Receptor
PDB id Resolution Class Description Source Keywords
4WKB 1.37 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF VIBRIO CHOLERAE 5'-METHYLTHIOADENOSINE/ HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH METHYLTHIO-I MMUCILLIN-A VIBRIO CHOLERAE SEROTYPE O1 HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: ACTIVE SITE AND REMOTE CONTRIBUTIONS TO CATALYSIS I METHYLTHIOADENOSINE NUCLEOSIDASES. BIOCHEMISTRY V. 54 2520 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
TDI B:301;
A:301;
Valid;
Valid;
none;
none;
Ki = 2.7 pM
293.388 C13 H19 N5 O S CSC[C...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4WKB 1.37 Å EC: 3.2.2.9 CRYSTAL STRUCTURE OF VIBRIO CHOLERAE 5'-METHYLTHIOADENOSINE/ HOMOCYSTEINE NUCLEOSIDASE (MTAN) COMPLEXED WITH METHYLTHIO-I MMUCILLIN-A VIBRIO CHOLERAE SEROTYPE O1 HYDROLASE HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Ref.: ACTIVE SITE AND REMOTE CONTRIBUTIONS TO CATALYSIS I METHYLTHIOADENOSINE NUCLEOSIDASES. BIOCHEMISTRY V. 54 2520 2015
Members (3)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 4 families.
1 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
2 3DP9 ic50 = 6 nM BIG C16 H25 N5 O S CCCCSC[C@H....
3 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
70% Homology Family (18)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 2 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 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
17 3DP9 ic50 = 6 nM BIG C16 H25 N5 O S CCCCSC[C@H....
18 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
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: TDI; Similar ligands found: 11
No: Ligand ECFP6 Tc MDL keys Tc
1 TDI 1 1
2 4F0 1 1
3 BIG 0.723684 0.903226
4 GMD 0.701299 0.857143
5 4EH 0.696203 0.857143
6 4CT 0.683544 0.818182
7 2EL 0.683544 0.818182
8 DF9 0.675 0.915254
9 HCE 0.650602 0.84375
10 3QA 0.614458 0.818182
11 AGV 0.512821 0.80303
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WKB; Ligand: TDI; Similar sites found: 46
This union binding pocket(no: 1) in the query (biounit: 4wkb.bio1) has 42 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 1MFA GLA MMA ABE 0.02332 0.40477 None
2 4QPW XYP XYP XYP 0.007962 0.40201 2.11268
3 5F7J ADE 0.000008835 0.52389 2.86885
4 5KJW 53C 0.01641 0.41513 2.86885
5 4QAR ADE 0.00000000175 0.72123 2.98507
6 3BJE URA 0.000002345 0.43641 3.27869
7 3SUT OAN 0.01265 0.41044 3.27869
8 3PA8 621 0.02349 0.4053 3.27869
9 3BJE R1P 0.0003458 0.40397 3.27869
10 1GZF NIR 0.01008 0.42429 3.31754
11 5FAW CHT 0.02168 0.4071 3.68852
12 3EUF BAU 0.000131 0.49497 4.09836
13 5KXE 6Y2 0.02738 0.40381 4.11523
14 3EGI ADP 0.02609 0.40293 4.36893
15 2FN1 PYR 0.02113 0.40529 4.5082
16 4JCA CIT 0.003852 0.45848 4.79042
17 1VMK GUN 0.000004914 0.43786 5.05415
18 4K6B GLU 0.02112 0.4077 5.59006
19 2P4S DIH 0.00003737 0.5268 5.7377
20 5A0U CHT 0.01914 0.40562 5.7377
21 1GPM AMP 0.03018 0.4045 5.7377
22 1G2O IMH 0.0000076 0.54544 6.55738
23 3DJF BC3 0.00005235 0.49041 6.55738
24 5ETJ IM5 0.0004707 0.46982 7.37705
25 1B8O IMH 0.00004122 0.45983 7.78689
26 1TF9 PHI 0.007778 0.41654 7.78689
27 4H2D FMN 0.01053 0.40278 7.87879
28 2A8Y MTA 0.000006672 0.52908 8.60656
29 1NW4 IMH 0.000004268 0.56399 9.83607
30 5IFK HPA 0.000002439 0.61825 10.5769
31 4TXJ THM 0.00003947 0.507 10.6557
32 5EWK P34 0.01274 0.42039 11
33 4YJK URA 0.00002429 0.56747 12.2951
34 2BVE PH5 0.02726 0.4128 12.605
35 1EOC 4NC 0.01414 0.40806 13.8756
36 1U1F 183 0.00008017 0.51275 16.4062
37 4K7O EKZ 0.013 0.4176 17.8571
38 3KVY URA 0.00005487 0.41397 23.3607
39 1JE1 GMP 0.00004118 0.41737 30.5085
40 1ODJ GMP 0.000009969 0.54689 32.3404
41 1VHW ADN 0.00001285 0.55633 32.377
42 3LGS SAH 0.0000000000195 0.77548 33.1967
43 3LGS ADE 0.0000000000195 0.77548 33.1967
44 3U40 ADN 0.0000004021 0.5305 36.3636
45 5MX4 HPA 0.00000006775 0.7024 38.1974
46 2FOI JPA 0.01056 0.41429 40
Pocket No.: 2; Query (leader) PDB : 4WKB; Ligand: TDI; 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: 4wkb.bio1) has 26 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
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