Receptor
PDB id Resolution Class Description Source Keywords
2JFZ 1.86 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR HELICOBACTER PYLORI CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDOGLYCAN SYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY IN GLUTAMATE RACEMASES NATURE V. 447 817 2007
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
003 A:1256;
B:1256;
Valid;
Valid;
none;
none;
Ki = 5.8 uM
439.509 C26 H25 N5 O2 CC(C)...
DGL A:1257;
B:1257;
Valid;
Valid;
none;
none;
submit data
147.129 C5 H9 N O4 C(CC(...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
2JFZ 1.86 Å EC: 5.1.1.3 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI GLUTAMATE RACEMASE IN COMPLEX WITH D-GLUTAMATE AND AN INHIBITOR HELICOBACTER PYLORI CELL WALL ISOMERASE CELL SHAPE GLUTAMATE RACEMASE PEPTIDOGLYCAN SYNTHESIS PEPTIDOGLYCAN BIOSYNTHESIS
Ref.: EXPLOITATION OF STRUCTURAL AND REGULATORY DIVERSITY IN GLUTAMATE RACEMASES NATURE V. 447 817 2007
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 10 families.
1 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
2 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
3 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
4 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
5 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 8 families.
1 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
2 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
3 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
4 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
5 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
50% Homology Family (15)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 2JFV - FLC C6 H5 O7 C(C(=O)[O-....
2 2JFQ - DGL C5 H9 N O4 C(CC(=O)O)....
3 2DWU - DGL C5 H9 N O4 C(CC(=O)O)....
4 2JFO - DGL C5 H9 N O4 C(CC(=O)O)....
5 2VVT ic50 = 5.8 uM I24 C22 H28 F2 N6 O2 CCCCOc1nc(....
6 2JFP - DGL C5 H9 N O4 C(CC(=O)O)....
7 2OHV Ki = 16 nM NHL C16 H17 N O4 c1ccc2cc(c....
8 1B74 Ki = 50 mM DGN C5 H10 N2 O3 C(CC(=O)N)....
9 1ZUW - DGL C5 H9 N O4 C(CC(=O)O)....
10 2GZM - DGL C5 H9 N O4 C(CC(=O)O)....
11 4B1F - KRH C25 H26 N6 O2 CC(C)CN1c2....
12 2JFY - DGL C5 H9 N O4 C(CC(=O)O)....
13 2JFZ Ki = 5.8 uM 003 C26 H25 N5 O2 CC(C)CN1c2....
14 2W4I ic50 = 0.5 uM VGA C22 H19 N3 O S c1ccc(cc1)....
15 2JFX - DGL C5 H9 N O4 C(CC(=O)O)....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 003; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 003 1 1
2 KRH 0.697917 0.983333
Ligand no: 2; Ligand: DGL; Similar ligands found: 53
No: Ligand ECFP6 Tc MDL keys Tc
1 GGL 1 1
2 GLU 1 1
3 DGL 1 1
4 DGN 0.62963 0.821429
5 GLN 0.62963 0.821429
6 ONL 0.586207 0.821429
7 UN1 0.566667 0.96
8 11C 0.566667 0.96
9 HCS 0.555556 0.714286
10 NPI 0.53125 0.923077
11 HGA 0.53125 0.666667
12 HSE 0.518519 0.758621
13 DAB 0.518519 0.666667
14 MEQ 0.515152 0.71875
15 3O3 0.513514 0.727273
16 NVA 0.5 0.740741
17 API 0.5 0.884615
18 DAS 0.481481 0.846154
19 ASP 0.481481 0.846154
20 TNA 0.463415 0.685714
21 DBB 0.461538 0.692308
22 ABA 0.461538 0.692308
23 DSN 0.461538 0.655172
24 SER 0.461538 0.655172
25 RGP 0.459459 0.648649
26 ORN 0.451613 0.689655
27 HOZ 0.451613 0.666667
28 AE5 0.447368 0.727273
29 DCY 0.444444 0.642857
30 C2N 0.444444 0.666667
31 CYS 0.444444 0.642857
32 NLE 0.4375 0.689655
33 2HG 0.433333 0.653846
34 S2G 0.433333 0.653846
35 ASN 0.428571 0.677419
36 26P 0.428571 0.857143
37 3GC 0.425 0.705882
38 DLY 0.424242 0.666667
39 MED 0.424242 0.625
40 MET 0.424242 0.625
41 MSE 0.424242 0.606061
42 BIX 0.418605 0.631579
43 MF3 0.416667 0.625
44 CBH 0.414634 0.774194
45 DHH 0.411765 0.851852
46 LYS 0.411765 0.645161
47 SHR 0.409091 0.774194
48 2NP 0.405405 0.71875
49 AS2 0.4 0.84
50 5OY 0.4 0.648649
51 ONH 0.4 0.611111
52 2JJ 0.4 0.648649
53 LEU 0.4 0.642857
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 2JFZ; Ligand: DGL; 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: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 2JFZ; Ligand: DGL; 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: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 2JFZ; Ligand: 003; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 3) in the query (biounit: 2jfz.bio1) has 57 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 2JFZ; Ligand: 003; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 2jfz.bio1) has 56 residues
No: Leader PDB Ligand Sequence Similarity
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