Receptor
PDB id Resolution Class Description Source Keywords
5arg 1.99 Å EC: 2.1.1.43 SMYD2 IN COMPLEX WITH SGC PROBE BAY-598 HOMO SAPIENS TRANSFERASE OXIDOREDUCTASE METHYLTRANSFERASE SET DOMAIN MOLECULE INHIBITOR SGC PROBE DRUG TARGET
Ref.: DISCOVERY AND CHARACTERIZATION OF A HIGHLY POTENT A SELECTIVE AMINOPYRAZOLINE-BASED IN VIVO PROBE (BAY-THE PROTEIN LYSINE METHYLTRANSFERASE SMYD2. J.MED.CHEM. V. 59 4578 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
SAM A:1434;
Invalid;
none;
submit data
398.437 C15 H22 N6 O5 S C[S@@...
ZN A:1003;
A:1005;
A:1004;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
GOL A:1433;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
H41 A:1432;
Valid;
none;
ic50 = 27 nM
525.335 C22 H20 Cl2 F2 N6 O3 CCN([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5KJK 1.93 Å EC: 2.1.1.43 SMYD2 IN COMPLEX WITH AZ370 HOMO SAPIENS SMYD2 HISTONE METHYLTRANSFERASE INHIBITOR TRANSFERASE TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: DESIGN, SYNTHESIS, AND BIOLOGICAL ACTIVITY OF SUBST COMPETITIVE SMYD2 INHIBITORS. J. MED. CHEM. V. 59 11079 2016
Members (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 37 families.
1 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
3 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
4 5ARF Kd = 540 nM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
5 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
6 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
8 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
9 3S7B Kd = 0.5 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
70% Homology Family (9)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 26 families.
1 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
3 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
4 5ARF Kd = 540 nM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
5 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
6 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
7 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
8 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
9 3S7B Kd = 0.5 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
50% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 21 families.
1 3PDN - SFG C15 H23 N7 O5 c1nc(c2c(n....
2 6P7Z - O41 C13 H19 N3 O4 S CS(=O)(=O)....
3 5CCM ic50 = 4 nM 4ZX C28 H34 Cl N5 O4 S c1ccc(cc1)....
4 5CCL - 4ZW C14 H17 N3 O2 c1cc2c(cc1....
5 5EX3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
6 3RU0 - SFG C15 H23 N7 O5 c1nc(c2c(n....
7 5HI7 Ki = 14 nM 62X C19 H32 N8 O5 CN(C)CCCN(....
8 6P6G Ki = 6 nM LUP C23 H35 F3 N4 O4 S c1c(onc1C(....
9 6P6K - SAM C15 H22 N6 O5 S C[S@@+](CC....
10 6PAF - O6A C19 H24 N4 O4 S c1cc(ccc1C....
11 6IJL - SAM C15 H22 N6 O5 S C[S@@+](CC....
12 3QWV - SAH C14 H20 N6 O5 S c1nc(c2c(n....
13 3QWW - SFG C15 H23 N7 O5 c1nc(c2c(n....
14 4WUY ic50 < 15 nM 3UJ C36 H42 N6 O Cc1cn(c2c1....
15 5ARF Kd = 540 nM I9H C22 H21 Cl F2 N6 O3 CCN([C@H]1....
16 5KJM ic50 = 0.065 uM 6TM C32 H37 Cl2 N7 O c1ccc(c(c1....
17 3TG4 - SAM C15 H22 N6 O5 S C[S@@+](CC....
18 5ARG ic50 = 27 nM H41 C22 H20 Cl2 F2 N6 O3 CCN([C@H]1....
19 5KJK ic50 = 0.012 uM 6T1 C30 H34 Cl2 N4 O2 c1ccc(c(c1....
20 3S7B Kd = 0.5 uM NH5 C29 H38 Cl2 N4 O4 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: H41; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 H41 1 1
2 I9H 0.794118 0.986842
Similar Ligands (3D)
Ligand no: 1; Ligand: H41; Similar ligands found: 0
No: Ligand Similarity coefficient
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5KJK; Ligand: 6T1; 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: 5kjk.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5KJK; Ligand: SAM; 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: 5kjk.bio1) has 43 residues
No: Leader PDB Ligand Sequence Similarity
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