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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 (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 291 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 = 138 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 = 230 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 247 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 = 138 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 = 230 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 209 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 = 138 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 = 230 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
Ligand no: 1; Ligand: 4YY; Similar ligands found: 19
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 DV5 0.594059 0.84507
15 TG0 0.556604 0.821918
16 EXE 0.528302 0.913043
17 3JK 0.440367 0.830986
18 3JG 0.405405 0.816901
19 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 with APoc: 35
This union binding pocket(no: 1) in the query (biounit: 5nvx.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4N14 WR7 4.12371
2 5DCH 1YO 6.18557
3 5FYR INS 6.18557
4 4FFG LBS 6.79012
5 1IND EOT 7.2165
6 4X5S AZM 7.40741
7 5G6U YJM 7.69231
8 3P7G MAN 7.69231
9 2OMN IPH 8.24742
10 2JIG PD2 8.64198
11 2GJ5 VD3 9.27835
12 3BMN AX3 9.27835
13 3F3E LEU 9.61539
14 1VA6 ADP 9.87654
15 1NX0 ALA LYS ALA ILE ALA 10.3093
16 5IVE 6E8 10.3093
17 3WSJ MK1 10.3448
18 2XK9 XK9 11.1111
19 3CQO FUC 11.3402
20 5EYP GTP 11.3402
21 5N9T 8QQ 12.3457
22 1I7L ATP 12.3711
23 5C3R AKG 12.5
24 5C3R HMU 12.5
25 5YBL AKG 13.4021
26 2XMY CDK 13.5802
27 1PVC ILE SER GLU VAL 14.1975
28 4OPC PGT 14.433
29 4OPC FDA 14.433
30 5W3X ACO 15.4639
31 5W3Y ACO 15.4639
32 5NC1 NAG 15.4639
33 4M1U A2G MBG 17.5258
34 3FXU TSU 19.5876
35 5JFS 6K0 25.9615
Pocket No.: 2; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found with APoc: 3
This union binding pocket(no: 2) in the query (biounit: 5nvx.bio2) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 1J71 THR ILE THR SER 12.3711
2 1PK8 ATP 21.6495
3 1ELI PYC 27.8351
Pocket No.: 3; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 5nvx.bio4) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5BTX CMP 5.47945
2 6F9G PUT 10.4938
3 1NX4 AKG 14.433
4 6GBV FMN 15.3846
5 4WUJ FMN 15.4639
Pocket No.: 4; Query (leader) PDB : 5NVX; Ligand: 4YY; Similar sites found with APoc: 2
This union binding pocket(no: 4) in the query (biounit: 5nvx.bio3) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 2WA4 069 8.24742
2 3G4Q MCH 15.4639
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