Receptor
PDB id Resolution Class Description Source Keywords
5vnf 2.41 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH A C- VV SORTING MOTIF HOMO SAPIENS COPII TRAFFICKING P24 ER RETENTION PROTEIN TRANSPORT
Ref.: ER RETENTION IS IMPOSED BY COPII PROTEIN SORTING AN ATTENUATED BY 4-PHENYLBUTYRATE. ELIFE V. 6 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN B:1101;
A:801;
 Part of Protein;
Part of Protein;
 none;
none;
 submit data
65.409 Zn [Zn+2...
VAL THR SER VAL VAL D:7;
 Valid;
 Atoms found LESS than expected: % Diff = 0.114;
 Kd = 14.2 uM
445.517 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5VNF 2.41 Å NON-ENZYME: TRANSPORT CRYSTAL STRUCTURE OF SEC23A/SEC24A/SEC22 COMPLEXED WITH A C- VV SORTING MOTIF HOMO SAPIENS COPII TRAFFICKING P24 ER RETENTION PROTEIN TRANSPORT
Ref.: ER RETENTION IS IMPOSED BY COPII PROTEIN SORTING AN ATTENUATED BY 4-PHENYLBUTYRATE. ELIFE V. 6 2017
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 232 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
70% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 197 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
50% Homology Family (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 165 families.
1 5VNF Kd = 14.2 uM VAL THR SER VAL VAL n/a n/a
2 5VNL - CLT C10 H12 O2 c1ccc(cc1)....
3 5VNN - CLT C10 H12 O2 c1ccc(cc1)....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: VAL THR SER VAL VAL; Similar ligands found: 27
No: Ligand ECFP6 Tc MDL keys Tc
1 VAL THR SER VAL VAL 1 1
2 ALA ALA ALA ALA SER ALA ALA 0.642857 0.973684
3 ALA LEU SER ARG 0.568965 0.947368
4 ALA LEU SER ARG GLN 0.55 0.947368
5 ALA ALA SER ALA SER ALA 0.55 0.923077
6 ALA SER VAL SER ALA 0.516129 0.948718
7 LYS GLN THR SER VAL 0.514286 0.883721
8 LYS ALA SER VAL GLY 0.506849 0.863636
9 ALA ILE ALA VAL 0.5 0.707317
10 ACE THR VAL ALA SER SER NH2 0.478261 0.925
11 ASP GLN ILE ILE 0.460317 0.682927
12 ILE LEU SER ALA LEU VAL GLY ILE VAL 0.454545 0.883721
13 SER THR SER ALA 0.454545 0.925
14 ALA ALA ALA 0.45283 0.684211
15 ALA ALA ALA ALA ALA ALA ALA 0.444444 0.684211
16 SER SER VAL THR 0.432836 0.925
17 ALA THR ALA ALA 0.42623 0.769231
18 ALA LEU ALA LEU 0.421875 0.794872
19 ALA SER ASN SER ILE ALA SER GLY 0.416667 0.782609
20 SER PRO SER ILE 0.412698 0.925
21 SER LYS SER MLZ ASP ARG LYS TYR THR LEU 0.411765 0.74
22 GLU GLU ILE ASP VAL VAL SER VAL 0.409091 0.844444
23 ALA ALA GLY ILE GLY ILE LEU THR VAL 0.404494 0.822222
24 THR SER THR THR SER VAL ALA SER SER TRP 0.40404 0.730769
25 ASN LEU VAL PRO SER VAL ALA THR VAL 0.403846 0.633333
26 GLY VAL VAL ALA SER GLN PRO ALA ARG VAL 0.401961 0.678571
27 ALA GLU ASP ASP VAL GLU 0.4 0.727273
Similar Ligands (3D)
Ligand no: 1; Ligand: VAL THR SER VAL VAL; 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 : 5VNF; Ligand: VAL THR SER VAL VAL; 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: 5vnf.bio1) has 15 residues
No: Leader PDB Ligand Sequence Similarity
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