Receptor
PDB id Resolution Class Description Source Keywords
4JV6 1.87 Å EC: 7.-.-.- THE CRYSTAL STRUCTURE OF PDE6D IN COMPLEX TO INHIBITOR-1 HOMO SAPIENS IMMUNOGLOBULIN-LIKE BETA-SANDWICH GDI-LIKE SOLUBILIZING FACPRENYL BINDING PROTEIN 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
18F B:201;
B:202;
 Valid;
Valid;
 none;
none;
 Kd = 217 nM
284.354 C20 H16 N2 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: 18F; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 18F 1 1
2 1M0 0.544304 0.717391
Similar Ligands (3D)
Ligand no: 1; Ligand: 18F; Similar ligands found: 45
No: Ligand Similarity coefficient
1 P57 0.9601
2 1M1 0.9539
3 SC3 0.9312
4 P59 0.9209
5 8HZ 0.9122
6 57Q 0.9107
7 5G7 0.9004
8 5UV 0.9000
9 G9J 0.8998
10 S3O 0.8977
11 FV4 0.8961
12 ZO9 0.8949
13 5UX 0.8941
14 7FL 0.8931
15 96X 0.8915
16 5DJ 0.8890
17 6Z8 0.8886
18 8JF 0.8870
19 5G5 0.8865
20 ALH 0.8864
21 AN1 0.8858
22 E2R 0.8852
23 KB8 0.8850
24 580 0.8842
25 MKY 0.8832
26 07U 0.8810
27 5G4 0.8785
28 5HW 0.8784
29 XIH 0.8765
30 5G3 0.8759
31 FPH 0.8714
32 5K0 0.8704
33 UIH 0.8698
34 F7T 0.8694
35 5J2 0.8693
36 RUM 0.8670
37 FLU 0.8669
38 K6W 0.8651
39 QVK 0.8650
40 369 0.8638
41 GOH 0.8634
42 1DZ 0.8610
43 3E2 0.8609
44 9KQ 0.8585
45 HXP 0.8569
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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