Receptor
PDB id Resolution Class Description Source Keywords
6QDX 2.1 Å EC: 2.1.1.266 STRUCTURE OF E.COLI RLMJ IN COMPLEX WITH A BISUBSTRATE ANALO ESCHERICHIA COLI RNA MTASES METHYLTRANSFERASE M6A TRANSITION STATE ANALOGUINHIBITOR RNA BINDING TRMK RLMJ M1A STRUCTURE. TRANSF
Ref.: BISUBSTRATE ANALOGUES AS STRUCTURAL TOOLS TO INVEST METHYLTRANSFERASE ACTIVE SITES. RNA BIOL. V. 16 798 2019
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
HY8 C:301;
B:301;
A:301;
D:301;
Valid;
Valid;
Valid;
Valid;
none;
none;
none;
Atoms found LESS than expected: % Diff = 0;
Kd = 30 uM
674.666 C27 H38 N12 O9 c1nc(...
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90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
6QE5 1.61 Å EC: 2.1.1.266 STRUCTURE OF E.COLI RLMJ IN COMPLEX WITH THE NATURAL COFACTO S-ADENOSYL-HOMOCYSTEINE (SAH) ESCHERICHIA COLI PCN033 RNA MTASES METHYLTRANSFERASE M6A TRANSITION STATE ANALOGUINHIBITOR RNA BINDING TRMK RLMJ M1A STRUCTURE. TRANSF
Ref.: BISUBSTRATE ANALOGUES AS STRUCTURAL TOOLS TO INVEST METHYLTRANSFERASE ACTIVE SITES. RNA BIOL. V. 16 798 2019
Members (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4BLW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 6QDX Kd = 30 uM HY8 C27 H38 N12 O9 c1nc(c2c(n....
3 6QE0 Kd = 25 uM HZ2 C26 H36 N12 O9 c1nc(c2c(n....
4 4BLV - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 6QE5 Kd = 7.5 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
70% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4BLW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 6QDX Kd = 30 uM HY8 C27 H38 N12 O9 c1nc(c2c(n....
3 6QE0 Kd = 25 uM HZ2 C26 H36 N12 O9 c1nc(c2c(n....
4 4BLV - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 6QE5 Kd = 7.5 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1 families.
1 4BLW - SAH C14 H20 N6 O5 S c1nc(c2c(n....
2 6QDX Kd = 30 uM HY8 C27 H38 N12 O9 c1nc(c2c(n....
3 6QE0 Kd = 25 uM HZ2 C26 H36 N12 O9 c1nc(c2c(n....
4 4BLV - SAM C15 H22 N6 O5 S C[S@@+](CC....
5 6QE5 Kd = 7.5 uM SAH C14 H20 N6 O5 S c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: HY8; Similar ligands found: 102
No: Ligand ECFP6 Tc MDL keys Tc
1 HY8 1 1
2 HZ2 0.86 1
3 K15 0.699029 0.883117
4 62X 0.68932 0.860759
5 KH3 0.637168 0.896104
6 OZP 0.612069 0.945205
7 KB1 0.589286 0.881579
8 SA8 0.576923 0.868421
9 F0P 0.532258 0.945205
10 S7M 0.522523 0.822785
11 ADN 0.5 0.847222
12 SFG 0.5 0.875
13 SAH 0.5 0.890411
14 5X8 0.5 0.863014
15 XYA 0.5 0.847222
16 RAB 0.5 0.847222
17 0UM 0.491379 0.906667
18 MHZ 0.490741 0.82716
19 SAI 0.486486 0.878378
20 EEM 0.477876 0.822785
21 EP4 0.47 0.779221
22 SXZ 0.46281 0.846154
23 6IA 0.45614 0.732558
24 A3S 0.454545 0.888889
25 GJV 0.453704 0.820513
26 TT8 0.452991 0.866667
27 6RE 0.45283 0.807692
28 SMM 0.444444 0.792683
29 SSA 0.444444 0.703297
30 SAM 0.443478 0.822785
31 KAA 0.442623 0.736264
32 DSZ 0.441667 0.703297
33 LSS 0.441667 0.652632
34 5CD 0.44 0.783784
35 3DH 0.438095 0.776316
36 DTA 0.436893 0.789474
37 MAO 0.436364 0.783133
38 6MD 0.435644 0.810811
39 A3T 0.433628 0.849315
40 J7C 0.431193 0.818182
41 GSU 0.430894 0.703297
42 LAD 0.430894 0.839506
43 5N5 0.43 0.847222
44 3US 0.427536 0.819277
45 YLP 0.427481 0.821429
46 A4D 0.425743 0.821918
47 XAH 0.425197 0.797619
48 5CA 0.425 0.703297
49 36A 0.424242 0.883117
50 A5A 0.423729 0.652174
51 M2T 0.423077 0.7375
52 LEU LMS 0.422764 0.645833
53 VRT 0.422414 0.866667
54 A3G 0.422018 0.902778
55 NEC 0.422018 0.797297
56 GEK 0.421488 0.855263
57 MTA 0.419048 0.776316
58 NSS 0.418033 0.684783
59 AMO 0.418033 0.790123
60 YLC 0.41791 0.819277
61 YLB 0.41791 0.821429
62 AMP 0.416667 0.728395
63 LMS 0.416667 0.648352
64 VMS 0.416667 0.638298
65 54H 0.416667 0.638298
66 A 0.416667 0.728395
67 ME8 0.416 0.755814
68 7MD 0.415385 0.841463
69 NVA LMS 0.414634 0.663158
70 AHX 0.414634 0.761905
71 S4M 0.414414 0.8375
72 D3Y 0.413223 0.890411
73 53H 0.413223 0.631579
74 TSB 0.413223 0.663043
75 F2R 0.413043 0.8
76 CA0 0.412281 0.756098
77 N37 0.410448 0.853333
78 SO8 0.410256 0.815789
79 N5O 0.409091 0.888889
80 DSH 0.409091 0.917808
81 HEJ 0.408696 0.731707
82 ATP 0.408696 0.731707
83 KG4 0.408696 0.756098
84 SRP 0.408333 0.790123
85 WAQ 0.408 0.814815
86 J4G 0.408 0.780488
87 5AS 0.40708 0.666667
88 AYB 0.405797 0.811765
89 45A 0.405405 0.710843
90 ABM 0.405405 0.710843
91 AQP 0.405172 0.731707
92 5FA 0.405172 0.731707
93 52H 0.404959 0.631579
94 NB8 0.404762 0.761905
95 ARG AMP 0.40458 0.788235
96 ZAS 0.40367 0.769231
97 SON 0.403509 0.768293
98 AN2 0.403509 0.722892
99 A7D 0.403509 0.876712
100 5AL 0.403361 0.743902
101 N5A 0.401786 0.861111
102 NVA 2AD 0.401709 0.855263
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 6QE5; Ligand: SAH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 1) in the query (biounit: 6qe5.bio2) has 38 residues
No: Leader PDB Ligand Sequence Similarity
Pocket No.: 2; Query (leader) PDB : 6QE5; Ligand: SAH; Similar sites found with APoc: No similar binding sites found, or similarity not calculated due to duplicate pocket.
This union binding pocket(no: 2) in the query (biounit: 6qe5.bio1) has 42 residues
No: Leader PDB Ligand Sequence Similarity
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