Receptor
PDB id Resolution Class Description Source Keywords
1ZOS 1.6 Å EC: 3.2.2.16 STRUCTURE OF 5'-METHYLTHIONADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE FROM S. PNEUMONIAE WITH A TRANSITION-STATE I NHIBITOR MT-IMMA STREPTOCOCCUS PNEUMONIAE R6 NUCLEOSIDASE PNEUMONIAE TRANSITION STATE INHIBITOR HYDROLASE
Ref.: STRUCTURE AND INHIBITION OF A QUORUM SENSING TARGET FROM STREPTOCOCCUS PNEUMONIAE. BIOCHEMISTRY V. 45 12929 2006
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
MTM A:301;
B:302;
C:303;
D:304;
E:305;
F:306;
Valid;
Valid;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
none;
none;
none;
Ki = 1 uM
297.377 C12 H19 N5 O2 S CSC[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
1ZOS 1.6 Å EC: 3.2.2.16 STRUCTURE OF 5'-METHYLTHIONADENOSINE/S-ADENOSYLHOMOCYSTEINE NUCLEOSIDASE FROM S. PNEUMONIAE WITH A TRANSITION-STATE I NHIBITOR MT-IMMA STREPTOCOCCUS PNEUMONIAE R6 NUCLEOSIDASE PNEUMONIAE TRANSITION STATE INHIBITOR HYDROLASE
Ref.: STRUCTURE AND INHIBITION OF A QUORUM SENSING TARGET FROM STREPTOCOCCUS PNEUMONIAE. BIOCHEMISTRY V. 45 12929 2006
Members (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ZOS Ki = 1 uM MTM C12 H19 N5 O2 S CSC[C@@H]1....
70% Homology Family (1)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 3 families.
1 1ZOS Ki = 1 uM MTM C12 H19 N5 O2 S CSC[C@@H]1....
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: MTM; Similar ligands found: 1
No: Ligand ECFP6 Tc MDL keys Tc
1 MTM 1 1
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: 54
This union binding pocket(no: 1) in the query (biounit: 1zos.bio2) has 19 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4CE5 PDG 0.01394 0.40338 1.73913
2 1IYE PGU 0.01878 0.40373 2.17391
3 5F7J ADE 0.000003111 0.5604 2.6087
4 1K27 MTM 0.000001295 0.52992 2.6087
5 3EUF BAU 0.00004481 0.50652 2.6087
6 3KVY URA 0.00001512 0.46083 2.6087
7 3KVY R2B 0.0001406 0.42672 2.6087
8 2A8Y MTA 0.000004099 0.5098 3.04348
9 4GLJ RHB 0.0001079 0.45357 3.04348
10 1GR0 NAD 0.01842 0.4075 3.04348
11 1G2O IMH 0.000003705 0.54833 3.47826
12 1Q0S SAH 0.007358 0.41478 3.47826
13 3HNB 768 0.01514 0.44344 3.77358
14 4UUG PXG 0.01281 0.40364 3.91304
15 4WZ8 3W7 0.03268 0.40206 3.91304
16 1FQK ALF 0.02156 0.40064 4.08163
17 2FLI DX5 0.005472 0.41574 4.54545
18 3BJE URA 0.0000006894 0.48924 4.78261
19 3BJE R1P 0.0006032 0.42097 4.78261
20 4RSL FAD 0.02506 0.4031 4.78261
21 3EGI ADP 0.01952 0.4023 4.85437
22 2P4S DIH 0.00001291 0.53807 5.21739
23 1I8T FAD 0.0238 0.40707 5.21739
24 5IFK HPA 0.0000007338 0.49228 5.65217
25 1B8O IMH 0.00001253 0.54455 6.52174
26 3P0F BAU 0.0000709 0.49158 6.52174
27 1C3X 8IG 0.0000191 0.43108 7.3913
28 4PIO AVI 0.01589 0.40949 7.82609
29 4PIO SAH 0.01675 0.40949 7.82609
30 5U3F 7TS 0.008096 0.40799 7.82609
31 3JYN NDP 0.01999 0.4047 8.26087
32 1MFA GLA MMA ABE 0.01177 0.41135 8.66142
33 2IV2 2MD 0.01127 0.41429 10.4348
34 1NW4 IMH 0.000002304 0.54729 10.8696
35 4Q3F TLA 0.02528 0.40315 11.1111
36 5ETJ IM5 0.0001371 0.51351 11.3043
37 2A0W DIH 0.01607 0.43616 11.3043
38 4QAR ADE 0.000000001218 0.68859 11.4428
39 1Z34 2FD 0.00001207 0.53944 11.7391
40 1VMK GUN 0.000001575 0.48427 11.9134
41 3DJF BC3 0.000009547 0.54566 13.0435
42 4TXJ THM 0.00001305 0.55144 13.913
43 4J56 FAD 0.03983 0.40024 27.8261
44 4DA6 GA2 0.000002182 0.54955 30
45 3U40 ADN 0.000000232 0.59079 30.8696
46 3QPB URA 0.0000482 0.43339 31.7391
47 3QPB R1P 0.002354 0.40437 31.7391
48 1VHW ADN 0.000008944 0.55315 32.4111
49 1ODJ GMP 0.000004119 0.5535 33.913
50 2AC7 ADN 0.000009792 0.55157 33.913
51 4YJK URA 0.00001607 0.4367 33.913
52 1JE1 GMP 0.000006932 0.56969 34.7826
53 1U1F 183 0.00005469 0.54161 36.087
54 5MX4 HPA 0.00000001334 0.72958 37.3913
Pocket No.: 2; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 1zos.bio2) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 3; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: 12
This union binding pocket(no: 3) in the query (biounit: 1zos.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1GPE FAD 0.01812 0.41494 3.47826
2 4Y2H SAH 0.02362 0.40413 3.91304
3 3UCL NAP 0.04682 0.40743 4.78261
4 3UCL CYH 0.04349 0.40743 4.78261
5 3UCL FAD 0.04349 0.40743 4.78261
6 1N4W FAD 0.02767 0.40431 5.21739
7 4ISS TAR 0.02309 0.40062 6.95652
8 2VPY MGD 0.03217 0.41355 7.50988
9 1G8K MGD 0.03038 0.41709 8.27068
10 2FKA BEF 0.01071 0.40176 10.8527
11 2R4J 13P 0.03192 0.40734 13.0435
12 2R4J FAD 0.03192 0.40734 13.0435
Pocket No.: 4; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 4) in the query (biounit: 1zos.bio1) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 5; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 5) in the query (biounit: 1zos.bio3) has 18 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
Pocket No.: 6; Query (leader) PDB : 1ZOS; Ligand: MTM; Similar sites found: 7
This union binding pocket(no: 6) in the query (biounit: 1zos.bio3) has 20 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 4L2I FAD 0.02177 0.40192 2.17391
2 1FNZ A2G 0.00912 0.42202 3.91304
3 1VBO MAN MAN MAN 0.02463 0.40197 8.69565
4 1PNO NAP 0.01746 0.40201 8.88889
5 2OOR TXP 0.01175 0.40621 9.1954
6 4K49 HFQ 0.01545 0.4068 16.1765
7 5BUK FAD 0.03025 0.40324 18.6957
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