Receptor
PDB id Resolution Class Description Source Keywords
3PN4 1.9 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PETIDE DEFORMYLASE (ATPDF1B) IN COMPLEX WITH ACTINONIN (CRYSTALLIZED IN PEG-55 ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B PDF N-TERMINAL EXCISION PATHWAY NINDUCED-FIT HYDROLASE-ANTIBIOTIC COMPLEX
Ref.: TRAPPING CONFORMATIONAL STATES ALONG LIGAND-BINDING OF PEPTIDE DEFORMYLASE: THE IMPACT OF INDUCED FIT O CATALYSIS. PLOS BIOL. V. 9 E1001 2011
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:501;
Valid;
none;
Kd = 140 nM
385.498 C19 H35 N3 O5 CCCCC...
ZN A:1001;
A:1002;
A:1003;
A:1004;
A:1005;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
3M6P 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLAS (ATPDF1B) IN COMPLEX WITH ACTINONIN ARABIDOPSIS THALIANA PEPTIDE DEFORMYLASE 1B PDF N-TERMINAL EXCISION PATHWAY NARABIDOPSIS THALIANA INDUCED-FIT HYDROLASE METAL-BINDINGMITOCHONDRION PROTEIN BIOSYNTHESIS TRANSIT PEPTIDE HYDROANTIBIOTIC COMPLEX
Ref.: TRAPPING CONFORMATIONAL STATES ALONG LIGAND-BINDING OF PEPTIDE DEFORMYLASE: THE IMPACT OF INDUCED FIT O CATALYSIS PLOS BIOL. V. 9 01066 2011
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
4 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
5 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
4 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
5 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
50% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3M6P Kd = 0.9 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 3M6R Kd = 32 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
3 3PN4 Kd = 140 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
4 3PN3 Ki = 400 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 3m6p.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
1 5MTE BB2 44.5255
Pocket No.: 2; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 3m6p.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
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