Receptor
PDB id Resolution Class Description Source Keywords
4YNB 2 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF HELICOBACTER PYLORI 5'-METHYLTHIOADENOS ADENOSYL HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH P YRAZINYLTHIO-DADME-IMMUCILLIN-A HELICOBACTER PYLORI 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
PEG A:304;
Invalid;
none;
submit data
106.12 C4 H10 O3 C(COC...
GOL A:303;
A:302;
Invalid;
Invalid;
none;
none;
submit data
92.094 C3 H8 O3 C(C(C...
4EH A:301;
Valid;
none;
Ki = 0.043 nM
357.433 C16 H19 N7 O S c1cnc...
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 4 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 2 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 (34)
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....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: 4EH; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 4EH 1 1
2 TDI 0.696203 0.857143
3 4F0 0.696203 0.857143
4 BIG 0.662791 0.830769
5 4CT 0.647727 0.920635
6 GMD 0.625 0.84375
7 DF9 0.622222 0.932203
8 HCE 0.619565 0.830769
9 2EL 0.611111 0.80597
10 3QA 0.536842 0.80597
11 AGV 0.444444 0.791045
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4FFS; Ligand: BIG; Similar sites found: 149
This union binding pocket(no: 1) in the query (biounit: 4ffs.bio1) has 49 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1DAK ADP 0.001647 0.41488 None
2 1DAK DPU 0.001647 0.41488 None
3 4INB 1F6 0.000279 0.4074 None
4 2ALG DAO 0.0003811 0.4072 None
5 2ALG HP6 0.0003811 0.4072 None
6 2PR5 FMN 0.00233 0.40248 None
7 2HGS GSH 0.00004946 0.41046 1.25523
8 1M5B BN1 0.005802 0.40891 1.25523
9 1V2X SAM 0.0003275 0.40517 1.54639
10 1V7R CIT 0.0102 0.44541 1.6129
11 4JTA NAP 0.00799 0.41164 1.67364
12 1EXB NDP 0.01071 0.40693 1.67364
13 2AMV BIN 0.004731 0.40743 2.09205
14 1LTH NAD 0.007963 0.40103 2.09205
15 2D37 FMN 0.0003922 0.41801 2.27273
16 2D37 NAD 0.000442 0.41801 2.27273
17 2E2R 2OH 0.0008718 0.4171 2.51046
18 1QF5 GDP 0.002644 0.41458 2.51046
19 1QF5 RPL 0.002644 0.41458 2.51046
20 1DLJ UGA 0.003461 0.41221 2.51046
21 3FS8 ACO 0.01151 0.41109 2.51046
22 4OYA 1VE 0.01947 0.4078 2.51046
23 1I0Z NAI 0.001154 0.40765 2.51046
24 3JYN NDP 0.001579 0.40729 2.51046
25 4O8A FAD 0.001346 0.4069 2.51046
26 1AL8 FMN 0.006452 0.40269 2.51046
27 3T1A 5MA 0.0003121 0.40196 2.51046
28 1AL8 DHP 0.01195 0.40157 2.51046
29 1U7Z PMT 0.001017 0.41357 2.65487
30 3LZW NAP 0.003203 0.4189 2.92887
31 3WBF NAP 0.0004927 0.41809 2.92887
32 2GYI HYA 0.006354 0.4116 2.92887
33 4FWE FAD 0.003282 0.40765 2.92887
34 2P2V CSF 0.005469 0.40521 2.92887
35 3WE0 FAD 0.003903 0.40506 2.92887
36 3TKA SAM 0.0005146 0.40268 2.92887
37 1MXI SAH 0.002417 0.40193 2.92887
38 2WA4 069 0.006587 0.40192 2.92887
39 4C0X AQN 0.0008454 0.41347 2.95567
40 1KOL NAD 0.001046 0.41697 3.01508
41 3P0F BAU 0.000000661 0.46466 3.34728
42 2V7T SAH 0.002249 0.44003 3.34728
43 4W6Z 8ID 0.0007063 0.42267 3.34728
44 1KY8 NAP 0.01285 0.41213 3.34728
45 4KGD FAD 0.009841 0.40771 3.34728
46 4KGD TDP 0.009485 0.40771 3.34728
47 1R37 NAD 0.001706 0.40745 3.34728
48 1WNG SAH 0.0002737 0.40707 3.34728
49 2YPO PHE 0.001231 0.40674 3.34728
50 4DEM YS4 0.01668 0.404 3.34728
51 2HGZ PBF 0.001134 0.40004 3.34728
52 1H6C SIN 0.0003302 0.43741 3.76569
53 1H6C NDP 0.0004224 0.43138 3.76569
54 2F2U M77 0.00182 0.42849 3.76569
55 1RYD NDP 0.0005434 0.42771 3.76569
56 1GR0 NAD 0.003491 0.42616 3.76569
57 3ZV6 NAD 0.001072 0.4223 3.76569
58 3UXL CFI 0.007461 0.42022 3.76569
59 1C0I FAD 0.002925 0.41125 3.76569
60 1C0I BE2 0.002925 0.41125 3.76569
61 1BUC CAA 0.0006881 0.40685 3.76569
62 3ZV6 4HB 0.004096 0.40339 3.76569
63 1YBH FAD 0.003442 0.40295 3.76569
64 1TOI HCI 0.001733 0.4005 3.76569
65 3I28 34N 0.006346 0.40044 3.76569
66 4P53 NAI 0.000101 0.43852 4.1841
67 1B8U OAA 0.0004724 0.42314 4.1841
68 2I7C AAT 0.0005562 0.4222 4.1841
69 2PT9 2MH 0.0008163 0.41804 4.1841
70 3T31 DCQ 0.004318 0.41351 4.1841
71 2PT9 S4M 0.0007659 0.40711 4.1841
72 4C12 ADP 0.008311 0.40037 4.1841
73 3ZOD FMN 0.001398 0.40046 4.18848
74 3ZOD HQE 0.001398 0.40046 4.18848
75 1G8S MET 0.01687 0.40809 4.34783
76 1SS4 GSH 0.0006141 0.53258 4.57516
77 1SS4 CIT 0.011 0.46967 4.57516
78 2GN4 NDP 0.008263 0.43918 4.60251
79 4E28 9MZ 0.007278 0.42473 4.60251
80 1RM0 D6P 0.002055 0.4193 4.60251
81 1RYI FAD 0.001535 0.41901 4.60251
82 1TDF NAP 0.006165 0.41581 4.60251
83 4IVG ANP 0.005729 0.4045 4.60251
84 1RM0 NAI 0.005256 0.40242 4.60251
85 3F3E LEU 0.003295 0.40144 4.60251
86 1VQ2 DDN 0.001477 0.43323 4.66321
87 1NNU NAD 0.01276 0.40839 4.80349
88 1SB8 UD2 0.008055 0.40085 5.02092
89 4CMF PXG 0.001795 0.42224 5.43933
90 2RGH FAD 0.001012 0.42206 5.43933
91 2NVK FAD 0.001498 0.41733 5.43933
92 1EP2 ORO 0.001076 0.41407 5.43933
93 1EP2 FMN 0.0009616 0.40721 5.43933
94 3WQM B29 0.0009122 0.40301 5.43933
95 2A0W DIH 0.000001035 0.51294 5.85774
96 2YBQ SAH 0.00006441 0.42525 5.85774
97 1REO FAD 0.001518 0.41499 5.85774
98 3O9P MHI 0.009586 0.40571 5.85774
99 2RHW C0E 0.009288 0.40429 5.85774
100 1I52 CTP 0.00134 0.40555 5.9322
101 3BW2 FMN 0.001346 0.40549 6.23306
102 2BLE 5GP 0.0003392 0.45473 6.27615
103 4AT0 FAD 0.001546 0.42272 6.27615
104 4NTD FAD 0.002043 0.40953 6.69456
105 2C31 ADP 0.009873 0.40824 6.69456
106 2C31 TZD 0.01023 0.40824 6.69456
107 9LDB NAD 0.001246 0.40799 6.69456
108 3I3X U22 0.009973 0.40217 6.69456
109 1Q0H NDP 0.006419 0.40112 6.69456
110 4IEN COA 0.001398 0.40968 6.74847
111 2GSD NAD 0.001474 0.41079 7.11297
112 3GE7 AFQ 0.001509 0.40794 7.11297
113 3IAE D7K 0.001925 0.40183 7.11297
114 4GLJ RHB 0.00002616 0.46427 7.53138
115 1EDO NAP 0.005624 0.41607 7.53138
116 3K3K A8S 0.0003641 0.40326 7.58294
117 1Q3Q ANP 0.004309 0.41354 7.94979
118 1T26 GBD 0.004885 0.42917 8.3682
119 1T26 NAI 0.004885 0.42917 8.3682
120 2V6O FAD 0.003599 0.42566 8.3682
121 4D7M TDC 0.001084 0.40398 8.75576
122 1PEA ACM 0.00278 0.45802 9.20502
123 1LVL FAD 0.001687 0.4176 9.20502
124 2BJF DXC 0.003871 0.40325 9.20502
125 1Z44 NPO 0.04757 0.41668 9.46746
126 1Z44 FMN 0.003835 0.40668 9.46746
127 2XVE FAD 0.003216 0.421 10.0418
128 2NCD ADP 0.008087 0.41709 10.0418
129 1GV0 NAD 0.001644 0.40267 10.0418
130 1GSA ADP 0.006072 0.40196 10.4603
131 2AQJ FAD 0.005816 0.41029 10.8787
132 2AQJ TRP 0.008546 0.40357 10.8787
133 1FL2 FAD 0.003833 0.40239 11.7155
134 3Q9T FAY 0.001642 0.41273 12.5523
135 1ZK7 FAD 0.0005389 0.43672 14.2259
136 4R33 SAH 0.0003849 0.42747 14.6444
137 4R33 TRP 0.0003849 0.42747 14.6444
138 3SHR CMP 0.003926 0.41519 15.0502
139 1G2O IMH 0.007174 0.44147 16.318
140 1K27 MTM 0.00000005114 0.55292 20.0837
141 1T8U UAP SGN IDS SGN 0.003091 0.40346 26.3598
142 4JK3 NAD 0.001742 0.40043 26.3598
143 1Z34 2FD 0.00001122 0.50077 29.7872
144 4DA6 GA2 0.000001269 0.53764 32.2176
145 1I2B NAD 0.02038 0.41384 33.4728
146 1I2B USQ 0.02038 0.41384 33.4728
147 1I2B UPG 0.02038 0.41384 33.4728
148 2AC7 ADN 0.000002012 0.51532 34.4681
149 1A69 FMB 0.00000852 0.51422 34.874
Feedback