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
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
Members (12)
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 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
3 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
4 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
5 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
6 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
8 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
9 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
10 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
11 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
12 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
70% Homology Family (14)
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 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
3 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
4 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
5 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
6 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
7 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
8 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
9 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
10 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
11 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
12 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
13 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
14 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
50% Homology Family (37)
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 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
19 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
20 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
21 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
22 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
23 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
24 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
25 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
26 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
27 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
28 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
29 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
30 3DP9 ic50 = 6 nM BIG C16 H25 N5 O S CCCCSC[C@H....
31 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
32 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
33 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
34 3BL6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
35 6AYR Ki = 4.1 nM BIG C16 H25 N5 O S CCCCSC[C@H....
36 6AYQ Ki = 6.5 nM TDI C13 H19 N5 O S CSC[C@H]1C....
37 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: 13
No: Ligand ECFP6 Tc MDL keys Tc
1 BIG 1 1
2 GMD 0.818182 0.888889
3 2EL 0.731707 0.848485
4 4F0 0.723684 0.903226
5 TDI 0.723684 0.903226
6 HCE 0.697674 0.846154
7 C1Y 0.688312 0.934426
8 DF9 0.662791 0.885246
9 4EH 0.662791 0.830769
10 4CT 0.651163 0.794118
11 3QA 0.588889 0.848485
12 AGV 0.45977 0.779412
13 4EZ 0.420455 0.731343
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FFS; Ligand: BIG; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 4ffs.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 4FFS; Ligand: BIG; 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: 4ffs.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
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