Receptor
PDB id Resolution Class Description Source Keywords
5JF0 1.6 Å EC: 3.5.1.88 CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIA COMPLEX WITH TRIPEPTIDE MET-ALA-ARG STREPTOCOCCUS AGALACTIAE PDF TYPE 2 NME N-TERMINAL METHIONINE EXCISION STREPTOCOCAGALACTIAE INHIBITOR TRIPEPTIDE 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
ACT A:301;
 Invalid;
 none;
 submit data
59.044 C2 H3 O2 CC(=O...
MET ALA ARG D:1;
 Valid;
 none;
 submit data
377.49 n/a S(CCC...
NI A:304;
A:305;
A:306;
A:307;
A:303;
A:308;
A:309;
A:302;
 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
58.693 Ni [Ni+2...
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 (22)
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 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
14 5JEZ - MET ALA SER n/a n/a
15 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
16 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
17 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
18 5JF0 - MET ALA ARG n/a n/a
19 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
20 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
21 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
22 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
50% Homology Family (23)
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 6OW7 ic50 = 1 nM N9Y C20 H29 N5 O4 c1ccnc(c1)....
7 4EOX ic50 = 0.28 nM 0S5 C22 H29 N3 O5 c1ccc(cc1)....
8 6OW2 ic50 = 3 nM NB4 C22 H36 F N7 O4 Cc1nc(c(c(....
9 3STR Ki = 334 nM 3LI C28 H33 Cl N10 O4 S Cc1cccc(c1....
10 3G6N - MET ALA SER n/a n/a
11 2OKL - BB2 C19 H35 N3 O5 CCCCC[C@H]....
12 1Q1Y - BB2 C19 H35 N3 O5 CCCCC[C@H]....
13 1LQY - BB2 C19 H35 N3 O5 CCCCC[C@H]....
14 5JF3 Ki = 38 nM SF5 C18 H23 N3 O5 CCCC[C@H](....
15 5JEZ - MET ALA SER n/a n/a
16 5JF7 Ki = 909 nM 6JU C17 H15 Br N2 O2 c1ccc(cc1)....
17 5JF2 Ki = 13 nM SF7 C16 H20 F N3 O3 CCCC[C@H](....
18 5JF5 Ki = 63 nM 7JT C19 H23 N3 O5 c1cc2c(cc1....
19 5JF0 - MET ALA ARG n/a n/a
20 5JF4 Ki = 65 nM 6JT C20 H23 N3 O4 c1ccc2c(c1....
21 5JF6 Ki = 62 nM BB4 C10 H9 Br N2 O2 c1cc2c(cc1....
22 5JF1 Ki = 64 nM BB2 C19 H35 N3 O5 CCCCC[C@H]....
23 5JF8 Ki = 1428 nM PN3 C15 H22 N2 O4 CC(C)(C)OC....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: MET ALA ARG; Similar ligands found: 35
No: Ligand ECFP6 Tc MDL keys Tc
1 MET ALA ARG 1 1
2 MET ALA ALA 0.5625 0.808511
3 ARG ARG ALA ALA 0.546667 0.875
4 ALA ARG 0.538462 0.851064
5 MET ARG THR GLY ASN ALA XSN 0.527778 0.893617
6 ARG SER ARG 0.520548 0.754717
7 MET ABA LEU ARG MET THR ALA VAL MET 0.509615 0.854545
8 API DAL C0O 0.507246 0.680851
9 VAL ALA ARG SER 0.506329 0.823529
10 LYS ALA LYS 0.5 0.714286
11 ALA ARG ALA ALA ALA ALA ALA ALA ALA 0.5 0.893617
12 MET CYS LEU ARG MET THR ALA VAL MET 0.495327 0.854545
13 MET CYS LEU ARG NLE THR ALA VAL MET 0.481818 0.839286
14 ARG GLU ALA ALA 0.481481 0.875
15 ARG ALA ARG 0.48 0.791667
16 LYS ARG LYS 0.474359 0.816327
17 ARG ARG GLY MET NH2 0.46988 0.862745
18 ARG ARG ALA THR LYS MET NH2 0.45 0.836364
19 GLU ALA GLN THR ARG LEU 0.445545 0.796296
20 GLU ARG GLY MET THR 0.4375 0.903846
21 PHE TYR ARG ALA LEU MET 0.4375 0.810345
22 VAL ARG MET 0.433735 0.916667
23 ALA ARG THR M3L GLN THR ALA ARG 0.431373 0.730159
24 MET CYS PRO ARG MET THR ALA VAL MET 0.430894 0.691176
25 CYS ALA ARG ALA TYR 0.43038 0.8125
26 GLN ARG ALA THR LYS MET NH2 0.428571 0.836364
27 ARG ASP ARG ALA ALA LYS LEU 0.428571 0.86
28 ARG ILE MET GLU NH2 0.425532 0.959184
29 ALA MET ARG VAL 0.418605 0.9375
30 ALA GLN PHE SER ALA SER ALA SER ARG 0.413462 0.736842
31 ARG ARG GLY LEU NH2 0.404762 0.803922
32 ARG ASP ALA ALA 0.402439 0.836735
33 ASN ARG LEU MET LEU THR GLY 0.401961 0.839286
34 ARG ARG GLY ILE NH2 0.4 0.803922
35 ARG LEU GLY GLU SER 0.4 0.8
Similar Ligands (3D)
Ligand no: 1; Ligand: MET ALA ARG; 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 : 5JF2; Ligand: SF7; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 5jf2.bio1) has 21 residues
No: Leader PDB Ligand Sequence Similarity
1 1G27 BB1 38.0952
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