Receptor
PDB id Resolution Class Description Source Keywords
6CD8 1.6 Å NON-ENZYME: OTHER COMPLEX OF GID4 FRAGMENT WITH SHORT PEPTIDE HOMO SAPIENS STRUCTURAL GENOMICS STRUCTURAL GENOMICS CONSORTIUM SGC PEBINDING PROTEIN
Ref.: MOLECULAR BASIS OF GID4-MEDIATED RECOGNITION OF DEG THE PRO/N-END RULE PATHWAY. NAT. CHEM. BIOL. V. 14 466 2018
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
UNX A:301;
A:308;
A:307;
B:304;
A:303;
B:305;
A:310;
B:303;
A:305;
A:302;
B:301;
B:306;
B:307;
B:308;
B:302;
A:306;
A:309;
A:311;
A:304;
 Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
 none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
none;
 submit data
n/a X *
PRO SER ARG VAL C:1;
D:1;
 Valid;
Valid;
 none;
Atoms found LESS than expected: % Diff = 0.125;
 Kd = 19.4 uM
458.54 n/a O=C([...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6CDG 1.6 Å NON-ENZYME: OTHER GID4 FRAGMENT IN COMPLEX WITH A PEPTIDE HOMO SAPIENS STRUCTURAL GENOMICS CONSORTIUM SGC PEPTIDE BINDING PROTEIN
Ref.: MOLECULAR BASIS OF GID4-MEDIATED RECOGNITION OF DEG THE PRO/N-END RULE PATHWAY. NAT. CHEM. BIOL. V. 14 466 2018
Members (7)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1610 families.
1 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
2 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
3 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
4 6CD9 - PRO SER ARG TRP n/a n/a
5 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
6 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
7 6CCT - PRO THR LEU VAL n/a n/a
70% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1331 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
5 6CD9 - PRO SER ARG TRP n/a n/a
6 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
7 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
8 6CCT - PRO THR LEU VAL n/a n/a
50% Homology Family (8)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 6CCU Kd = 35.2 uM PRO HIS ARG VAL n/a n/a
2 6CD8 Kd = 19.4 uM PRO SER ARG VAL n/a n/a
3 6CDG Kd = 1.9 uM PRO GLY LEU TRP LYS SER n/a n/a
4 6WZZ - VAL GLY LEU TRP LYS SER n/a n/a
5 6CD9 - PRO SER ARG TRP n/a n/a
6 6WZX - ILE GLY LEU TRP LYS SER n/a n/a
7 6CDC Kd = 2.5 uM PRO GLY LEU TRP n/a n/a
8 6CCT - PRO THR LEU VAL n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: PRO SER ARG VAL; Similar ligands found: 44
No: Ligand ECFP6 Tc MDL keys Tc
1 PRO SER ARG VAL 1 1
2 LEU PRO PRO PRO GLU SER GLU SER LYS VAL 0.604396 0.844828
3 PRO SER ARG TRP 0.588235 0.83871
4 THR PRO THR ARG ASP VAL ALA THR SER PRO 0.487395 0.833333
5 PRO SER ILE ASP ARG SER THR LYS PRO 0.484375 0.794118
6 PRO HIS ARG VAL 0.474747 0.725806
7 PRO LEU SER LYS 0.473118 0.859649
8 PRO VAL LYS ARG ARG LEU ASP LEU GLU 0.470588 0.864407
9 ARG ARG ARG GLU THR GLN VAL 0.464646 0.79661
10 VAL ALA ARG SER 0.460674 0.836364
11 PRO SER M3L PHE NLW 0.457944 0.695652
12 LEU PRO PRO GLU GLU ARG LEU ILE 0.457627 0.757576
13 PRO PRO LYS ARG ILE ALA 0.453782 0.753846
14 LYS GLY PRO PRO LEU PRO ARG PRO ARG VAL 0.45045 0.738462
15 PRO THR SER SER GLU GLN ILE 0.447619 0.8
16 PRO ILE VAL 0.445783 0.77193
17 VAL ARG SER ARG ARG CYS LEU ARG LEU 0.445545 0.813559
18 PRO GLN ILE ILE ASN ARG PRO GLN ASN 0.445378 0.731343
19 PRO LEU GLU PSA ARG LEU 0.44 0.885246
20 PRO ARG ARG PRO VAL ILE MET ARG ARG 0.44 0.685714
21 VAL ARG SER ARG ARG ABA LEU ARG LEU 0.436893 0.813559
22 ARG VAL 0.435897 0.763636
23 LYS ARG ARG LYS SEP VAL 0.435644 0.734375
24 PRO PRO LYS LYS LYS ARG LYS VAL 0.433628 0.761905
25 ALA ARG 9AT 0.428571 0.803571
26 ARG LEU GLN ARG ARG ARG GLU THR GLN VAL 0.427273 0.783333
27 ALA ASN SER ARG VAL PRO THR SER ILE ILE 0.42623 0.846154
28 PRO THR GLU PUK ARG GLU 0.423077 0.83871
29 ACE LYS ARG ARG LYS SEP VAL 0.419048 0.734375
30 5JP PRO LYS ARG ILE ALA 0.418803 0.815385
31 ARG SER ARG 0.418605 0.803571
32 ARG GLU ARG SER PRO THR ARG 0.415094 0.825397
33 ALA ASN SER ARG VAL GLN ASP SER ILE ILE 0.413793 0.786885
34 MBN ABN RNG GLY VAL ARG 0.411765 0.769231
35 PRO THR VAL GLU GLU VAL ASP 0.411765 0.827586
36 GLY LEU LEU GLY SER PRO VAL ARG ALA 0.41129 0.857143
37 ILE GLN GLN SER ILE GLU ARG ILE 0.409091 0.79661
38 SER HIS PRO ARG PRO ILE ARG VAL 0.409091 0.797101
39 PRO PRO PRO VAL PRO PRO ARG ARG ARG ARG 0.408696 0.75
40 SER PRO LYS ARG ILE ALA 0.408696 0.84127
41 PRO ALA ILE ILE ASN ARG PRO GLN ASN 0.408333 0.731343
42 ALA ASN SER ARG TRP GLN VAL THR ARG VAL 0.40625 0.80303
43 ACE GLN GLU ARG GLU VAL PRO CYS 0.403361 0.769231
44 LYS PRO VAL LEU ARG THR ALA 0.4 0.84375
Similar Ligands (3D)
Ligand no: 1; Ligand: PRO SER ARG 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 : 6CDG; Ligand: PRO GLY LEU TRP LYS SER; 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: 6cdg.bio1) has 28 residues
No: Leader PDB Ligand Sequence Similarity
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