Receptor
PDB id Resolution Class Description Source Keywords
5TDC 1.61 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE HUMAN UBR-BOX DOMAIN FROM UBR1 IN C WITH MONOMETHYLATED ARGININE PEPTIDE. HOMO SAPIENS UBR-BOX N-END RULE N-DEGRON MONOMETHYLATED ARGININE LIGA
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN C:201;
A:203;
A:202;
C:203;
C:202;
A:201;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
NMM ILE PHE SER D:1;
B:1;
Valid;
Valid;
Atoms found LESS than expected: % Diff = 0.053;
Atoms found LESS than expected: % Diff = 0.184;
Kd = 12.88 uM
433.577 n/a O=C(N...
SO4 C:204;
A:204;
Invalid;
Invalid;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5TDC 1.61 Å EC: 6.3.2.- CRYSTAL STRUCTURE OF THE HUMAN UBR-BOX DOMAIN FROM UBR1 IN C WITH MONOMETHYLATED ARGININE PEPTIDE. HOMO SAPIENS UBR-BOX N-END RULE N-DEGRON MONOMETHYLATED ARGININE LIGA
Ref.: BOUND WATERS MEDIATE BINDING OF DIVERSE SUBSTRATES UBIQUITIN LIGASE. STRUCTURE V. 25 719 2017
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 41 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 27 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
3 3NY3 Ka = 51900 M^-1 ARG ILE PHE SER n/a n/a
4 5TDA - ARG LEU TRP SER n/a n/a
5 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
50% Homology Family (12)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 12 families.
1 5TDC Kd = 12.88 uM NMM ILE PHE SER n/a n/a
2 3NIL - ARG ASP ALA ALA n/a n/a
3 3NIJ - HIS ILE ALA ALA n/a n/a
4 3NIH - ARG ILE ALA ALA ALA n/a n/a
5 3NII - LYS ILE ALA ALA n/a n/a
6 3NIM Kd = 17.7 uM ARG ARG ALA ALA n/a n/a
7 3NIK Kd = 358.8 uM ARG GLU ALA ALA n/a n/a
8 3NIN - ARG LEU GLY GLU SER n/a n/a
9 5TDB Kd = 1.45 uM DA2 ILE PHE SER n/a n/a
10 3NY3 Ka = 51900 M^-1 ARG ILE PHE SER n/a n/a
11 5TDA - ARG LEU TRP SER n/a n/a
12 5TDD Kd = 34 uM HIS ILE PHE SER n/a n/a
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: NMM ILE PHE SER; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 NMM ILE PHE SER 1 1
2 ARG ILE PHE SER 0.595745 0.882353
3 ARG ILE ALA ALA ALA 0.481928 0.87234
4 ALA VAL GLY ILE GLY ALA VAL PHE LEU 0.480392 0.77551
5 ILE MET ILE SER PHE 0.48 0.678571
6 ALA ALA PHE 0.45679 0.617021
7 LYS LEU LEU PHE 0.456522 0.77551
8 ARG ARG LEU ILE PHE NH2 0.443396 0.918367
9 ARG ABA PHE ILE PHE ALA ASN ILE 0.423729 0.818182
10 HIS ILE PHE SER 0.413462 0.625
11 ARG ABA VAL ILE PHE ALA ASN ILE 0.413223 0.833333
12 LYS ILE ALA ALA 0.404762 0.729167
Similar Ligands (3D)
Ligand no: 1; Ligand: NMM ILE PHE SER; 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 : 5TDC; Ligand: NMM ILE PHE 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: 5tdc.bio2) has 12 residues
No: Leader PDB Ligand Sequence Similarity
APoc FAQ
Feedback