2NVA - PL2 C13 H24 N5 O5 P [H]/N=C(/N....
2 2NV9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
70% Homology Family (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 2NVA - PL2 C13 H24 N5 O5 P [H]/N=C(/N....
2 2NV9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2NVA - PL2 C13 H24 N5 O5 P [H]/N=C(/N....
2 2NV9 - PLP C8 H10 N O6 P Cc1c(c(c(c....
3 1NJJ Ki = 8 mM GET C20 H40 N4 O10 C[C@H]([C@....
4 1F3T - PLP PUT n/a n/a
5 2OO0 Kd = 0.05 uM PLP C8 H10 N O6 P Cc1c(c(c(c....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PLP; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 PLP 1 1
2 PZP 0.729167 0.843137
3 EXT 0.62069 0.8
4 AN7 0.603448 0.918367
5 EPC 0.603448 0.862745
6 FOO 0.59322 0.849057
7 PLR 0.58 0.895833
8 4LM 0.57377 0.818182
9 0JO 0.57377 0.803571
10 P3D 0.571429 0.704918
11 MPM 0.564516 0.814815
12 KOU 0.555556 0.836364
13 HCP 0.546875 0.77193
14 6DF 0.545455 0.811321
15 PXL 0.541667 0.659574
16 Z98 0.537313 0.75
17 PXP 0.537037 0.862745
18 PMP 0.527273 0.767857
19 P0P 0.527273 0.916667
20 PL6 0.522388 0.818182
21 GT1 0.517857 0.830189
22 PFM 0.514706 0.803571
23 LLP 0.5 0.737705
24 PL5 0.479452 0.775862
25 PUS 0.479452 0.707692
26 MPL 0.473684 0.836364
27 PLG 0.46875 0.75
28 IN5 0.46875 0.758621
29 P89 0.466667 0.714286
30 PLP PUT 0.463768 0.684211
31 5DK 0.460526 0.725806
32 O1G 0.454545 0.75
33 PLP ABU 0.450704 0.706897
34 PLT 0.439024 0.762712
35 X04 0.431034 0.851852
36 PP3 0.426471 0.762712
37 P1T 0.426471 0.714286
38 PDD 0.426471 0.762712
39 PDA 0.426471 0.762712
40 IK2 0.42029 0.714286
41 33P 0.42029 0.745763
42 2BO 0.414286 0.793103
43 PLS 0.414286 0.779661
44 PMH 0.414286 0.619718
45 5PA 0.414286 0.714286
46 TLP 0.414286 0.793103
47 2BK 0.414286 0.793103
48 C6P 0.408451 0.75
49 PPD 0.408451 0.75
50 QLP 0.405405 0.681818
51 MP5 0.403509 0.666667
52 PY5 0.402778 0.703125
53 PLA 0.402778 0.703125
54 HEY 0.4 0.703125
55 PLP PHE 0.4 0.732143
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: 34
This union binding pocket(no: 1) in the query (biounit: 2nva.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3LJU IP9 0.02617 0.40164 1.34409
2 3WQD PLP 999 0.007921 0.41123 1.6129
3 2YGM GLA NAG GAL FUC 0.02686 0.40407 1.9774
4 3GLC R5P 0.003299 0.44103 2.71186
5 5A5W GUO 0.005011 0.41431 2.7668
6 2F6U CIT 0.01701 0.41864 2.99145
7 1V6A TRE 0.03559 0.40331 3.01205
8 2Y88 2ER 0.001853 0.42781 3.27869
9 1FQK ALF 0.04049 0.40178 3.38462
10 1M5W DXP 0.01204 0.42652 3.7037
11 5TVM PUT 0.01168 0.42837 4.21053
12 4UTU LRY 0.01298 0.40837 4.36681
13 1DBT U5P 0.004846 0.41734 4.60251
14 4FFG LBS 0.006515 0.43077 4.83871
15 3AIH BMA MAN MAN 0.03123 0.40226 4.83871
16 1C1X HFA 0.01543 0.40844 5.07042
17 3LL5 IP8 0.01799 0.41371 5.22088
18 2YPI PGA 0.001124 0.46892 5.66802
19 3EXS 5RP 0.004717 0.43797 5.88235
20 3N29 NSD 0.002265 0.447 6.1828
21 3B0P FMN 0.01052 0.40907 6.57143
22 2VD9 IN5 0.01175 0.40685 6.72043
23 2R2N PMP 0.02051 0.4024 6.72043
24 2VD9 EPC 0.01321 0.40112 6.72043
25 3EB9 FLC 0.02084 0.40206 6.76692
26 3OVR 5SP 0.001801 0.40371 7.45614
27 4NAE 1GP 0.0001687 0.52229 8
28 1XVB BBU 0.006669 0.40498 8.82353
29 5KAX RHQ 0.03378 0.40288 11.4458
30 4EWN 0VR 0.01337 0.40423 13.0435
31 1YRO UDP 0.03179 0.40598 23.5772
32 1TUF AZ1 0.000000001046 0.65368 34.4086
33 5GJO PLP 0.000000000005111 0.64423 45.4301
34 2PLK P3D 0.00000000000879 0.70095 45.6989
Pocket No.: 2; Query (leader) PDB : 2NVA; Ligand: PL2; 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: 2nva.bio2) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: 8
This union binding pocket(no: 3) in the query (biounit: 2nva.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2IF8 ADP 0.0321 0.40406 1.92837
2 1NVM OXL 0.01788 0.40095 2.88462
3 2Y7P SAL 0.03525 0.4019 3.66972
4 4M26 AKG 0.03603 0.40046 3.84615
5 3L6C MLI 0.01942 0.41688 4.03226
6 1WQ1 AF3 0.04423 0.40046 8.43373
7 2CJU PHX 0.02458 0.40481 9.09091
8 4RJD TFP 0.0381 0.4001 9.09091
Pocket No.: 4; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2nva.bio4) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: 6
This union binding pocket(no: 5) in the query (biounit: 2nva.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3RGA LSB 0.01576 0.4009 2.4735
2 4BHL ARG 0.009441 0.43214 3.65169
3 5FS0 5JC 0.02946 0.402 5.21327
4 2FLI DX5 0.001717 0.40058 9.09091
5 5C3R HMU 0.01238 0.40241 9.62099
6 5C3R AKG 0.01238 0.40241 9.62099
Pocket No.: 6; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 6) in the query (biounit: 2nva.bio1) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 7; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: 2
This union binding pocket(no: 7) in the query (biounit: 2nva.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4R08 URI 0.0184 0.40113 1.34409
2 1GXU 2HP 0.02635 0.40247 6.59341
Pocket No.: 8; Query (leader) PDB : 2NVA; Ligand: PL2; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 8) in the query (biounit: 2nva.bio3) has 27 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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