Receptor
PDB id Resolution Class Description Source Keywords
4YO8 2.1 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOS ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH ((5 H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)(HEXYL)AMINO)METHANO HELICOBACTER PYLORI HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: NEW ANTIBIOTIC CANDIDATES AGAINST HELICOBACTER PYLO J.AM.CHEM.SOC. V. 137 14275 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
4EZ A:301;
B:301;
 Valid;
Valid;
 none;
none;
 Ki = 0.03 nM
277.365 C14 H23 N5 O CCCCC...
ZN A:302;
 Part of Protein;
 none;
 submit data
65.409 Zn [Zn+2...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6DYV 1.62 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOS ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH (3( (4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)-4-((PENT-YL THIO)METHYL)PYRROLIDIN-3-OL HELICOBACTER PYLORI MTAN ENZYME DUODENAL ULCERS STOMACH CANCER HYDROLASE-HYDRINHIBITOR COMPLEX
Ref.: SELECTIVE INHIBITORS OF HELICOBACTER PYLORI METHYLTHIOADENOSINE NUCLEOSIDASE AND HUMAN METHYLTHIOADENOSINE PHOSPHORYLASE. J. MED. CHEM. V. 62 3286 2019
Members (16)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 6 families.
1 4WKP - 3QA C17 H27 N5 O3 S c1c(c2c([n....
2 6DYV Kd = 0.026 nM OS3 C17 H23 N5 O S C#CCCCSC[C....
3 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
4 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
5 6DYY Kd = 0.028 nM OS6 C21 H32 N8 O S CCCCn1cc(n....
6 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
7 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
8 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
10 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
11 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
12 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
13 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
14 6DYW Kd = 0.036 nM OS5 C24 H30 N8 O S c1ccc(cc1)....
15 6DYU Kd = 0.055 nM OS2 C15 H19 N5 O S C#CCSC[C@H....
16 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4WKP - 3QA C17 H27 N5 O3 S c1c(c2c([n....
2 6DYV Kd = 0.026 nM OS3 C17 H23 N5 O S C#CCCCSC[C....
3 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
4 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
5 6DYY Kd = 0.028 nM OS6 C21 H32 N8 O S CCCCn1cc(n....
6 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
7 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
8 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
9 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
10 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
11 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
12 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
13 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
14 6DYW Kd = 0.036 nM OS5 C24 H30 N8 O S c1ccc(cc1)....
15 6DYU Kd = 0.055 nM OS2 C15 H19 N5 O S C#CCSC[C@H....
16 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
17 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
18 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (41)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 3DF9 - DF9 C19 H23 N5 O S c1ccc(cc1)....
2 4F1W - ADE C5 H5 N5 c1[nH]c2c(....
3 1Y6Q Ki = 2 pM TDI C13 H19 N5 O S CSC[C@H]1C....
4 4YML Ki = 4.5 nM 4F0 C13 H19 N5 O S CSC[C@@H]1....
5 1NC3 Ki = 10 uM FMC C10 H13 N5 O4 c1nc2c(c(n....
6 4WKC Ki = 0.21 pM BIG C16 H25 N5 O S CCCCSC[C@H....
7 1JYS Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
8 4F2W Ki = 5 pM TDI C13 H19 N5 O S CSC[C@H]1C....
9 1NC1 Ki = 0.75 uM MTH C12 H16 N4 O3 S CSC[C@@H]1....
10 1Z5N Ki = 300 uM ADE C5 H5 N5 c1[nH]c2c(....
11 4F2P Ki = 5 pM 2EL C16 H25 N5 O3 S c1c(c2c([n....
12 1Y6R Ki = 77 pM MTM C12 H19 N5 O2 S CSC[C@@H]1....
13 4F3C Ki = 1.5 pM BIG C16 H25 N5 O S CCCCSC[C@H....
14 4F3K Ki = 69 pM HCE C16 H24 N6 O3 S c1c(c2c([n....
15 1Z5O - MTA C11 H15 N5 O3 S CSC[C@@H]1....
16 1ZOS Ki = 1 uM MTM C12 H19 N5 O2 S CSC[C@@H]1....
17 4WKP - 3QA C17 H27 N5 O3 S c1c(c2c([n....
18 6DYV Kd = 0.026 nM OS3 C17 H23 N5 O S C#CCCCSC[C....
19 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
20 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
21 6DYY Kd = 0.028 nM OS6 C21 H32 N8 O S CCCCn1cc(n....
22 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
23 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
24 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
25 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
26 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
27 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
28 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
29 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
30 6DYW Kd = 0.036 nM OS5 C24 H30 N8 O S c1ccc(cc1)....
31 6DYU Kd = 0.055 nM OS2 C15 H19 N5 O S C#CCSC[C@H....
32 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
33 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
34 3DP9 Kd = 208 pM BIG C16 H25 N5 O S CCCCSC[C@H....
35 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
36 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
37 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
38 3BL6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
39 6AYR Ki = 4.1 nM BIG C16 H25 N5 O S CCCCSC[C@H....
40 6AYQ Ki = 6.5 nM TDI C13 H19 N5 O S CSC[C@H]1C....
41 6AYO Ki = 5.1 nM C1Y C14 H21 N5 O CCC[C@H]1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: 4EZ; Similar ligands found: 3
No: Ligand ECFP6 Tc MDL keys Tc
1 4EZ 1 1
2 BIG 0.420455 0.731343
3 C1Y 0.402439 0.727273
Similar Ligands (3D)
Ligand no: 1; Ligand: 4EZ; Similar ligands found: 8
No: Ligand Similarity coefficient
1 OS2 0.9105
2 AMP 0.8839
3 4F0 0.8719
4 MTA 0.8708
5 MTM 0.8701
6 TDI 0.8667
7 MTH 0.8626
8 FMP 0.8570
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6DYV; Ligand: OS3; Similar sites found with APoc: 1
This union binding pocket(no: 1) in the query (biounit: 6dyv.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
1 4QAR ADE 8.95522
Pocket No.: 2; Query (leader) PDB : 6DYV; Ligand: OS3; 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: 6dyv.bio1) has 51 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 6DYV; Ligand: OS3; Similar sites found with APoc: 6
This union binding pocket(no: 3) in the query (biounit: 6dyv.bio2) has 52 residues
No: Leader PDB Ligand Sequence Similarity
1 4QAR ADE 8.95522
2 4QAR ADE 8.95522
3 3LGS SAH 42.0408
4 3LGS SAH 42.0408
5 3LGS ADE 42.0408
6 3LGS ADE 42.0408
Pocket No.: 4; Query (leader) PDB : 6DYV; Ligand: OS3; 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: 6dyv.bio2) has 52 residues
No: Leader PDB Ligand Sequence Similarity
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