Receptor
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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PL2 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
361.334 C13 H24 N5 O5 P [H]/N...
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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: PL2; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 PL2 1 1
2 PLG 0.611111 0.794118
3 33P 0.558442 0.791045
4 P1T 0.545455 0.760563
5 EA5 0.542169 0.84058
6 IN5 0.526316 0.776119
7 PDD 0.525641 0.753623
8 PDA 0.525641 0.753623
9 PP3 0.525641 0.753623
10 IK2 0.518987 0.760563
11 QLP 0.518072 0.802817
12 PE1 0.517647 0.865672
13 PMP 0.514286 0.84127
14 PLS 0.5125 0.794118
15 TLP 0.5125 0.753623
16 5PA 0.5125 0.785714
17 2BO 0.5125 0.753623
18 2BK 0.5125 0.753623
19 HEY 0.511905 0.774648
20 PPD 0.506173 0.794118
21 C6P 0.506173 0.794118
22 ILP 0.506024 0.757143
23 ORX 0.505882 0.865672
24 PXP 0.5 0.75
25 PY5 0.5 0.8
26 PLA 0.5 0.75
27 PY6 0.494118 0.802817
28 PMH 0.493827 0.65
29 PL4 0.488636 0.865672
30 3LM 0.488372 0.72973
31 N5F 0.488372 0.838235
32 PSZ 0.488372 0.693333
33 PGU 0.488095 0.823529
34 7XF 0.488095 0.823529
35 CBA 0.488095 0.722222
36 PDG 0.488095 0.823529
37 GT1 0.486111 0.701493
38 PMG 0.482353 0.777778
39 76U 0.476744 0.811594
40 7TS 0.470588 0.619048
41 PL8 0.466667 0.727273
42 9YM 0.465909 0.797101
43 DCS 0.465116 0.666667
44 KAM 0.461538 0.811594
45 7B9 0.456522 0.756757
46 PXG 0.455556 0.742857
47 RW2 0.455556 0.763889
48 5DK 0.445652 0.878788
49 AQ3 0.427083 0.75
50 PPG 0.419355 0.838235
51 PLP 2KZ 0.418605 0.714286
52 PLP ALO 0.406977 0.714286
53 PLR 0.402778 0.661538
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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