Receptor
PDB id Resolution Class Description Source Keywords
3m6q 2.4 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF ARABIDOPSIS THALIANA PEPTIDE DEFORMYLAS (ATPDF1B) G41Q MUTANT 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
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BB2 A:194;
 Valid;
 none;
 Kd = 48 nM
385.498 C19 H35 N3 O5 CCCCC...
ZN A:195;
A:196;
A:197;
A:198;
A:199;
 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 Ki = 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 Ki = 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 Ki = 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 Ki = 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 (14)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1144 families.
1 1G2A ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
2 1BS8 - MET ALA SER n/a n/a
3 2AI8 ic50 = 0.16 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 1G27 ic50 = 7 nM BB1 C16 H31 N3 O4 CCCC[C@H](....
5 1LRU - BB2 C19 H35 N3 O5 CCCCC[C@H]....
6 1BS6 - MET ALA SER n/a n/a
7 2EW6 ic50 = 10.8 uM Y13 C17 H17 N O4 c1cc(ccc1C....
8 2EW5 ic50 = 1.25 uM Y12 C21 H21 N O5 CC(=O)Oc1c....
9 3UWB ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1RL4 ic50 = 130 nM BL5 C38 H62 N8 O4 CCCC[C@@H]....
11 1S17 ic50 < 5 nM GNR C10 H10 N2 O3 S c1ccc2c(c1....
12 1IX1 - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 4DR9 ic50 = 10 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 3M6Q Kd = 48 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: BB2; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 BB2 1 1
Similar Ligands (3D)
Ligand no: 1; Ligand: BB2; Similar ligands found: 1
No: Ligand Similarity coefficient
1 BB1 0.8743
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: 2
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
2 5MTE BB2 44.5255
Pocket No.: 2; Query (leader) PDB : 3M6P; Ligand: BB2; Similar sites found with APoc: 2
This union binding pocket(no: 2) in the query (biounit: 3m6p.bio2) has 19 residues
No: Leader PDB Ligand Sequence Similarity
1 5MTE BB2 44.5255
2 5MTE BB2 44.5255
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