Receptor
PDB id Resolution Class Description Source Keywords
4Z1D 1.65 Å EC: 2.5.1.55 STRUCTURE OF PEP AND ZINC BOUND KDO8PS FROM H.PYLORI HELICOBACTER PYLORI (STRAIN ATCC 7003926695) HELICOBACTER PYLORI LIPOPOLYSACCHARIDE BIOSYNTHESIS LIGANDTRANSFERASE
Ref.: IDENTIFICATION OF NOVEL SCAFFOLDS FOR POTENTIAL ANTI-HELICOBACTER PYLORI AGENTS BASED ON THE CRYSTA STRUCTURE OF H. PYLORI 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE (HPKDO8PS). EUR.J.MED.CHEM. V. 108 188 2016
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PEP B:300;
A:300;
Valid;
Valid;
none;
none;
submit data
168.042 C3 H5 O6 P C=C(C...
ZN A:301;
B:301;
Part of Protein;
Part of Protein;
none;
none;
submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4Z1D 1.65 Å EC: 2.5.1.55 STRUCTURE OF PEP AND ZINC BOUND KDO8PS FROM H.PYLORI HELICOBACTER PYLORI (STRAIN ATCC 7003926695) HELICOBACTER PYLORI LIPOPOLYSACCHARIDE BIOSYNTHESIS LIGANDTRANSFERASE
Ref.: IDENTIFICATION OF NOVEL SCAFFOLDS FOR POTENTIAL ANTI-HELICOBACTER PYLORI AGENTS BASED ON THE CRYSTA STRUCTURE OF H. PYLORI 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE (HPKDO8PS). EUR.J.MED.CHEM. V. 108 188 2016
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4Z1D - PEP C3 H5 O6 P C=C(C(=O)O....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 4Z1D - 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
Ligand no: 1; Ligand: PEP; Similar ligands found: 2
No: Ligand ECFP6 Tc MDL keys Tc
1 PEP 1 1
2 UVW 0.44 0.709677
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4Z1D; Ligand: PEP; Similar sites found: 33
This union binding pocket(no: 1) in the query (biounit: 4z1d.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3W9Z FMN 0.01952 0.40521 None
2 2Q3R FMN 0.02204 0.40279 2.17391
3 4UMA GZ3 0.0000003638 0.63822 2.53623
4 4DV8 0LX 0.04708 0.40187 2.6616
5 4A3U FMN 0.02645 0.40096 2.89855
6 3U6W KIV 0.002658 0.43412 3.26087
7 1RE8 BD2 0.02333 0.43094 3.26087
8 2Q3O FMN 0.007786 0.43706 3.62319
9 4EN4 ATP 0.03033 0.4152 3.62319
10 4EN4 GT1 0.03033 0.4152 3.62319
11 4EN4 GT0 0.03033 0.4152 3.62319
12 2F2H XTG 0.01993 0.41115 3.62319
13 3FHQ BMA NGT MAN MAN 0.01519 0.40541 3.62319
14 4MZU COA 0.01356 0.41993 3.98551
15 5T9C G3P 0.007363 0.40383 4.10448
16 5C8W PCG 0.004996 0.42288 4.1958
17 3T7V MD0 0.007629 0.41144 4.34783
18 1T90 NAD 0.04946 0.40041 4.34783
19 1VKF CIT 0.004227 0.42293 4.71014
20 1SR9 KIV 0.002888 0.41927 4.71014
21 2GJ5 VD3 0.04507 0.40746 4.93827
22 3VP6 HLD 0.01403 0.42207 5.43478
23 4B0T ADP 0.01819 0.41488 5.43478
24 5JNN 6LM 0.001842 0.47148 6.31579
25 3R1Z ALA DGL 0.01721 0.40081 6.52174
26 1OF8 PEP 0.0000002614 0.6412 7.6087
27 1OF8 G3P 0.0000007884 0.62687 7.6087
28 1U6R ADP 0.01969 0.40308 8.69565
29 4B1L FRU 0.004183 0.41528 9.05797
30 1XG4 ICT 0.0129 0.41814 10.8696
31 5CKS 52L 0.0000009851 0.51768 16.3043
32 4AIA ADK 0.005146 0.42264 19.1489
33 4C1K PEP 0.0001533 0.53356 47.7099
Pocket No.: 2; Query (leader) PDB : 4Z1D; Ligand: PEP; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 4z1d.bio1) has 12 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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