data_M8M
#
_chem_comp.id M8M
_chem_comp.name "5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H23 N7 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-31
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 353.377
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code M8M
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3DZ5
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
M8M N1 N1 N 0 1 N N N N N N -21.012 -10.251 9.476 -2.770 3.941 0.377 N1 M8M 1
M8M O2 O2 O 0 1 N N N N N N -19.731 -9.753 9.810 -3.405 2.839 -0.347 O2 M8M 2
M8M C4 C4 C 0 1 N N N N N N -18.988 -9.341 8.554 -4.242 2.015 0.467 C4 M8M 3
M8M C5 C5 C 0 1 N N N N N N -17.618 -8.795 8.823 -4.850 0.903 -0.389 C5 M8M 4
M8M N2 N2 N 0 1 N N N N N N -16.824 -8.707 7.553 -3.782 0.020 -0.877 N2 M8M 5
M8M C6 C6 C 0 1 N N N N N N -16.252 -10.048 7.284 -4.259 -0.824 -1.980 C6 M8M 6
M8M "C5'" "C5'" C 0 1 N N N N N N -15.711 -7.710 7.687 -3.236 -0.798 0.214 "C5'" M8M 7
M8M "C4'" "C4'" C 0 1 N N R N N N -14.865 -7.612 6.426 -1.973 -1.514 -0.269 "C4'" M8M 8
M8M "O4'" "O4'" O 0 1 N N N N N N -15.633 -7.218 5.233 -0.937 -0.553 -0.533 "O4'" M8M 9
M8M "C1'" "C1'" C 0 1 N N R N N N -15.234 -5.924 5.062 0.317 -1.180 -0.186 "C1'" M8M 10
M8M N5 N5 N 0 1 Y N N N N N -16.528 -5.076 4.783 1.347 -0.168 0.067 N5 M8M 11
M8M C11 C11 C 0 1 Y N N N N N -17.657 -5.294 5.574 2.645 -0.203 -0.376 C11 M8M 12
M8M N4 N4 N 0 1 Y N N N N N -17.812 -6.172 6.593 3.366 -1.049 -1.104 N4 M8M 13
M8M C10 C10 C 0 1 Y N N N N N -19.044 -6.096 7.123 4.630 -0.797 -1.370 C10 M8M 14
M8M N3 N3 N 0 1 Y N N N N N -20.067 -5.296 6.774 5.242 0.290 -0.937 N3 M8M 15
M8M C9 C9 C 0 1 Y N N N N N -19.884 -4.424 5.747 4.602 1.194 -0.202 C9 M8M 16
M8M N7 N7 N 0 1 N N N N N N -20.896 -3.628 5.398 5.252 2.330 0.248 N7 M8M 17
M8M C12 C12 C 0 1 Y N N N N N -18.623 -4.407 5.098 3.250 0.969 0.108 C12 M8M 18
M8M N6 N6 N 0 1 Y N N N N N -18.128 -3.654 4.042 2.308 1.645 0.808 N6 M8M 19
M8M C7 C7 C 0 1 Y N N N N N -16.894 -4.084 3.892 1.189 0.982 0.780 C7 M8M 20
M8M "C2'" "C2'" C 0 1 N N R N N N -14.396 -5.376 5.953 -0.014 -1.958 1.112 "C2'" M8M 21
M8M "O2'" "O2'" O 0 1 N N N N N N -13.509 -4.335 5.600 0.882 -3.057 1.290 "O2'" M8M 22
M8M "C3'" "C3'" C 0 1 N N S N N N -13.726 -6.614 6.502 -1.452 -2.458 0.833 "C3'" M8M 23
M8M "O3'" "O3'" O 0 1 N N N N N N -12.657 -6.999 5.637 -1.431 -3.808 0.366 "O3'" M8M 24
M8M C8 C8 C 0 1 N N N N N N -15.905 -3.597 2.873 -0.093 1.420 1.442 C8 M8M 25
M8M HN1 HN1 H 0 1 N N N N N N -21.552 -10.369 10.309 -2.238 3.598 1.162 HN1 M8M 26
M8M HN1A HN1A H 0 0 N N N N N N -21.473 -9.604 8.869 -2.191 4.492 -0.239 HN1A M8M 27
M8M H4 H4 H 0 1 N N N N N N -18.884 -10.227 7.911 -3.649 1.574 1.268 H4 M8M 28
M8M H4A H4A H 0 1 N N N N N N -19.571 -8.539 8.078 -5.040 2.620 0.897 H4A M8M 29
M8M H5 H5 H 0 1 N N N N N N -17.711 -7.789 9.259 -5.553 0.325 0.211 H5 M8M 30
M8M H5A H5A H 0 1 N N N N N N -17.098 -9.469 9.520 -5.374 1.342 -1.238 H5A M8M 31
M8M H6 H6 H 0 1 N N N N N N -16.110 -10.176 6.201 -4.540 -0.195 -2.825 H6 M8M 32
M8M H6A H6A H 0 1 N N N N N N -15.282 -10.142 7.794 -3.466 -1.507 -2.284 H6A M8M 33
M8M H6B H6B H 0 1 N N N N N N -16.939 -10.821 7.658 -5.125 -1.397 -1.651 H6B M8M 34
M8M "H5'" "H5'" H 0 1 N N N N N N -16.150 -6.722 7.891 -2.989 -0.157 1.061 "H5'" M8M 35
M8M "H5'A" "H5'A" H 0 0 N N N N N N -15.057 -8.043 8.506 -3.977 -1.536 0.521 "H5'A" M8M 36
M8M "H4'" "H4'" H 0 1 N N N N N N -14.476 -8.638 6.344 -2.191 -2.082 -1.173 "H4'" M8M 37
M8M "H1'" "H1'" H 0 1 N N N N N N -14.547 -5.924 4.203 0.636 -1.861 -0.975 "H1'" M8M 38
M8M H10 H10 H 0 1 N N N N N N -19.240 -6.771 7.943 5.188 -1.506 -1.964 H10 M8M 39
M8M HN7 HN7 H 0 1 N N N N N N -21.457 -3.429 6.202 6.186 2.474 0.027 HN7 M8M 40
M8M HN7A HN7A H 0 0 N N N N N N -20.534 -2.774 5.024 4.774 2.983 0.783 HN7A M8M 41
M8M "H2'" "H2'" H 0 1 N N N N N N -14.965 -4.750 6.656 0.008 -1.297 1.978 "H2'" M8M 42
M8M "HO2'" "HO2'" H 0 0 N N N N N N -13.310 -3.814 6.369 0.715 -3.575 2.090 "HO2'" M8M 43
M8M "H3'" "H3'" H 0 1 N N N N N N -13.287 -6.507 7.505 -2.066 -2.373 1.730 "H3'" M8M 44
M8M "HO3'" "HO3'" H 0 0 N N N N N N -12.983 -7.084 4.749 -1.112 -4.445 1.019 "HO3'" M8M 45
M8M H8 H8 H 0 1 N N N N N N -16.407 -3.478 1.902 -0.127 1.031 2.460 H8 M8M 46
M8M H8A H8A H 0 1 N N N N N N -15.494 -2.628 3.194 -0.135 2.509 1.468 H8A M8M 47
M8M H8B H8B H 0 1 N N N N N N -15.089 -4.328 2.776 -0.943 1.037 0.878 H8B M8M 48
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
M8M N1 O2 SING N N 1
M8M O2 C4 SING N N 2
M8M C4 C5 SING N N 3
M8M C5 N2 SING N N 4
M8M N2 C6 SING N N 5
M8M N2 "C5'" SING N N 6
M8M "C5'" "C4'" SING N N 7
M8M "C4'" "O4'" SING N N 8
M8M "C4'" "C3'" SING N N 9
M8M "O4'" "C1'" SING N N 10
M8M "C1'" N5 SING N N 11
M8M "C1'" "C2'" SING N N 12
M8M N5 C11 SING Y N 13
M8M N5 C7 SING Y N 14
M8M C11 N4 DOUB Y N 15
M8M C11 C12 SING Y N 16
M8M N4 C10 SING Y N 17
M8M C10 N3 DOUB Y N 18
M8M N3 C9 SING Y N 19
M8M C9 N7 SING N N 20
M8M C9 C12 DOUB Y N 21
M8M C12 N6 SING Y N 22
M8M N6 C7 DOUB Y N 23
M8M C7 C8 SING N N 24
M8M "C2'" "O2'" SING N N 25
M8M "C2'" "C3'" SING N N 26
M8M "C3'" "O3'" SING N N 27
M8M N1 HN1 SING N N 28
M8M N1 HN1A SING N N 29
M8M C4 H4 SING N N 30
M8M C4 H4A SING N N 31
M8M C5 H5 SING N N 32
M8M C5 H5A SING N N 33
M8M C6 H6 SING N N 34
M8M C6 H6A SING N N 35
M8M C6 H6B SING N N 36
M8M "C5'" "H5'" SING N N 37
M8M "C5'" "H5'A" SING N N 38
M8M "C4'" "H4'" SING N N 39
M8M "C1'" "H1'" SING N N 40
M8M C10 H10 SING N N 41
M8M N7 HN7 SING N N 42
M8M N7 HN7A SING N N 43
M8M "C2'" "H2'" SING N N 44
M8M "O2'" "HO2'" SING N N 45
M8M "C3'" "H3'" SING N N 46
M8M "O3'" "HO3'" SING N N 47
M8M C8 H8 SING N N 48
M8M C8 H8A SING N N 49
M8M C8 H8B SING N N 50
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
M8M SMILES ACDLabs 10.04 "n2c1c(ncnc1n(c2C)C3OC(C(O)C3O)CN(CCON)C)N"
M8M SMILES_CANONICAL CACTVS 3.341 "CN(CCON)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23"
M8M SMILES CACTVS 3.341 "CN(CCON)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23"
M8M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCON)O)O)N"
M8M SMILES "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCON)O)O)N"
M8M InChI InChI 1.03 "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"
M8M InChIKey InChI 1.03 MIGFZONTOHGZMB-IDTAVKCVSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
M8M "SYSTEMATIC NAME" ACDLabs 10.04 "5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine"
M8M "SYSTEMATIC NAME" "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"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
M8M "Create component" 2008-07-31 RCSB
M8M "Modify aromatic_flag" 2011-06-04 RCSB
M8M "Modify descriptor" 2011-06-04 RCSB
M8M "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id M8M
_pdbx_chem_comp_pcm.modified_residue_id PYR
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid backbone"
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_pdbx_chem_comp_pcm.comp_id_linking_atom N1
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom CA
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#