Receptor
PDB id Resolution Class Description Source Keywords
5ML3 1.4 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF PDE6D IN COMPLEX TO DELTASONAMIDE1 HOMO SAPIENS PRENYL BINDING PROTEIN FARNESYLATED KRAS PLASMA MEMBRANE LIPID BINDING PROTEIN
Ref.: A PDE6 DELTA-KRAS INHIBITOR CHEMOTYPE WITH UP TO SE H-BONDS AND PICOMOLAR AFFINITY THAT PREVENTS EFFICI INHIBITOR RELEASE BY ARL2. ANGEW. CHEM. INT. ED. ENGL. V. 56 2423 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
DL3 B:201;
Valid;
none;
Kd = 203 pM
647.251 C30 H39 Cl N6 O4 S2 CNc1n...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5ML3 1.4 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF PDE6D IN COMPLEX TO DELTASONAMIDE1 HOMO SAPIENS PRENYL BINDING PROTEIN FARNESYLATED KRAS PLASMA MEMBRANE LIPID BINDING PROTEIN
Ref.: A PDE6 DELTA-KRAS INHIBITOR CHEMOTYPE WITH UP TO SE H-BONDS AND PICOMOLAR AFFINITY THAT PREVENTS EFFICI INHIBITOR RELEASE BY ARL2. ANGEW. CHEM. INT. ED. ENGL. V. 56 2423 2017
Members (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 293 families.
1 5X72 Kd = 467 nM P59 C20 H15 F N2 O c1ccc(cc1)....
2 5ML2 Kd = 13 nM NH6 C25 H27 Cl N2 O4 S2 c1ccc(cc1)....
3 5ML6 Kd = 358 pM 9GD C32 H39 Cl N4 O6 S2 c1cc(ccc1C....
4 5X74 Kd = 2.3 nM JAY C35 H33 F2 N5 O2 c1ccc(c(c1....
5 5ML3 Kd = 203 pM DL3 C30 H39 Cl N6 O4 S2 CNc1nccc(n....
6 4JV6 Kd = 165 nM 18F C20 H16 N2 c1ccc(cc1)....
7 5ML4 Kd < 2 nM RRQ C33 H41 Cl N4 O6 S2 CNc1cc(ccc....
8 5E8F Kd = 2.3 nM LYS SER LYS THR CMT GER n/a n/a
9 4JVB Kd = 39 nM 1M0 C38 H32 N4 O C=CC[C@H](....
10 3T5I - CYS SER GLN GLN GLY LYS SER SER CMT FAR n/a n/a
11 4JVF Kd = 10 nM 17X C40 H42 N6 O2 c1ccc(cc1)....
12 5X73 Kd = 184 nM P59 C20 H15 F N2 O c1ccc(cc1)....
13 4JV8 - 1M1 C19 H14 N4 c1ccc2c(c1....
70% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 250 families.
1 5X72 Kd = 467 nM P59 C20 H15 F N2 O c1ccc(cc1)....
2 5ML2 Kd = 13 nM NH6 C25 H27 Cl N2 O4 S2 c1ccc(cc1)....
3 5ML6 Kd = 358 pM 9GD C32 H39 Cl N4 O6 S2 c1cc(ccc1C....
4 5X74 Kd = 2.3 nM JAY C35 H33 F2 N5 O2 c1ccc(c(c1....
5 5ML3 Kd = 203 pM DL3 C30 H39 Cl N6 O4 S2 CNc1nccc(n....
6 4JV6 Kd = 165 nM 18F C20 H16 N2 c1ccc(cc1)....
7 5ML4 Kd < 2 nM RRQ C33 H41 Cl N4 O6 S2 CNc1cc(ccc....
8 5E8F Kd = 2.3 nM LYS SER LYS THR CMT GER n/a n/a
9 4JVB Kd = 39 nM 1M0 C38 H32 N4 O C=CC[C@H](....
10 3T5I - CYS SER GLN GLN GLY LYS SER SER CMT FAR n/a n/a
11 4JVF Kd = 10 nM 17X C40 H42 N6 O2 c1ccc(cc1)....
12 5X73 Kd = 184 nM P59 C20 H15 F N2 O c1ccc(cc1)....
13 4JV8 - 1M1 C19 H14 N4 c1ccc2c(c1....
50% Homology Family (13)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 204 families.
1 5X72 Kd = 467 nM P59 C20 H15 F N2 O c1ccc(cc1)....
2 5ML2 Kd = 13 nM NH6 C25 H27 Cl N2 O4 S2 c1ccc(cc1)....
3 5ML6 Kd = 358 pM 9GD C32 H39 Cl N4 O6 S2 c1cc(ccc1C....
4 5X74 Kd = 2.3 nM JAY C35 H33 F2 N5 O2 c1ccc(c(c1....
5 5ML3 Kd = 203 pM DL3 C30 H39 Cl N6 O4 S2 CNc1nccc(n....
6 4JV6 Kd = 165 nM 18F C20 H16 N2 c1ccc(cc1)....
7 5ML4 Kd < 2 nM RRQ C33 H41 Cl N4 O6 S2 CNc1cc(ccc....
8 5E8F Kd = 2.3 nM LYS SER LYS THR CMT GER n/a n/a
9 4JVB Kd = 39 nM 1M0 C38 H32 N4 O C=CC[C@H](....
10 3T5I - CYS SER GLN GLN GLY LYS SER SER CMT FAR n/a n/a
11 4JVF Kd = 10 nM 17X C40 H42 N6 O2 c1ccc(cc1)....
12 5X73 Kd = 184 nM P59 C20 H15 F N2 O c1ccc(cc1)....
13 4JV8 - 1M1 C19 H14 N4 c1ccc2c(c1....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: DL3; Similar ligands found: 4
No: Ligand ECFP6 Tc MDL keys Tc
1 DL3 1 1
2 RRQ 0.62963 0.8375
3 9GD 0.587156 0.802469
4 NH6 0.424528 0.767123
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5ML3; Ligand: DL3; 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: 5ml3.bio1) has 37 residues
No: Leader PDB Ligand Sequence Similarity
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