Receptor
PDB id Resolution Class Description Source Keywords
1phw 2.36 Å EC: 2.5.1.55 CRYSTAL STRUCTURE OF KDO8P SYNTHASE IN ITS BINARY COMPLEX WI SUBSTRATE ANALOG 1-DEOXY-A5P ESCHERICHIA COLI BETA-ALPHA-BARRELS LYASE LIPOPOLYSACCHARIDE A5P ANALOG TRANSFERASE
Ref.: CRYSTAL STRUCTURES OF ESCHERICHIA COLI KDO8P SYNTHA COMPLEXES REVEAL THE SOURCE OF CATALYTIC IRREVERSIB J.MOL.BIOL. V. 351 641 2005
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
N A:70;
 Valid;
 none;
 Ki = 0.5 mM
214.11 C5 H11 O7 P C1[C@...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1G7V 2.4 Å EC: 2.5.1.55 CRYSTAL STRUCTURES OF KDO8P SYNTHASE IN ITS BINARY COMPLEXES MECHANISM-BASED INHIBITOR ESCHERICHIA COLI BETA-ALPHA-BARRELS LYASE LIPOPOLYSACCHARIDE
Ref.: CRYSTAL STRUCTURES OF KDOP SYNTHASE IN ITS BINARY C WITH THE SUBSTRATE PHOSPHOENOLPYRUVATE AND WITH A MECHANISM-BASED INHIBITOR. BIOCHEMISTRY V. 40 6326 2001
Members (2)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
3 3FYP - PEP C3 H5 O6 P C=C(C(=O)O....
4 3FYO - PEP C3 H5 O6 P C=C(C(=O)O....
50% Homology Family (34)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 1PHW Ki = 0.5 mM N C5 H11 O7 P C1[C@@H]([....
2 1G7V Kd = 0.4 uM PAI C9 H23 N O13 P2 C([C@H]([C....
3 4Z1D - PEP C3 H5 O6 P C=C(C(=O)O....
4 2A2I Kd = 0.04 uM A5P C5 H13 O8 P C([C@H]([C....
5 1LRQ - PEP C3 H5 O6 P C=C(C(=O)O....
6 1ZJI - R5P C5 H11 O8 P C(C(C(C(C=....
7 1FY6 - A5P C5 H13 O8 P C([C@H]([C....
8 3E12 - KD0 C8 H15 O11 P C([C@H]([C....
9 1ZHA Kd = 0.04 uM PEP C3 H5 O6 P C=C(C(=O)O....
10 2NWS Kd = 5.44 uM A5P C5 H13 O8 P C([C@H]([C....
11 1T8X - PEP C3 H5 O6 P C=C(C(=O)O....
12 2NWR - PEP C3 H5 O6 P C=C(C(=O)O....
13 1FXQ - PEP C3 H5 O6 P C=C(C(=O)O....
14 1FWN - PEP C3 H5 O6 P C=C(C(=O)O....
15 1JCY - PEP C3 H5 O6 P C=C(C(=O)O....
16 1LRO - PEP C3 H5 O6 P C=C(C(=O)O....
17 1PCK - PEZ C4 H9 O6 P CCC(C(=O)O....
18 3E0I - PEP C3 H5 O6 P C=C(C(=O)O....
19 2NXG Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
20 2NXI - PEP C3 H5 O6 P C=C(C(=O)O....
21 2NX3 Kd = 17 uM A5P C5 H13 O8 P C([C@H]([C....
22 1T96 - PEP C3 H5 O6 P C=C(C(=O)O....
23 2NXH - PEP C3 H5 O6 P C=C(C(=O)O....
24 2EF9 Kd = 14.18 uM A5P C5 H13 O8 P C([C@H]([C....
25 1FWT - E4P C4 H9 O7 P C([C@H]([C....
26 1PE1 - 2PG C3 H7 O7 P C([C@H](C(....
27 2A21 - PEP C3 H5 O6 P C=C(C(=O)O....
28 2NX1 Kd = 0.02 uM RP5 C5 H11 O8 P C([C@@H]1[....
29 1JCX Ki = 7 uM PAI C9 H23 N O13 P2 C([C@H]([C....
30 1FWW - PEP C3 H5 O6 P C=C(C(=O)O....
31 1FWS - PEP C3 H5 O6 P C=C(C(=O)O....
32 1PCW - H4P C7 H19 N O11 P2 C([C@H]([C....
33 3FYP - PEP C3 H5 O6 P C=C(C(=O)O....
34 3FYO - PEP C3 H5 O6 P C=C(C(=O)O....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: N; Similar ligands found: 21
No: Ligand ECFP6 Tc MDL keys Tc
1 N 1 1
2 CU0 0.666667 0.953488
3 GDP MG 0.590909 0.906977
4 D6G 0.478261 0.822222
5 ABF 0.47619 0.860465
6 RP5 0.47619 0.860465
7 HSX 0.47619 0.860465
8 AHG 0.475 0.928571
9 R1X 0.472222 0.674419
10 M6D 0.444444 0.777778
11 A6P 0.444444 0.777778
12 BG6 0.444444 0.777778
13 BGP 0.444444 0.777778
14 M6P 0.444444 0.777778
15 G6P 0.444444 0.777778
16 RF5 0.444444 0.765957
17 50A 0.444444 0.765957
18 FDQ 0.425532 0.952381
19 GRF 0.422222 0.698113
20 GLP 0.408163 0.660377
21 4R1 0.408163 0.660377
Similar Ligands (3D)
Ligand no: 1; Ligand: N; 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 : 1G7V; Ligand: PAI; 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: 1g7v.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 1G7V; Ligand: PAI; 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: 1g7v.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1G7V; Ligand: PAI; 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: 1g7v.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 4; Query (leader) PDB : 1G7V; Ligand: PAI; 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: 1g7v.bio2) has 20 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1G7V; Ligand: PAI; 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: 1g7v.bio1) has 20 residues
No: Leader PDB Ligand Sequence Similarity
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