Receptor
PDB id Resolution Class Description Source Keywords
5nw2 2.2 Å NON-ENZYME: TRANSCRIPT_TRANSLATE PVHL:ELOB:ELOC IN COMPLEX WITH (2S,4R)-1-((S)-3,3-DIMETHYL-2 3-CARBOXAMIDO)BUTANOYL)-4-HYDROXY-N-(4-(4-METHYLTHIAZOL-5-YP YRROLIDINE-2-CARBOXAMIDE (LIGAND 19) 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
9B8 L:301;
C:301;
I:301;
F:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
Kd = 232 nM
514.637 C26 H34 N4 O5 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 (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 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 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
70% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 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 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 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 6GFZ Kd = 3080 nM EXE C24 H31 F N4 O4 S Cc1c(scn1)....
4 5NW1 Kd = 210 nM 9BH C27 H36 N4 O4 S Cc1c(scn1)....
5 5LLI Kd = 90 nM 6Z3 C27 H33 N5 O4 S Cc1c(scn1)....
6 5NVV Kd = 105 nM 9BT C24 H32 N4 O5 S Cc1c(scn1)....
7 4W9L Kd = 9.52 uM 3JJ C30 H43 N5 O5 S Cc1c(scn1)....
8 4W9C Kd = 22.2 uM 3JG C21 H27 N3 O4 CC(C)(C)CC....
9 5NW0 Kd = 128 nM 9BK C28 H37 N5 O5 S Cc1c(scn1)....
10 5NVW Kd = 132 nM 9BW C26 H34 N4 O4 S Cc1c(scn1)....
11 4W9D Kd = 10.2 uM 3JK C22 H29 N3 O4 Cc1c(ocn1)....
12 4AWJ Kd ~ 10000 uM V6F C8 H14 N2 O3 CC(=O)N1C[....
13 6FMJ Kd = 0.76 uM DV5 C21 H26 N4 O3 S2 Cc1c(scn1)....
14 4W9I Kd = 1.1 uM 3JS C23 H28 N4 O5 S Cc1c(scn1)....
15 5NW2 Kd = 232 nM 9B8 C26 H34 N4 O5 S Cc1c(scn1)....
16 4BKT Kd = 240 uM QD0 C12 H17 N3 O4 Cc1cc(on1)....
17 4W9K Kd = 0.291 uM 3JO C33 H41 N5 O5 S Cc1c(scn1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 9B8; Similar ligands found: 20
No: Ligand ECFP6 Tc MDL keys Tc
1 9B8 1 1
2 9BW 0.863636 0.875
3 9BH 0.844444 0.901408
4 3JF 0.806818 0.9
5 9BT 0.771739 0.888889
6 3JJ 0.747368 0.887324
7 4YY 0.72449 0.828947
8 9BK 0.72 0.84
9 6Z3 0.717172 0.84
10 3JH 0.71 0.863014
11 3JO 0.663551 0.863014
12 3JU 0.638298 0.887324
13 3JS 0.608247 0.847222
14 DV5 0.6 0.833333
15 TG0 0.576923 0.810811
16 EXE 0.518868 0.797297
17 GBW 0.480263 0.788235
18 3JK 0.457944 0.84507
19 X6C 0.419048 0.763889
20 3JG 0.409091 0.830986
Similar Ligands (3D)
Ligand no: 1; Ligand: 9B8; 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 : 5NVX; Ligand: 4YY; 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: 5nvx.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 5NVX; Ligand: 4YY; 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: 5nvx.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found with APoc: 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 Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 5nvx.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
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