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: 54
No: Ligand ECFP6 Tc MDL keys Tc
1 DGL 1 1
2 GLU 1 1
3 GGL 1 1
4 GLN 0.62963 0.821429
5 DGN 0.62963 0.821429
6 ONL 0.586207 0.821429
7 11C 0.566667 0.96
8 UN1 0.566667 0.96
9 HCS 0.555556 0.714286
10 KSN 0.552632 0.774194
11 NPI 0.53125 0.923077
12 HGA 0.53125 0.666667
13 HSE 0.518519 0.758621
14 DAB 0.518519 0.666667
15 MEQ 0.515152 0.71875
16 3O3 0.513514 0.727273
17 NVA 0.5 0.740741
18 API 0.5 0.884615
19 ASP 0.481481 0.846154
20 DAS 0.481481 0.846154
21 TNA 0.463415 0.685714
22 SER 0.461538 0.655172
23 ABA 0.461538 0.692308
24 DBB 0.461538 0.692308
25 DSN 0.461538 0.655172
26 RGP 0.459459 0.648649
27 ORN 0.451613 0.689655
28 HOZ 0.451613 0.666667
29 AE5 0.447368 0.727273
30 DCY 0.444444 0.642857
31 CYS 0.444444 0.642857
32 C2N 0.444444 0.666667
33 NLE 0.4375 0.689655
34 2HG 0.433333 0.653846
35 S2G 0.433333 0.653846
36 26P 0.428571 0.857143
37 ASN 0.428571 0.677419
38 3GC 0.425 0.705882
39 MED 0.424242 0.625
40 MSE 0.424242 0.606061
41 DLY 0.424242 0.666667
42 MET 0.424242 0.625
43 BIX 0.418605 0.631579
44 MF3 0.416667 0.625
45 CBH 0.414634 0.774194
46 LYS 0.411765 0.645161
47 DHH 0.411765 0.851852
48 SHR 0.409091 0.774194
49 2NP 0.405405 0.71875
50 ONH 0.4 0.611111
51 5OY 0.4 0.648649
52 LEU 0.4 0.642857
53 AS2 0.4 0.84
54 2JJ 0.4 0.648649
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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