Receptor
PDB id Resolution Class Description Source Keywords
5NVX 2.2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE PVHL:ELOB:ELOC IN COMPLEX WITH (2S,4R)-1-((S)-2-(1- FLUOROCYCLOPROPANECARBOXAMIDO)-3,3-DIMETHYLBUTANOYL)-4-HYDR( 4-METHYLTHIAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE (LIG HOMO SAPIENS PROTEIN COMPLEX UBIQUITIN LIGASE HYPOXIA INDUCIBLE FACTOR
Ref.: GROUP-BASED OPTIMIZATION OF POTENT AND CELL-ACTIVE INHIBITORS OF THE VON HIPPEL-LINDAU (VHL) E3 UBIQUI LIGASE: STRUCTURE-ACTIVITY RELATIONSHIPS LEADING TO CHEMICAL PROBE (2S,4R)-1-((S)-2-(1-CYANOCYCLOPROPANECARBOXAMIDO)-3 3-DIMETHYLBUTANOYL)-4-HYDROX
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4YY C:301;
F:301;
L:301;
I:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 44 nM
516.628 C26 H33 F N4 O4 S Cc1c(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5NVX 2.2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE PVHL:ELOB:ELOC IN COMPLEX WITH (2S,4R)-1-((S)-2-(1- FLUOROCYCLOPROPANECARBOXAMIDO)-3,3-DIMETHYLBUTANOYL)-4-HYDR( 4-METHYLTHIAZOL-5-YL)BENZYL)PYRROLIDINE-2-CARBOXAMIDE (LIG HOMO SAPIENS PROTEIN COMPLEX UBIQUITIN LIGASE HYPOXIA INDUCIBLE FACTOR
Ref.: GROUP-BASED OPTIMIZATION OF POTENT AND CELL-ACTIVE INHIBITORS OF THE VON HIPPEL-LINDAU (VHL) E3 UBIQUI LIGASE: STRUCTURE-ACTIVITY RELATIONSHIPS LEADING TO CHEMICAL PROBE (2S,4R)-1-((S)-2-(1-CYANOCYCLOPROPANECARBOXAMIDO)-3 3-DIMETHYLBUTANOYL)-4-HYDROX
Members (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 257 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
4 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
5 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
6 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
7 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
8 5NW0 Kd = 138 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
9 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
10 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
11 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
12 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
13 5NW2 Kd = 230 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
14 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
15 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
70% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 222 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
4 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
5 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
6 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
7 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
8 5NW0 Kd = 138 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
9 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
10 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
11 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
12 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
13 5NW2 Kd = 230 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
14 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
15 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 185 families.
1 5NVX Kd = 44 nM 4YY C26 H33 F N4 O4 S Cc1c(scn1)....
2 4W9J Kd = 0.588 uM 3JH C30 H43 N5 O5 S Cc1c(scn1)....
3 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
4 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
5 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
6 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
7 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
8 5NW0 Kd = 138 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
9 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
10 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
11 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
12 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
13 5NW2 Kd = 230 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
14 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
15 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4YY; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 4YY 1 1
2 6Z3 0.8 0.902778
3 3JF 0.797753 0.913043
4 9BK 0.783505 0.902778
5 9BT 0.763441 0.875
6 9BH 0.757895 0.914286
7 9BW 0.755319 0.942029
8 3JJ 0.739583 0.9
9 9B8 0.72449 0.828947
10 3JH 0.70297 0.875
11 3JO 0.657407 0.875
12 3JU 0.648936 0.9
13 3JS 0.602041 0.833333
14 TG0 0.556604 0.821918
15 3JK 0.440367 0.830986
16 3JG 0.405405 0.816901
17 X6C 0.401869 0.75
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found: 13
This union binding pocket(no: 1) in the query (biounit: 5nvx.bio1) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4HIA FMN 0.02522 0.40756 3.84615
2 5DCH 1YO 0.01689 0.40192 6.18557
3 4FFG LBS 0.01304 0.40851 6.79012
4 4X5S AZM 0.01792 0.40132 7.40741
5 3P7G MAN 0.007319 0.42942 7.69231
6 3F3E LEU 0.03545 0.40303 9.61539
7 5EYP GTP 0.02346 0.40089 11.3402
8 1I7L ATP 0.01516 0.40587 12.3711
9 2XMY CDK 0.04214 0.41541 13.5802
10 4OPC PGT 0.04191 0.43226 14.433
11 4OPC FDA 0.03895 0.43136 14.433
12 5W3X ACO 0.005376 0.42856 15.4639
13 5JFS 6K0 0.02515 0.41161 25.9615
Pocket No.: 2; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found: 1
This union binding pocket(no: 2) in the query (biounit: 5nvx.bio2) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4J36 FAD 0.03679 0.40025 9.87654
Pocket No.: 3; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 5nvx.bio4) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found: 1
This union binding pocket(no: 4) in the query (biounit: 5nvx.bio3) has 17 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 2GJ5 VD3 0.006493 0.43944 9.27835
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