Receptor
PDB id Resolution Class Description Source Keywords
3H0W 1.81 Å EC: 4.1.1.50 HUMAN ADOMETDC WITH 5'-DEOXY-5'-[(N-DIMETHYL)AMINO]-8-METHYL HOMO SAPIENS ADOMETDC WITH COMPETITIVE SUBSTRATE ANALOGS AUTOCATALYTIC CDECARBOXYLASE LYASE PHOSPHOPROTEIN POLYAMINE BIOSYNTHESIPYRUVATE S-ADENOSYL-L-METHIONINE SCHIFF BASE SPERMIDINE BIOSYNTHESIS ZYMOGEN
Ref.: ROLE OF THE SULFONIUM CENTER IN DETERMINING THE LIG SPECIFICITY OF HUMAN S-ADENOSYLMETHIONINE DECARBOXY BIOCHEMISTRY V. 48 6423 2009
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
N8M A:368;
Valid;
none;
ic50 = 600 nM
308.336 C13 H20 N6 O3 Cc1nc...
PUT B:350;
Valid;
none;
submit data
88.151 C4 H12 N2 C(CCN...
PYR A:68;
Invalid;
none;
submit data
88.062 C3 H4 O3 CC(=O...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3DZ6 1.83 Å EC: 4.1.1.50 HUMAN ADOMETDC WITH 5'-[(4-AMINOOXYBUTYL)METHYLAMINO]-5'DEOX ETHYLADENOSINE HOMO SAPIENS COMPLEXES OF ADOMETDC WITH 8-SUBSTITUTED LIGANDS DECARBOXYLLYASE PYRUVATE S-ADENOSYL-L-METHIONINE SPERMIDINE BIOSYNZYMOGEN
Ref.: NEW INSIGHTS INTO THE DESIGN OF INHIBITORS OF HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE: STUDIES OF ADEN SUBSTITUTION IN STRUCTURAL ANALOGUES OF S-ADENOSYLM J.MED.CHEM. V. 52 1388 2009
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 1I7B - PUT C4 H12 N2 C(CCN)CN
2 3H0V ic50 = 15 uM M2T C12 H19 N5 O3 S CS(C)C[C@@....
3 3EPB Ka = 10000 M^-1 PUT C4 H12 N2 C(CCN)CN
4 1I72 - PUT C4 H12 N2 C(CCN)CN
5 3DZ4 ic50 = 400 nM C8M C15 H23 N7 O4 Cc1nc2c(nc....
6 3DZ5 - PUT C4 H12 N2 C(CCN)CN
7 1I7C ic50 = 0.4 uM MGB C5 H12 N8 [H]/N=C(N)....
8 3H0W ic50 = 600 nM N8M C13 H20 N6 O3 Cc1nc2c(nc....
9 3DZ6 ic50 = 15 nM M8E C17 H27 N7 O4 C[N@@](CCC....
10 3DZ7 - PUT C4 H12 N2 C(CCN)CN
11 1I79 - PUT C4 H12 N2 C(CCN)CN
12 3EPA Ka = 2000 M^-1 PUT C4 H12 N2 C(CCN)CN
13 3DZ2 ic50 = 70 uM A8M C15 H25 N7 O3 Cc1nc2c(nc....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: N8M; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 N8M 1 1
2 A8M 0.753623 0.866667
3 O8M 0.742857 0.942029
4 M8M 0.732394 0.822785
5 C8M 0.722222 0.902778
6 EP4 0.493151 0.984848
7 3BH 0.492754 0.830986
8 5NB 0.486111 0.821918
9 M8E 0.47191 0.761905
10 Z8B 0.439024 0.769231
11 8BR 0.416667 0.7375
Ligand no: 2; Ligand: PUT; Similar ligands found: 6
No: Ligand ECFP6 Tc MDL keys Tc
1 PUT 1 1
2 13D 0.666667 0.8
3 N2P 0.636364 0.947368
4 16D 0.636364 0.9
5 DIA 0.583333 0.9
6 AML 0.5 0.652174
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3DZ6; Ligand: PUT; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 3dz6.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 3DZ6; Ligand: M8E; 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: 3dz6.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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