Chemical Components in the PDB

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M8M : Summary

Code

M8M

One-letter code

X

Molecule name

5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine
OpenEye OEToolkits 1.5.0 (2R,3R,4S,5R)-2-(6-amino-8-methyl-purin-9-yl)-5-[(2-aminooxyethyl-methyl-amino)methyl]oxolane-3,4-diol

Formula

C14 H23 N7 O4

Formal charge

0

Molecular weight

353.377 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 n2c1c(ncnc1n(c2C)C3OC(C(O)C3O)CN(CCON)C)N
SMILES CACTVS 3.341 CN(CCON)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23
SMILES OpenEye OEToolkits 1.5.0 Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCON)O)O)N
Canonical SMILES CACTVS 3.341 CN(CCON)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCON)O)O)N

IUPAC InChI

InChI=1S/C14H23N7O4/c1-7-19-9-12(15)17-6-18-13(9)21(7)14-11(23)10(22)8(25-14)5-20(2)3-4-24-16/h6,8,10-11,14,22-23H,3-5,16H2,1-2H3,(H2,15,17,18)/t8-,10-,11-,14-/m1/s1

IUPAC InChI key

MIGFZONTOHGZMB-IDTAVKCVSA-N
M8M

wwPDB Information

Atom count

48 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-07-31

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



M8M : Atoms of Molecule

Total Number of Atoms: 48
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -2.77 3.941 0.377
2 O2 O O2 N N N 0 -3.405 2.839 -0.347
3 C4 C C4 N N N 0 -4.242 2.015 0.467
4 C5 C C5 N N N 0 -4.85 0.903 -0.389
5 N2 N N2 N N N 0 -3.782 0.02 -0.877
6 C6 C C6 N N N 0 -4.259 -0.824 -1.98
7 C5' C C5' N N N 0 -3.236 -0.798 0.214
8 C4' C C4' R N N 0 -1.973 -1.514 -0.269
9 O4' O O4' N N N 0 -0.937 -0.553 -0.533
10 C1' C C1' R N N 0 0.317 -1.18 -0.186
11 N5 N N5 N Y N 0 1.347 -0.168 0.067
12 C11 C C11 N Y N 0 2.645 -0.203 -0.376
13 N4 N N4 N Y N 0 3.366 -1.049 -1.104
14 C10 C C10 N Y N 0 4.63 -0.797 -1.37
15 N3 N N3 N Y N 0 5.242 0.29 -0.937
16 C9 C C9 N Y N 0 4.602 1.194 -0.202
17 N7 N N7 N N N 0 5.252 2.33 0.248
18 C12 C C12 N Y N 0 3.25 0.969 0.108
19 N6 N N6 N Y N 0 2.308 1.645 0.808
20 C7 C C7 N Y N 0 1.189 0.982 0.78
21 C2' C C2' R N N 0 -0.014 -1.958 1.112
22 O2' O O2' N N N 0 0.882 -3.057 1.29
23 C3' C C3' S N N 0 -1.452 -2.458 0.833
24 O3' O O3' N N N 0 -1.431 -3.808 0.366
25 C8 C C8 N N N 0 -0.093 1.42 1.442
26 HN1 H HN1 N N N 0 -2.238 3.598 1.162
27 HN1A H HN1A N N N 0 -2.191 4.492 -0.239
28 H4 H H4 N N N 0 -3.649 1.574 1.268
29 H4A H H4A N N N 0 -5.04 2.62 0.897
30 H5 H H5 N N N 0 -5.553 0.325 0.211
31 H5A H H5A N N N 0 -5.374 1.342 -1.238
32 H6 H H6 N N N 0 -4.54 -0.195 -2.825
33 H6A H H6A N N N 0 -3.466 -1.507 -2.284
34 H6B H H6B N N N 0 -5.125 -1.397 -1.651
35 H5' H H5' N N N 0 -2.989 -0.157 1.061
36 H5'A H H5'A N N N 0 -3.977 -1.536 0.521
37 H4' H H4' N N N 0 -2.191 -2.082 -1.173
38 H1' H H1' N N N 0 0.636 -1.861 -0.975
39 H10 H H10 N N N 0 5.188 -1.506 -1.964
40 HN7 H HN7 N N N 0 6.186 2.474 0.027
41 HN7A H HN7A N N N 0 4.774 2.983 0.783
42 H2' H H2' N N N 0 0.008 -1.297 1.978
43 HO2' H HO2' N N N 0 0.715 -3.575 2.09
44 H3' H H3' N N N 0 -2.066 -2.373 1.73
45 HO3' H HO3' N N N 0 -1.112 -4.445 1.019
46 H8 H H8 N N N 0 -0.127 1.031 2.46
47 H8A H H8A N N N 0 -0.135 2.509 1.468
48 H8B H H8B N N N 0 -0.943 1.037 0.878



M8M : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 O2 N O sing 1.46 N N
2 O2 C4 O C sing 1.43 N N
3 C4 C5 C C sing 1.53 N N
4 C5 N2 C N sing 1.47 N N
5 N2 C6 N C sing 1.47 N N
6 N2 C5' N C sing 1.47 N N
7 C5' C4' C C sing 1.53 N N
8 C4' O4' C O sing 1.44 N N
9 C4' C3' C C sing 1.54 N N
10 O4' C1' O C sing 1.44 N N
11 C1' N5 C N sing 1.47 N N
12 C1' C2' C C sing 1.55 N N
13 N5 C11 N C sing 1.37 N Y
14 N5 C7 N C sing 1.36 N Y
15 C11 N4 C N doub 1.33 N Y
16 C11 C12 C C sing 1.4 N Y
17 N4 C10 N C sing 1.32 N Y
18 C10 N3 C N doub 1.32 N Y
19 N3 C9 N C sing 1.33 N Y
20 C9 N7 C N sing 1.38 N N
21 C9 C12 C C doub 1.41 N Y
22 C12 N6 C N sing 1.35 N Y
23 N6 C7 N C doub 1.3 N Y
24 C7 C8 C C sing 1.51 N N
25 C2' O2' C O sing 1.43 N N
26 C2' C3' C C sing 1.55 N N
27 C3' O3' C O sing 1.43 N N
28 N1 HN1 N H sing 1.01 N N
29 N1 HN1A N H sing 1.01 N N
30 C4 H4 C H sing 1.09 N N
31 C4 H4A C H sing 1.09 N N
32 C5 H5 C H sing 1.09 N N
33 C5 H5A C H sing 1.09 N N
34 C6 H6 C H sing 1.09 N N
35 C6 H6A C H sing 1.09 N N
36 C6 H6B C H sing 1.09 N N
37 C5' H5' C H sing 1.09 N N
38 C5' H5'A C H sing 1.09 N N
39 C4' H4' C H sing 1.09 N N
40 C1' H1' C H sing 1.09 N N
41 C10 H10 C H sing 1.08 N N
42 N7 HN7 N H sing 0.97 N N
43 N7 HN7A N H sing 0.97 N N
44 C2' H2' C H sing 1.09 N N
45 O2' HO2' O H sing 0.97 N N
46 C3' H3' C H sing 1.09 N N
47 O3' HO3' O H sing 0.97 N N
48 C8 H8 C H sing 1.09 N N
49 C8 H8A C H sing 1.09 N N
50 C8 H8B C H sing 1.09 N N



M8M : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
M8M 3dz5 Open in New Window Bound ligand 1 1