Receptor
PDB id Resolution Class Description Source Keywords
1GG1 2 Å EC: 4.1.2.15 CRYSTAL STRUCTURE ANALYSIS OF DAHP SYNTHASE IN COMPLEX WITH MN2+ AND 2-PHOSPHOGLYCOLATE ESCHERICHIA COLI BETA-ALPHA-BARREL LYASE
Ref.: STRUCTURE OF 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM ESCHERICHIA COLI: COMPARISON OF THE MN(2+)*2-PHOSPHOGLYCOLATE AND THE PB(2+)*2-PHOSPHOENOLPYRUVATE COMPLEXES AND IMPLICATIONS FOR CATALYSIS. J.MOL.BIOL. V. 301
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MN A:371;
B:371;
C:371;
D:371;
Part of Protein;
Part of Protein;
Part of Protein;
Part of Protein;
none;
none;
none;
none;
submit data
54.938 Mn [Mn+2...
PGA A:372;
B:372;
C:372;
D:372;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
submit data
156.031 C2 H5 O6 P C(C(=...
SO4 A:1373;
A:1374;
B:2373;
B:2374;
C:3373;
C:3374;
D:4373;
D:4374;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
Invalid;
none;
none;
none;
none;
none;
none;
none;
none;
submit data
96.063 O4 S [O-]S...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
5CKS 2.12 Å EC: 4.1.2.15 DAHP (3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE) SYNTHASE I WITH DAHP OXIME. ESCHERICHIA COLI (STRAIN K12) DAHP SYNTHASE INHIBITOR COMPLEX TRANSITION STATE MIMIC TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
Ref.: POTENT INHIBITION OF 3-DEOXY-D-ARABINOHEPTULOSONATE-7-PHOSPHATE (DAHP) S BY DAHP OXIME, A PHOSPHATE GROUP MIMIC. BIOCHEMISTRY V. 55 6617 2016
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 families.
1 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
2 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
3 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
70% Homology Family (11)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
10 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
11 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
50% Homology Family (17)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4UMB Ki = 99 uM 0V5 C3 H7 O6 P C[C@H](C(=....
2 4UMC Ki = 360 uM PEQ C3 H7 O6 P C[C@@H](C(....
3 4HSO Kd = 22 uM TYR C9 H11 N O3 c1cc(ccc1C....
4 4UCG - PEP C3 H5 O6 P C=C(C(=O)O....
5 5DCE - TRP C11 H12 N2 O2 c1ccc2c(c1....
6 4UC5 - PHE C9 H11 N O2 c1ccc(cc1)....
7 4HSN - PEP C3 H5 O6 P C=C(C(=O)O....
8 4UMA Ki = 3.9 uM GZ3 C4 H7 O5 P C/C(=CP(=O....
9 1OAB - PEP C3 H5 O6 P C=C(C(=O)O....
10 1OFO - PGA C2 H5 O6 P C(C(=O)O)O....
11 1OF6 - DTY C9 H11 N O3 c1cc(ccc1C....
12 1OF8 - G3P C3 H9 O6 P C([C@H](CO....
13 1OFA - PEP C3 H5 O6 P C=C(C(=O)O....
14 1HFB - PEP C3 H5 O6 P C=C(C(=O)O....
15 1N8F - PEP C3 H5 O6 P C=C(C(=O)O....
16 1GG1 - PGA C2 H5 O6 P C(C(=O)O)O....
17 5CKS Ki = 1.5 uM 52L C7 H14 N O10 P C([C@H]([C....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: PGA; Similar ligands found: 9
No: Ligand ECFP6 Tc MDL keys Tc
1 PGA 1 1
2 HPV 0.555556 0.903226
3 13P 0.5 0.818182
4 PGH 0.482759 0.651163
5 3PG 0.433333 0.90625
6 3PP 0.423077 0.866667
7 PAE 0.416667 0.806452
8 EFS 0.416667 0.741935
9 SEP 0.40625 0.710526
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 5CKS; Ligand: 52L; Similar sites found with APoc: 3
This union binding pocket(no: 1) in the query (biounit: 5cks.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 5UXM PEP 5.98291
2 4C1K PEP 24.4275
3 3TFC PEP 27.3504
Pocket No.: 2; Query (leader) PDB : 5CKS; Ligand: GAL; 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: 5cks.bio1) has 11 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 5CKS; Ligand: 52L; 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: 5cks.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 5CKS; Ligand: GAL; 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: 5cks.bio1) has 10 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 5CKS; Ligand: GAL; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 5cks.bio1) has 3 residues
No: Leader PDB Ligand Sequence Similarity
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