Receptor
PDB id Resolution Class Description Source Keywords
5Y24 1.92 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF AIMR FROM BACILLUS PHAGE SPBETA IN COMP ITS SIGNALLING PEPTIDE BACILLUS PHAGE SPBETA DNA BINDING PROTEIN PEPTIDE BINDING PROTEIN COMPLEX WITH P
Ref.: STRUCTURAL BASIS OF THE ARBITRIUM PEPTIDE-AIMR COMM SYSTEM IN THE PHAGE LYSIS-LYSOGENY DECISION. NAT MICROBIOL V. 3 1266 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BR B:401;
A:401;
A:402;
A:403;
B:402;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
submit data
79.904 Br [Br-]
GLY MET PRO ARG GLY ALA D:1;
C:1;
Valid;
Valid;
none;
none;
Kd = 4.6 nM
573.72 n/a S(CCC...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5Y24 1.92 Å NON-ENZYME: TRANSCRIPT_TRANSLATE CRYSTAL STRUCTURE OF AIMR FROM BACILLUS PHAGE SPBETA IN COMP ITS SIGNALLING PEPTIDE BACILLUS PHAGE SPBETA DNA BINDING PROTEIN PEPTIDE BINDING PROTEIN COMPLEX WITH P
Ref.: STRUCTURAL BASIS OF THE ARBITRIUM PEPTIDE-AIMR COMM SYSTEM IN THE PHAGE LYSIS-LYSOGENY DECISION. NAT MICROBIOL V. 3 1266 2018
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 308 families.
1 5Y24 Kd = 4.6 nM GLY MET PRO ARG GLY ALA n/a n/a
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 266 families.
1 5Y24 Kd = 4.6 nM GLY MET PRO ARG GLY ALA n/a n/a
50% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 220 families.
1 5Y24 Kd = 4.6 nM GLY MET PRO ARG GLY ALA n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: GLY MET PRO ARG GLY ALA; Similar ligands found: 55
No: Ligand ECFP6 Tc MDL keys Tc
1 GLY MET PRO ARG GLY ALA 1 1
2 GLY LEU LEU GLY SER PRO VAL ARG ALA 0.527132 0.808824
3 VAL MET LEU PRO GLY ARG GLY VAL PRO 0.507143 0.9375
4 GLY LEU LEU GLY SEP PRO VAL ARG ALA 0.492754 0.743243
5 THR PRO ARG VAL THR GLY GLY GLY ALA MET 0.489209 0.871429
6 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.487805 0.859375
7 PRO ARG ARG PRO VAL ILE MET ARG ARG 0.474453 0.907692
8 THR PRO ARG ARG SER MLZ SER ALA 0.468254 0.855072
9 GLN PRO PRO VAL PRO PRO GLN ARG PRO MET 0.467626 0.909091
10 VAL MET ALA PRO ARG ALA LEU LEU LEU 0.455224 0.9375
11 ARG PRO GLN VAL PRO LEU ARG PRO MET 0.453901 0.909091
12 ARG PRO LYS PRO LEU VAL ASP PRO 0.452381 0.859375
13 MET CYS PRO ARG MET THR ALA VAL MET 0.451389 0.842857
14 GLY PRO ARG PRO 0.45045 0.825397
15 SER SER TYR ARG ARG PRO VAL GLY ILE 0.44898 0.736842
16 GLY PHE ARG PRO 0.445378 0.8
17 ALA MET ALA PRO ARG THR LEU LEU LEU 0.445255 0.869565
18 MET TRP ARG PRO TRP 0.444444 0.852941
19 GLY HIS ARG PRO 0.439024 0.791045
20 VAL PRO LEU ARG PRO MET THR TYR 0.436242 0.786667
21 ASN PRO ARG ALA MET GLN ALA LEU LEU 0.435714 0.895522
22 ARG ARG GLY MET NH2 0.435185 0.758065
23 ARG PRO PRO GLY PHE SER PRO PHE ALA 0.432432 0.75
24 ARG PRO MET THR TYR LYS GLY ALA LEU 0.432099 0.824324
25 GLY ARG PRO ARG THR THR SER PHE ALA GLU 0.431373 0.763889
26 LEU ASP PRO ARG 0.430894 0.846154
27 GLY ARG LEU LEU PRO 0.428571 0.887097
28 SER PRO LYS ARG ILE ALA 0.426357 0.794118
29 PRO PRO PRO VAL PRO PRO ARG ARG ARG ARG 0.426357 0.84375
30 ARG PRO PRO LYS PRO ARG PRO ARG 0.426357 0.809524
31 ARG PRO MET THR PHE LYS GLY ALA LEU 0.425926 0.859155
32 VAL PRO PRO PRO ARG PRO PRO PRO PRO GLU 0.425197 0.830769
33 5JP PRO LYS ARG ILE ALA 0.424242 0.823529
34 ALA PRO PRO PRO ARG PRO PRO LYS PRO 0.421875 0.84127
35 HIS HIS ALA SER PRO ARG LYS 0.418919 0.746479
36 GLY GLU ARG THR ILE PRO ILE THR ARG GLU 0.41844 0.8
37 THR LYS PRO ARG 0.417391 0.809524
38 DPN PRO DAR ILE NH2 0.414062 0.84375
39 DPN PRO DAR DTH NH2 0.414062 0.753623
40 ALA ILE MET PRO ALA ARG PHE TYR PRO LYS 0.413174 0.797297
41 LYS ARG ARG ARG HIS PRO SER GLY 0.412587 0.736111
42 GLY ASP CYS PHE SER LYS PRO ARG 0.410596 0.760563
43 MET SER LEU PRO GLY ARG TRP LYS PRO LYS 0.408046 0.789474
44 ARG PRO LYS ARG ILE ALA 0.407407 0.846154
45 PHE ASN ARG PRO VAL 0.407407 0.782609
46 PRO PRO LYS LYS LYS ARG LYS VAL 0.40458 0.857143
47 LYS ARG ARG ARG HIS PRO SER 0.404255 0.742857
48 ASP VAL GLN THR GLY ARG ARG PRO TYR GLU 0.403846 0.733333
49 ARG MET PHE PRO ASN ALA PRO TYR LEU 0.403727 0.792208
50 ALA PRO ASP THR ARG PRO ALA PRO 0.402985 0.8
51 GLN VAL PRO LEU ARG PRO MET THR TYR LYS 0.402367 0.8
52 DMG PRO ARG ARG ARG SER ARG LYS PRO 0.401575 0.84058
53 DPN PRO DAR CYS NH2 0.401575 0.8125
54 SER ALA PRO ASP THR ARG PRO ALA 0.4 0.788732
55 ARG VAL ALA SER PRO THR SER GLY VAL 0.4 0.760563
Similar Ligands (3D)
Ligand no: 1; Ligand: GLY MET PRO ARG GLY ALA; 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 : 5Y24; Ligand: GLY MET PRO ARG GLY ALA; 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: 5y24.bio2) has 25 residues
No: Leader PDB Ligand Sequence Similarity
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