Receptor
PDB id Resolution Class Description Source Keywords
4x24 1.5 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 (STRAIN AT/ CLASSICAL OGAWA 395 / O395) 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
PGE A:302;
Invalid;
none;
submit data
150.173 C6 H14 O4 C(COC...
TDI B:301;
A:301;
Valid;
Valid;
none;
none;
Ki = 166 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 6 families.
1 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
2 3DP9 Kd = 208 pM 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 4 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 = 0.21 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 Kd = 208 pM 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 (41)
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 = 0.21 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 6DYV Kd = 0.026 nM OS3 C17 H23 N5 O S C#CCCCSC[C....
19 4YNB Ki = 0.043 nM 4EH C16 H19 N7 O S c1cnc(cn1)....
20 4FFS Kd = 36 pM BIG C16 H25 N5 O S CCCCSC[C@H....
21 6DYY Kd = 0.028 nM OS6 C21 H32 N8 O S CCCCn1cc(n....
22 3NM6 - TRS C4 H12 N O3 C(C(CO)(CO....
23 4WKN Ki = 0.19 nM TDI C13 H19 N5 O S CSC[C@H]1C....
24 4OY3 - SAH C14 H20 N6 O5 S c1nc(c2c(n....
25 5KB3 Kd = 570 pM 4CT C18 H20 Cl N5 O S c1cc(ccc1S....
26 4YO8 Ki = 0.03 nM 4EZ C14 H23 N5 O CCCCCCN(Cc....
27 4P54 - MTA C11 H15 N5 O3 S CSC[C@@H]1....
28 3NM5 - FMC C10 H13 N5 O4 c1nc2c(c(n....
29 4WKO Ki = 0.34 nM GMD C16 H25 N5 O2 S c1c(c2c([n....
30 6DYW Kd = 0.036 nM OS5 C24 H30 N8 O S c1ccc(cc1)....
31 6DYU Kd = 0.055 nM OS2 C15 H19 N5 O S C#CCSC[C@H....
32 4OJT - ADE C5 H5 N5 c1[nH]c2c(....
33 4X24 Ki = 166 pM TDI C13 H19 N5 O S CSC[C@H]1C....
34 3DP9 Kd = 208 pM BIG C16 H25 N5 O S CCCCSC[C@H....
35 4WKB Ki = 2.7 pM TDI C13 H19 N5 O S CSC[C@H]1C....
36 4BMZ - MTA C11 H15 N5 O3 S CSC[C@@H]1....
37 4BMX - ADE C5 H5 N5 c1[nH]c2c(....
38 3BL6 - FMC C10 H13 N5 O4 c1nc2c(c(n....
39 6AYR Ki = 4.1 nM BIG C16 H25 N5 O S CCCCSC[C@H....
40 6AYQ Ki = 6.5 nM TDI C13 H19 N5 O S CSC[C@H]1C....
41 6AYO Ki = 5.1 nM C1Y C14 H21 N5 O CCC[C@H]1C....
Polypharmacology
Similar Ligands (2D)
Ligand no: 1; Ligand: TDI; Similar ligands found: 16
No: Ligand ECFP6 Tc MDL keys Tc
1 TDI 1 1
2 4F0 1 1
3 C1Y 0.728571 0.933333
4 BIG 0.723684 0.903226
5 OS2 0.72 0.9
6 GMD 0.701299 0.857143
7 4EH 0.696203 0.857143
8 2EL 0.683544 0.818182
9 4CT 0.683544 0.818182
10 DF9 0.675 0.915254
11 OS3 0.666667 0.870968
12 HCE 0.650602 0.84375
13 3QA 0.614458 0.818182
14 OS6 0.561224 0.823529
15 OS5 0.514286 0.80597
16 AGV 0.512821 0.80303
Similar Ligands (3D)
Ligand no: 1; Ligand: TDI; Similar ligands found: 49
No: Ligand Similarity coefficient
1 MTA 0.9356
2 MTM 0.9345
3 MTI 0.9298
4 MTH 0.9295
5 DIH 0.9190
6 IM5 0.9108
7 B5A 0.9049
8 FMC 0.8994
9 AX8 0.8895
10 BC3 0.8872
11 0QV 0.8867
12 MQS 0.8862
13 GA2 0.8839
14 ADN 0.8830
15 FMB 0.8830
16 MDR 0.8829
17 TAL 0.8826
18 5F1 0.8804
19 JYN 0.8797
20 VIB 0.8793
21 1Q4 0.8780
22 SNP 0.8762
23 2FD 0.8755
24 GU7 0.8749
25 NOS 0.8730
26 XYA 0.8730
27 GNG 0.8729
28 CWP 0.8729
29 KWK 0.8718
30 43O 0.8715
31 QEI 0.8707
32 3D1 0.8701
33 IMH 0.8688
34 5CD 0.8678
35 4EZ 0.8667
36 ASE 0.8661
37 TBN 0.8652
38 FM1 0.8646
39 AMP 0.8643
40 0XR 0.8637
41 EXP 0.8624
42 DE7 0.8621
43 ZEZ 0.8608
44 IGP 0.8605
45 RAB 0.8595
46 JMQ 0.8572
47 2FA 0.8566
48 JFX 0.8550
49 3L1 0.8533
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4WKB; Ligand: TDI; Similar sites found with APoc: 5
This union binding pocket(no: 1) in the query (biounit: 4wkb.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 4QAR ADE 2.98507
2 3LGS SAH 33.1967
3 3LGS ADE 33.1967
4 3LGS SAH 33.1967
5 3LGS ADE 33.1967
Pocket No.: 2; Query (leader) PDB : 4WKB; Ligand: TDI; Similar sites found with APoc: 5
This union binding pocket(no: 2) in the query (biounit: 4wkb.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 4QAR ADE 2.98507
2 3LGS ADE 33.1967
3 3LGS SAH 33.1967
4 3LGS ADE 33.1967
5 3LGS SAH 33.1967
APoc FAQ
Feedback