Receptor
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
ZN A:310;
A:308;
A:306;
A:311;
A:307;
A:304;
A:305;
A:309;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
65.409 Zn [Zn+2...
IMD A:303;
Invalid;
none;
submit data
69.085 C3 H5 N2 c1c[n...
ACT A:302;
Invalid;
none;
submit data
59.044 C2 H3 O2 CC(=O...
SF7 A:301;
Valid;
Atoms found LESS than expected: % Diff = 0;
Ki = 13 nM
321.347 C16 H20 F N3 O3 CCCC[...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5JF2 2 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH INHIBITOR AT002 STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR AT002 HYDROLASE
Ref.: A UNIQUE PEPTIDE DEFORMYLASE PLATFORM TO RATIONALLY AND CHALLENGE NOVEL ACTIVE COMPOUNDS. SCI REP V. 6 35429 2016
Members (10)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 14 families.
1 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
2 5JEZ - MET ALA SER n/a n/a
3 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
4 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
5 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
6 5JF0 - MET ALA ARG n/a n/a
7 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
8 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
9 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
70% Homology Family (20)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
12 5JEZ - MET ALA SER n/a n/a
13 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
14 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
15 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
16 5JF0 - MET ALA ARG n/a n/a
17 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
18 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
19 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
20 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (21)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 5 families.
1 3SW8 Ki = 25910 nM 5LI C10 H10 Cl2 N2 O3 c1cc(c(c(c....
2 3SVJ Ki = 117 nM 4LI C27 H32 Cl N9 O2 S Cc1cccc(c1....
3 2AI7 ic50 = 0.4 uM SB7 C10 H15 N O2 c1ccc(cc1)....
4 2AIE ic50 = 2.2 uM SB9 C10 H14 N2 O2 Cc1cccc(n1....
5 2AIA ic50 = 3.9 uM SB8 C16 H15 N O4 c1ccc(cc1)....
6 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
7 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
8 3G6N - MET ALA SER n/a n/a
9 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
10 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
11 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
13 5JEZ - MET ALA SER n/a n/a
14 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
15 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
16 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
17 5JF0 - MET ALA ARG n/a n/a
18 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
19 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
20 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
21 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: SF7; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 SF7 1 1
2 SF5 0.736842 0.835821
3 7JT 0.40404 0.742857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5JF2; Ligand: SF7; 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: 5jf2.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
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