Receptor
PDB id Resolution Class Description Source Keywords
6N19 1.5 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ578 HOMO SAPIENS FRAGMENT BASED DRUG DESIGN ANTI-CANCER DRUG DESIGN DNA BINPROTEIN HYDROLASE
Ref.: IDENTIFICATION OF A LIGAND BINDING HOT SPOT AND STR MOTIFS REPLICATING ASPECTS OF TYROSYL-DNA PHOSPHODI I (TDP1) PHOSPHORYL RECOGNITION BY CRYSTALLOGRAPHIC COCKTAIL SCREENING. NUCLEIC ACIDS RES. V. 47 10134 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
K8V B:701;
A:701;
 Valid;
Valid;
 Atoms found LESS than expected: % Diff = 0.19;
none;
 ic50 = 0.96 mM
295.245 C13 H13 N O7 c1cc(...
EDO B:702;
A:702;
B:703;
 Invalid;
Invalid;
Invalid;
 none;
none;
none;
 submit data
62.068 C2 H6 O2 C(CO)...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DJJ 1.74 Å EC: 3.1.4.- CRYSTAL STRUCTURE OF TDP1 CATALYTIC DOMAIN IN COMPLEX WITH C XZ532 HOMO SAPIENS FRAGMENT-BASED DRUG DESIGN HYDROLASE
Ref.: IDENTIFICATION OF A LIGAND BINDING HOT SPOT AND STR MOTIFS REPLICATING ASPECTS OF TYROSYL-DNA PHOSPHODI I (TDP1) PHOSPHORYL RECOGNITION BY CRYSTALLOGRAPHIC COCKTAIL SCREENING. NUCLEIC ACIDS RES. V. 47 10134 2019
Members (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 13 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
70% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
50% Homology Family (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 6DJH - GNM C10 H6 Br N O3 c1cc2c(c(c....
2 6DJE - GNY C13 H13 N O3 CC(C)c1ccc....
3 6MJ5 - JTA C10 H6 N2 O5 c1cc2c(c(c....
4 6N17 ic50 = 1.01 mM K8Y C12 H11 N O7 c1cc(c(cc1....
5 6DIM - GJP C10 H7 N O3 c1ccc2c(c1....
6 6DJF - GNV C11 H7 N O5 c1cc2c(c(c....
7 6N19 ic50 = 0.96 mM K8V C13 H13 N O7 c1cc(c(cc1....
8 6DIE ic50 = 0.74 mM GHM C9 H6 O6 c1cc(c(cc1....
9 6DJI ic50 = 3.1 mM GOG C8 H6 O5 c1cc(c(c(c....
10 6DHU - GHM C9 H6 O6 c1cc(c(cc1....
11 6DJG - GNJ C10 H7 N O6 S c1cc2c(c(c....
12 6DJD ic50 = 7.2 mM GJP C10 H7 N O3 c1ccc2c(c1....
13 6DJJ ic50 = 80 uM GM7 C8 H7 N O4 c1cc(c(cc1....
14 6DIH ic50 = 1.9 mM GJS C8 H6 O5 c1cc(c(cc1....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: K8V; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 K8V 1 1
2 K8Y 0.729167 0.941176
3 BZH 0.476923 0.615385
4 SPB 0.444444 0.837838
Similar Ligands (3D)
Ligand no: 1; Ligand: K8V; 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 : 6DJJ; Ligand: GM7; 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: 6djj.bio2) has 16 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6DJJ; Ligand: GM7; 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: 6djj.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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