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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 with APoc: 97
This union binding pocket(no: 1) in the query (biounit: 4z1d.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3W9Z FMN None
2 4S3F 43W 1.08696
3 3ATY FMN 1.81159
4 5F3I 5UJ 1.81159
5 4NVP 7CH 1.91388
6 2WQP WQP 2.17391
7 4N02 FNR 2.17391
8 2Q3R FMN 2.17391
9 1O68 KIV 2.18182
10 5E2N V14 2.28137
11 4UMA GZ3 2.53623
12 5OCS FMN 2.53623
13 1FA2 DOM 2.53623
14 4WOE ADP 2.53623
15 4DV8 0LX 2.6616
16 4N9I PCG 2.85714
17 2XG9 NOJ GLC 2.89855
18 3OYZ ACO 2.89855
19 4A3U FMN 2.89855
20 3B00 16A 2.94118
21 1OFD FMN 3.26087
22 1OFD AKG 3.26087
23 1RE8 BD2 3.26087
24 3U6W KIV 3.26087
25 6EJI UD2 3.26087
26 1Z44 FMN 3.26087
27 1Z41 FMN 3.26087
28 1Z48 FMN 3.26087
29 2Q3O FMN 3.62319
30 4EN4 GT0 3.62319
31 4EN4 ATP 3.62319
32 4EN4 GT1 3.62319
33 3SHR CMP 3.62319
34 2F2H XTG 3.62319
35 3FHQ BMA NGT MAN MAN 3.62319
36 5OSW DIU 3.62319
37 5ABH YWN 3.62319
38 1UJP CIT 3.69004
39 5ETR APC 3.72671
40 5ETR 5RW 3.72671
41 1M3U KPL 3.78788
42 4MZU COA 3.98551
43 5IVE 6E8 3.98551
44 2OD9 A1R NCA 3.98551
45 5T9C G3P 4.10448
46 5C8W PCG 4.1958
47 1EP2 ORO 4.21456
48 1EP2 FMN 4.21456
49 2JLB UDM 4.34783
50 3T7V MD0 4.34783
51 1T90 NAD 4.34783
52 1SR9 KIV 4.71014
53 1VKF CIT 4.71014
54 3S5Y DGJ 4.71014
55 1EC9 XYH 4.71014
56 4RW3 IPD 5.07246
57 4M5P FMN 5.15971
58 3PNA CMP 5.19481
59 1TB3 FMN 5.43478
60 3VP6 HLD 5.43478
61 4B0T ADP 5.43478
62 2PTM CMP 5.7971
63 2R5V HHH 5.7971
64 2J62 GSZ 5.7971
65 6AM8 PLT 6.15942
66 6CUZ FEV 6.15942
67 1TKK ALA GLU 6.15942
68 5JNN 6LM 6.31579
69 6MPT C30 6.52174
70 3R1Z ALA DGL 6.52174
71 3WVR AMP 6.88406
72 3OCP CMP 7.19424
73 1OF8 PEP 7.6087
74 1OF8 G3P 7.6087
75 1AL8 FMN 7.6087
76 4BPZ GLC BGC BGC 7.8125
77 2CXS F6P 7.97101
78 1P4A PCP 7.97101
79 1U6R ADP 8.69565
80 4B1L FRU 9.05797
81 4GZP G39 9.05797
82 1SJD NPG 9.78261
83 2P8B NSK 9.78261
84 1QPR PPC 10.8696
85 1XG4 ICT 10.8696
86 3OGV PTQ 12.3188
87 3DER ALA LYS 12.6812
88 4KU7 PCG 13.7255
89 4QXB OGA 16.1765
90 4MUV PCG 16.1972
91 5CKS 52L 16.3043
92 5UXM PEP 17.029
93 4AIA ADK 19.1489
94 5JAX 6J7 22.2222
95 1RZM PEP 44.5652
96 3TFC PEP 44.9275
97 4C1K PEP 47.7099
Pocket No.: 2; Query (leader) PDB : 4Z1D; Ligand: PEP; Similar sites found with APoc: 24
This union binding pocket(no: 2) in the query (biounit: 4z1d.bio1) has 12 residues
No: Leader PDB Ligand Sequence Similarity
1 3JYY PPV 2.17391
2 4QYS PLP SEP 2.53623
3 1ICP FMN 2.89855
4 2RDT 2RD 2.89855
5 2RDT FMN 2.89855
6 4IAW LIZ 3.19149
7 1OYB FMN 3.26087
8 1Z45 NAD 3.62319
9 1SZD APR 3.98551
10 3H55 GLA 3.98551
11 4BG4 ADP 3.98551
12 2TPS TPS 5.7971
13 2C29 DQH 5.7971
14 2OKL BB2 5.94595
15 1P1M MET 6.52174
16 4EXO PYR 6.84932
17 4TMC FMN 7.24638
18 3B6R ADP 7.97101
19 1NYW DAU 8.62944
20 1L1Q 9DA 9.13978
21 5UR1 YY9 9.42029
22 3KF3 FRU 11.9565
23 2FLI DX5 15
24 3ZO7 K6H 17.0213
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