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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: 80
This union binding pocket(no: 1) in the query (biounit: 4ffs.bio1) has 49 residues
No: Leader PDB Ligand Sequence Similarity
1 1MFA GLA MMA ABE None
2 1GPM AMP 2.09205
3 4U36 TNR 2.09205
4 4WCX MET 2.09205
5 4B9E FAH 2.09205
6 5KJW 53C 2.09205
7 3PA8 621 2.51046
8 1FNZ A2G 2.53165
9 2PEL LAT 2.54237
10 2PEL LBT 2.54237
11 5TZO 7V7 2.65957
12 3EGI ADP 2.91262
13 3BJE URA 2.92887
14 3BJE R1P 2.92887
15 1YFS ALA 2.92887
16 4PTN GXV 2.92887
17 5EXA 5SO 3.04348
18 3P0F BAU 3.34728
19 5KXE 6Y2 3.34728
20 4AGS GSH 3.34728
21 4LOC OXM 3.34728
22 5XPI 8C3 3.82166
23 1RJW ETF 4.1841
24 5XNC MTA 4.1841
25 2BVE PH5 4.20168
26 4PL9 ADP 4.37158
27 6AYU F6P 4.60251
28 1VKF CIT 4.78723
29 1B8O IMH 5.02092
30 5WBF LAC 5.02092
31 1J1R ADE 5.02092
32 6ACS CIT 5.43933
33 1FQK ALF 5.43933
34 3KIF GDL 5.66038
35 2A0W DIH 5.85774
36 5ETJ IM5 5.85774
37 4JCA CIT 5.98802
38 3EUF BAU 6.27615
39 2P4S DIH 6.27615
40 3WD6 GSH 6.27615
41 1C3X 8IG 6.69456
42 3DJF BC3 6.69456
43 5TBS ADE 6.69456
44 4FXQ G9L 7.11297
45 5YSI NCA 7.23684
46 3NB0 G6P 7.31034
47 4GLJ RHB 7.53138
48 4FK7 P34 8.29694
49 3KVY URA 8.3682
50 3KVY R2B 8.3682
51 4QAR ADE 8.95522
52 2J5V PCA 9.20502
53 1JE1 GMP 10.1695
54 2X65 M1P 10.8787
55 5IFK HPA 11.2971
56 1G2O IMH 16.318
57 2UVO NDG 16.3743
58 4AML GYU 16.3743
59 1GZF NIR 17.5355
60 2A8Y MTA 17.9916
61 5F7J ADE 18.41
62 1K27 MTM 20.0837
63 5CIC 51R 20.0837
64 1VMK GUN 23.1047
65 4YJK URA 28.0335
66 1U1F 183 28.8703
67 3U40 ADN 29.7071
68 1ODJ GMP 29.7872
69 1Z34 2FD 29.7872
70 3QPB URA 30.9623
71 3QPB R1P 30.9623
72 4DA6 GA2 32.2176
73 1NW4 IMH 32.2176
74 4TXJ THM 34.3096
75 2AC7 ADN 34.4681
76 1VHW ADN 34.728
77 1A69 FMB 34.874
78 6F4W FMC 37.2385
79 3LGS SAH 43.0962
80 3LGS ADE 43.0962
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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