Receptor
PDB id Resolution Class Description Source Keywords
4JV8 1.45 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF PDE6D IN COMPLEX WITH RAC-S1 HOMO SAPIENS IMMUNOGLOBULIN-LIKE BETA-SANDWICH GDI-LIKE SOLUBILIZING FACPRENYL BINDING PROTEIN BINDING-INHIBITOR COMPLEX
Ref.: SMALL MOLECULE INHIBITION OF THE KRAS PDED INTERACT IMPAIRS ONCOGENIC KRAS SIGNALLING NATURE V. 497 638 2013
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
1M1 B:201;
B:202;
 Valid;
Valid;
 none;
none;
 submit data
298.341 C19 H14 N4 c1ccc...
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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 319 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 = 217 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 271 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 = 217 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 223 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 = 217 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 (2D)
Ligand no: 1; Ligand: 1M1; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 1M1 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: 1M1; Similar ligands found: 43
No: Ligand Similarity coefficient
1 18F 0.9539
2 P59 0.9321
3 57Q 0.9296
4 3RH 0.9164
5 E2R 0.9141
6 P57 0.9119
7 1JR 0.9034
8 UIH 0.8994
9 JVE 0.8992
10 LZL 0.8960
11 M2N 0.8957
12 ET 0.8932
13 MKY 0.8923
14 ALH 0.8903
15 FLU 0.8852
16 2BZ 0.8842
17 07U 0.8842
18 IR1 0.8830
19 96X 0.8811
20 3E2 0.8800
21 P69 0.8788
22 MRX 0.8764
23 KB8 0.8748
24 AO6 0.8739
25 9KQ 0.8726
26 FID 0.8722
27 SC3 0.8710
28 8JF 0.8706
29 S3O 0.8706
30 6VK 0.8682
31 GOH 0.8680
32 M4V 0.8668
33 982 0.8656
34 F7T 0.8653
35 HXP 0.8647
36 65A 0.8607
37 8HZ 0.8607
38 IA7 0.8603
39 VKE 0.8590
40 KLB 0.8587
41 IRG 0.8584
42 FW7 0.8583
43 IEO 0.8510
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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