Receptor
PDB id Resolution Class Description Source Keywords
4FFS 1.9 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF 5'-METHYLTHIOADENOSINE/S-ADENOSYLHOMOCY NUCLEOSIDASE FROM HELICOBACTER PYLORI WITH BUTYL-THIO-DADMEI MMUCILLIN-A HELICOBACTER PYLORI L-METHIONINE BIOSYNTHETIC PROCESS FROM S-ADENOSYLMETHIONINEMETHIONINE SALVAGE FROM METHYLTHIOADENOSINE 5-prime - METHYLTHIOADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE ADENOSYLHOMOCYSTEINE NUCLEOSIDASE ACTIVITY METHYLTHIOADENONUCLEOSIDASE ACTIVITY HYDROLASE ACTIVITY ACTING ON GLYCOSHYDROLASE
Ref.: A PICOMOLAR TRANSITION STATE ANALOGUE INHIBITOR OF SPECIFIC ANTIBIOTIC FOR HELICOBACTER PYLORI. BIOCHEMISTRY V. 51 6892 2012
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
BIG A:301;
Valid;
none;
Kd = 36 pM
335.468 C16 H25 N5 O S CCCCS...
CL A:302;
Invalid;
none;
submit data
35.453 Cl [Cl-]
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 5 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 3 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 = 0.2 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 ic50 = 6 nM 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
Ligand no: 1; Ligand: BIG; Similar ligands found: 17
No: Ligand ECFP6 Tc MDL keys Tc
1 BIG 1 1
2 GMD 0.818182 0.888889
3 OS3 0.777778 0.903226
4 2EL 0.731707 0.848485
5 4F0 0.723684 0.903226
6 TDI 0.723684 0.903226
7 OS6 0.705263 0.909091
8 OS2 0.703704 0.870968
9 HCE 0.697674 0.846154
10 C1Y 0.688312 0.934426
11 4EH 0.662791 0.830769
12 DF9 0.662791 0.885246
13 4CT 0.651163 0.794118
14 OS5 0.6 0.835821
15 3QA 0.588889 0.848485
16 AGV 0.45977 0.779412
17 4EZ 0.420455 0.731343
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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