Receptor
PDB id Resolution Class Description Source Keywords
5MX4 2.31 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF H. PYLORI PURINE NUCLEOSIDE PHOSPHORYLA CLINICAL ISOLATE HPPNP-1 HELICOBACTER PYLORI R018C PURINE NUCLEOSIDE PHOSPHORYLASE CLINICAL ISOLATE HELICOBACPYLORI DEAD-END-COMPLEX TRANSFERASE
Ref.: STRUCTURAL CHARACTERIZATION OF PURINE NUCLEOSIDE PHOSPHORYLASE FROM HUMAN PATHOGEN HELICOBACTER PYLO INT. J. BIOL. MACROMOL. V. 101 518 2017
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
PO4 C:301;
Invalid;
none;
submit data
94.971 O4 P [O-]P...
HPA C:300;
Valid;
none;
submit data
136.111 C5 H4 N4 O c1[nH...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6F4W 2.29 Å EC: 2.4.2.1 CRYSTAL STRUCTURE OF H. PYLORI PURINE NUCLEOSIDE PHOSPHORYLA COMPLEX WITH FORMYCIN A HELICOBACTER PYLORI PURINE NUCLEOSIDE PHOSPHORYLASE H. PYLORI FORMYCIN A HYDR
Ref.: HELICOBACTER PYLORI PURINE NUCLEOSIDE PHOSPHORYLASE NEW DISTRIBUTION PATTERNS OF OPEN AND CLOSED ACTIVE CONFORMATIONS AND UNUSUAL BIOCHEMICAL FEATURES. FEBS J. V. 285 1305 2018
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 18 families.
1 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
2 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
3 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
4 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
5 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
70% Homology Family (39)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 9 families.
1 1Z35 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
2 1Z34 ic50 = 0.42 mM 2FD C10 H12 F N5 O3 c1nc2c(nc(....
3 1Z38 - NOS C10 H12 N4 O5 c1nc2c(n1[....
4 1PR1 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
5 1OUM - TAL C12 H16 N4 O4 Cc1c2c(ncn....
6 1PR2 - MDR C11 H14 N4 O3 Cc1c2c(ncn....
7 1PR5 Ki = 120 uM TBN C11 H14 N4 O4 c1cn(c2c1c....
8 1PKE - 2FD C10 H12 F N5 O3 c1nc2c(nc(....
9 1PR6 - XYA C10 H13 N5 O4 c1nc(c2c(n....
10 1PR0 - NOS C10 H12 N4 O5 c1nc2c(n1[....
11 1PK9 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
12 1OV6 - DBM C12 H16 N4 O4 Cc1c2c(ncn....
13 1PR4 - MTP C11 H14 N4 O4 S CSc1c2c(nc....
14 1PK7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
15 1OVG - MDR C11 H14 N4 O3 Cc1c2c(ncn....
16 1OU4 - 6MP C6 H6 N4 Cc1c2c(nc[....
17 1OTY - 6MP C6 H6 N4 Cc1c2c(nc[....
18 3UT6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
19 1PW7 - RAB C10 H13 N5 O4 c1nc(c2c(n....
20 1K9S - FM2 C11 H16 N5 O4 C[n+]1cnc2....
21 1A69 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
22 1VHW - ADN C10 H13 N5 O4 c1nc(c2c(n....
23 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
24 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
25 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
26 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
27 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
28 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
29 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
30 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
31 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
32 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
33 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
34 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
35 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
36 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
37 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
38 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
39 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
50% Homology Family (45)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 1Z35 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
2 1Z34 ic50 = 0.42 mM 2FD C10 H12 F N5 O3 c1nc2c(nc(....
3 1Z38 - NOS C10 H12 N4 O5 c1nc2c(n1[....
4 1PR1 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
5 1OUM - TAL C12 H16 N4 O4 Cc1c2c(ncn....
6 1PR2 - MDR C11 H14 N4 O3 Cc1c2c(ncn....
7 1PR5 Ki = 120 uM TBN C11 H14 N4 O4 c1cn(c2c1c....
8 1PKE - 2FD C10 H12 F N5 O3 c1nc2c(nc(....
9 1PR6 - XYA C10 H13 N5 O4 c1nc(c2c(n....
10 1PR0 - NOS C10 H12 N4 O5 c1nc2c(n1[....
11 1PK9 - 2FA C10 H12 F N5 O4 c1nc2c(nc(....
12 1OV6 - DBM C12 H16 N4 O4 Cc1c2c(ncn....
13 1PR4 - MTP C11 H14 N4 O4 S CSc1c2c(nc....
14 1PK7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
15 1OVG - MDR C11 H14 N4 O3 Cc1c2c(ncn....
16 1OU4 - 6MP C6 H6 N4 Cc1c2c(nc[....
17 1OTY - 6MP C6 H6 N4 Cc1c2c(nc[....
18 3UT6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
19 1PW7 - RAB C10 H13 N5 O4 c1nc(c2c(n....
20 1K9S - FM2 C11 H16 N5 O4 C[n+]1cnc2....
21 1A69 Ki = 5 uM FMB C10 H12 N4 O5 C1=Nc2c(n[....
22 1VHW - ADN C10 H13 N5 O4 c1nc(c2c(n....
23 5MX4 - HPA C5 H4 N4 O c1[nH]c2c(....
24 5MX6 - HPA C5 H4 N4 O c1[nH]c2c(....
25 5MX8 - HPA C5 H4 N4 O c1[nH]c2c(....
26 6F4X Kd = 10.7 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
27 6F4W Kd = 2.95 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
28 1JDT - MTA C11 H15 N5 O3 S CSC[C@@H]1....
29 1JE1 - GMP C10 H13 N5 O5 c1nc2c(n1[....
30 1JDZ - FMB C10 H12 N4 O5 C1=Nc2c(n[....
31 2AC7 - ADN C10 H13 N5 O4 c1nc(c2c(n....
32 3UAZ - NOS C10 H12 N4 O5 c1nc2c(n1[....
33 3UAY - ADN C10 H13 N5 O4 c1nc(c2c(n....
34 3UAX - NOS C10 H12 N4 O5 c1nc2c(n1[....
35 3UAW - ADN C10 H13 N5 O4 c1nc(c2c(n....
36 1ODI Kd = 62 uM ADN C10 H13 N5 O4 c1nc(c2c(n....
37 1ODJ Kd = 80 uM GMP C10 H13 N5 O5 c1nc2c(n1[....
38 4DAO - ADE C5 H5 N5 c1[nH]c2c(....
39 4DA6 - GA2 C9 H13 N5 O4 c1nc2c(n1C....
40 4DA7 - AC2 C8 H11 N5 O3 c1nc2c(n1C....
41 4DAE - 6CR C10 H12 Cl N5 O4 c1nc2c(n1[....
42 4D9H - ADN C10 H13 N5 O4 c1nc(c2c(n....
43 4D8V - ADE C5 H5 N5 c1[nH]c2c(....
44 4DAB - HPA C5 H4 N4 O c1[nH]c2c(....
45 3U40 - ADN C10 H13 N5 O4 c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HPA; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 HPA 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 9
This union binding pocket(no: 1) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
2 4TXJ THM 18.8841
3 4TXJ THM 18.8841
4 1U1F 183 39.0558
5 1U1F 183 39.0558
6 1U1F 183 39.0558
7 1U1F 183 39.0558
8 1U1F 183 39.0558
9 1U1F 183 39.0558
Pocket No.: 2; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 9
This union binding pocket(no: 2) in the query (biounit: 6f4w.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
2 1U1F 183 39.0558
3 1U1F 183 39.0558
4 1U1F 183 39.0558
5 1U1F 183 39.0558
6 1U1F 183 39.0558
7 1U1F 183 39.0558
8 4YJK URA 43.7768
9 4YJK URA 43.7768
Pocket No.: 3; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 5
This union binding pocket(no: 3) in the query (biounit: 6f4w.bio1) has 17 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
2 4TXJ THM 18.8841
3 4TXJ THM 18.8841
4 1U1F 183 39.0558
5 1U1F 183 39.0558
Pocket No.: 4; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 13
This union binding pocket(no: 4) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
2 4TXJ THM 18.8841
3 4TXJ THM 18.8841
4 4TXJ THM 18.8841
5 1U1F 183 39.0558
6 1U1F 183 39.0558
7 1U1F 183 39.0558
8 1U1F 183 39.0558
9 1U1F 183 39.0558
10 1U1F 183 39.0558
11 4YJK URA 43.7768
12 4YJK URA 43.7768
13 4YJK URA 43.7768
Pocket No.: 5; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 11
This union binding pocket(no: 5) in the query (biounit: 6f4w.bio1) has 16 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
2 4TXJ THM 18.8841
3 4TXJ THM 18.8841
4 4TXJ THM 18.8841
5 1U1F 183 39.0558
6 1U1F 183 39.0558
7 1U1F 183 39.0558
8 1U1F 183 39.0558
9 1U1F 183 39.0558
10 1U1F 183 39.0558
11 4YJK URA 43.7768
Pocket No.: 6; Query (leader) PDB : 6F4W; Ligand: FMC; Similar sites found with APoc: 1
This union binding pocket(no: 6) in the query (biounit: 6f4w.bio1) has 18 residues
No: Leader PDB Ligand Sequence Similarity
1 4TXJ THM 18.8841
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