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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 5 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 3 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 (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: TDI; Similar ligands found: 12
No: Ligand ECFP6 Tc MDL keys Tc
1 4F0 1 1
2 TDI 1 1
3 C1Y 0.728571 0.933333
4 BIG 0.723684 0.903226
5 GMD 0.701299 0.857143
6 4EH 0.696203 0.857143
7 2EL 0.683544 0.818182
8 4CT 0.683544 0.818182
9 DF9 0.675 0.915254
10 HCE 0.650602 0.84375
11 3QA 0.614458 0.818182
12 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 with APoc: 104
This union binding pocket(no: 1) in the query (biounit: 4wkb.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
1 1MFA GLA MMA ABE None
2 2WL9 MBD 1.63934
3 1C3X 8IG 2.04918
4 4QPW XYP XYP XYP 2.11268
5 2PEL LAT 2.11864
6 2PEL LBT 2.11864
7 5F7J ADE 2.86885
8 5KJW 53C 2.86885
9 4ZS4 ATP 2.86885
10 6CFC BLG 2.86885
11 4QAR ADE 2.98507
12 1G8K MGD 3.00752
13 3BJE URA 3.27869
14 3BJE R1P 3.27869
15 6ACS CIT 3.27869
16 3SUT OAN 3.27869
17 3PA8 621 3.27869
18 5LQ8 GB 3.27869
19 5O2J 2PO 3.27869
20 1GZF NIR 3.31754
21 4A34 FUL 3.40136
22 3N8K D1X 3.48837
23 3PCJ INO 3.5
24 5XHA FRU 3.68852
25 5FAW CHT 3.68852
26 5LY1 PPI 3.68852
27 1KYZ SAH 3.68852
28 3EUF BAU 4.09836
29 4FXQ G9L 4.09836
30 2HIM ASN 4.09836
31 2IZ1 ATR 4.09836
32 5KXE 6Y2 4.11523
33 4FK7 P34 4.36681
34 3EGI ADP 4.36893
35 5OES ADP 4.5082
36 2FN1 PYR 4.5082
37 1VKF CIT 4.78723
38 4JCA CIT 4.79042
39 1VMK GUN 5.05415
40 5YSI NCA 5.26316
41 5TZO 7V7 5.31915
42 5TBS ADE 5.32787
43 3NB0 G6P 5.32787
44 3CL5 SIO 5.32787
45 4K6B GLU 5.59006
46 2P4S DIH 5.7377
47 1GPM AMP 5.7377
48 1PVN MZP 5.7377
49 5A0U CHT 5.7377
50 6EOM ALA LYS 5.7377
51 3UZO PLP 6.14754
52 4GLJ RHB 6.39731
53 1G2O IMH 6.55738
54 3DJF BC3 6.55738
55 1RJW ETF 6.55738
56 5Y0T TAT 6.55738
57 6GNO XDI 6.66667
58 1FNZ A2G 6.75105
59 2CBO TH2 6.95652
60 4LHD GLY 6.96721
61 2A0W DIH 7.37705
62 5ETJ IM5 7.37705
63 2NYA MGD 7.37705
64 5XNC MTA 7.37705
65 4AML GYU 7.60234
66 1B8O IMH 7.78689
67 1TF9 PHI 7.78689
68 5WBF LAC 7.78689
69 4H2D FMN 7.87879
70 1QXO FMN 7.98969
71 2A8Y MTA 8.60656
72 5OVK NDP 9.01639
73 1NW4 IMH 9.83607
74 5IFK HPA 10.5769
75 4TXJ THM 10.6557
76 4UCF GLA 11.0656
77 5GZZ GSH 11.8852
78 4YJK URA 12.2951
79 2BVE PH5 12.605
80 3QPB URA 12.7049
81 3QPB R1P 12.7049
82 1FUR MLT 13.1148
83 2ZJ1 NAD 13.5246
84 2ZJ1 ARJ 13.5246
85 6CI9 F3V 14.3443
86 4R3U 5AD 14.557
87 1Z34 2FD 15.7447
88 1U1F 183 16.4062
89 1K27 MTM 17.2131
90 4K7O EKZ 17.8571
91 3KVY URA 23.3607
92 3KVY R2B 23.3607
93 4DA6 GA2 30.3279
94 1JE1 GMP 30.5085
95 1ODJ GMP 32.3404
96 1VHW ADN 32.377
97 3P0F BAU 32.7869
98 3LGS ADE 33.1967
99 3LGS SAH 33.1967
100 3U40 ADN 36.3636
101 1A69 FMB 36.4754
102 2AC7 ADN 37.0213
103 6F4W FMC 38.1974
104 2FOI JPA 40
Pocket No.: 2; Query (leader) PDB : 4WKB; Ligand: TDI; Similar sites found with APoc: 19
This union binding pocket(no: 2) in the query (biounit: 4wkb.bio1) has 26 residues
No: Leader PDB Ligand Sequence Similarity
1 3GUZ PAF 2.27273
2 4ZVV GN0 2.45902
3 4ZVV NAD 2.45902
4 5H9O GLC 2.45902
5 6CZI 38E 2.67857
6 1RM0 NAI 2.86885
7 5JVB 2PO 3.27869
8 2VPY MGD 4.34783
9 4I4S LAT 4.79452
10 5Y4R C2E 4.82759
11 1SO0 GAL 4.91803
12 5TE1 7A2 4.91803
13 1ZX5 LFR 5.32787
14 1I1E DM2 5.32787
15 4U36 TNR 6.25
16 1H0H 2MD 6.54206
17 2F2U M77 8.60656
18 2VGD XYP XYP 8.7156
19 1OGD RIP 15.2672
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