data_C8M
#
_chem_comp.id C8M
_chem_comp.name
;3-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]propanamid
e
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H23 N7 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "5'-[(2-carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2008-07-31
_chem_comp.pdbx_modified_date 2020-06-17
_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 365.388
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code C8M
_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 3DZ4
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
# #
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.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
C8M N1 N1 N 0 1 N N N -30.472 -6.830 40.609 -6.834 2.836 -0.670 N1 C8M 1
C8M C1 C1 C 0 1 N N N -29.585 -6.388 41.530 -6.142 1.854 -0.058 C1 C8M 2
C8M C4 C4 C 0 1 N N N -28.334 -6.987 41.873 -4.963 1.220 -0.750 C4 C8M 3
C8M C5 C5 C 0 1 N N N -27.159 -6.237 41.490 -4.360 0.143 0.154 C5 C8M 4
C8M N2 N2 N 0 1 N N N -26.782 -6.213 40.190 -3.210 -0.475 -0.520 N2 C8M 5
C8M C6 C6 C 0 1 N N N -26.749 -7.386 39.468 -3.637 -1.218 -1.713 C6 C8M 6
C8M "C5'" "C5'" C 0 1 N N N -25.561 -5.532 39.962 -2.464 -1.342 0.401 "C5'" C8M 7
C8M "C4'" "C4'" C 0 1 N N R -25.090 -5.244 38.556 -1.147 -1.767 -0.252 "C4'" C8M 8
C8M "O4'" "O4'" O 0 1 N N N -25.668 -4.832 37.672 -0.293 -0.623 -0.420 "O4'" C8M 9
C8M "C1'" "C1'" C 0 1 N N R -25.445 -3.595 37.364 1.064 -1.081 -0.242 "C1'" C8M 10
C8M N5 N5 N 0 1 Y N N -26.529 -2.750 37.211 1.944 0.037 0.109 N5 C8M 11
C8M C11 C11 C 0 1 Y N N -27.530 -2.708 38.069 3.194 0.278 -0.403 C11 C8M 12
C8M N4 N4 N 0 1 Y N N -27.840 -3.288 39.141 3.978 -0.327 -1.289 N4 C8M 13
C8M C10 C10 C 0 1 Y N N -28.822 -3.128 39.823 5.165 0.162 -1.580 C10 C8M 14
C8M N3 N3 N 0 1 Y N N -29.809 -2.265 39.553 5.635 1.261 -1.018 N3 C8M 15
C8M C9 C9 C 0 1 Y N N -29.621 -1.567 38.431 4.924 1.934 -0.120 C9 C8M 16
C8M N7 N7 N 0 1 N N N -30.570 -0.622 38.012 5.426 3.083 0.464 N7 C8M 17
C8M C12 C12 C 0 1 Y N N -28.437 -1.801 37.666 3.650 1.450 0.224 C12 C8M 18
C8M N6 N6 N 0 1 Y N N -27.914 -1.354 36.583 2.672 1.857 1.069 N6 C8M 19
C8M C7 C7 C 0 1 Y N N -26.868 -1.877 36.340 1.668 1.032 0.999 C7 C8M 20
C8M "C2'" "C2'" C 0 1 N N R -24.425 -3.139 38.404 0.957 -2.081 0.937 "C2'" C8M 21
C8M "O2'" "O2'" O 0 1 N N N -23.613 -2.260 38.186 2.021 -3.034 0.896 "O2'" C8M 22
C8M "C3'" "C3'" C 0 1 N N S -23.767 -4.503 38.798 -0.406 -2.762 0.661 "C3'" C8M 23
C8M "O3'" "O3'" O 0 1 N N N -22.864 -4.802 37.981 -0.215 -4.010 -0.009 "O3'" C8M 24
C8M C8 C8 C 0 1 N N N -26.209 -1.459 35.179 0.390 1.157 1.788 C8 C8M 25
C8M O1 O1 O 0 1 N N N -29.884 -5.399 42.120 -6.469 1.481 1.048 O1 C8M 26
C8M HN1 HN1 H 0 1 N N N -30.137 -7.665 40.173 -6.573 3.134 -1.555 HN1 C8M 27
C8M HN1A HN1A H 0 0 N N N -31.341 -6.384 40.394 -7.595 3.241 -0.226 HN1A C8M 28
C8M H4 H4 H 0 1 N N N -28.311 -7.102 42.967 -5.290 0.768 -1.686 H4 C8M 29
C8M H4A H4A H 0 1 N N N -28.286 -7.935 41.317 -4.211 1.982 -0.958 H4A C8M 30
C8M H5 H5 H 0 1 N N N -27.353 -5.192 41.775 -4.032 0.595 1.090 H5 C8M 31
C8M H5A H5A H 0 1 N N N -26.334 -6.758 41.997 -5.112 -0.619 0.362 H5A C8M 32
C8M H6 H6 H 0 1 N N N -26.740 -7.155 38.393 -4.126 -0.537 -2.410 H6 C8M 33
C8M H6A H6A H 0 1 N N N -25.842 -7.952 39.729 -2.766 -1.666 -2.193 H6A C8M 34
C8M H6B H6B H 0 1 N N N -27.638 -7.988 39.706 -4.335 -2.003 -1.422 H6B C8M 35
C8M "H5'" "H5'" H 0 1 N N N -25.667 -4.552 40.451 -2.253 -0.798 1.322 "H5'" C8M 36
C8M "H5'A" "H5'A" H 0 0 N N N -24.805 -6.235 40.343 -3.058 -2.227 0.630 "H5'A" C8M 37
C8M "H4'" "H4'" H 0 1 N N N -25.151 -6.238 38.088 -1.346 -2.227 -1.220 "H4'" C8M 38
C8M "H1'" "H1'" H 0 1 N N N -25.077 -3.536 36.329 1.422 -1.581 -1.142 "H1'" C8M 39
C8M H10 H10 H 0 1 N N N -28.912 -3.726 40.718 5.777 -0.354 -2.305 H10 C8M 40
C8M HN7 HN7 H 0 1 N N N -31.176 -0.397 38.775 6.307 3.407 0.219 HN7 C8M 41
C8M HN7A HN7A H 0 0 N N N -30.102 0.206 37.703 4.897 3.566 1.119 HN7A C8M 42
C8M "H2'" "H2'" H 0 1 N N N -24.959 -2.569 39.179 0.944 -1.557 1.892 "H2'" C8M 43
C8M "HO2'" "HO2'" H 0 0 N N N -23.401 -1.815 38.998 1.997 -3.682 1.613 "HO2'" C8M 44
C8M "H3'" "H3'" H 0 1 N N N -23.256 -4.640 39.763 -0.955 -2.908 1.592 "H3'" C8M 45
C8M "HO3'" "HO3'" H 0 0 N N N -23.236 -4.878 37.110 0.247 -4.674 0.521 "HO3'" C8M 46
C8M H8 H8 H 0 1 N N N -26.938 -1.349 34.362 0.494 0.625 2.733 H8 C8M 47
C8M H8A H8A H 0 1 N N N -25.718 -0.492 35.364 0.185 2.209 1.983 H8A C8M 48
C8M H8B H8B H 0 1 N N N -25.453 -2.207 34.897 -0.433 0.726 1.217 H8B C8M 49
# #
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
C8M N1 C1 SING N N 1
C8M C1 C4 SING N N 2
C8M C1 O1 DOUB N N 3
C8M C4 C5 SING N N 4
C8M C5 N2 SING N N 5
C8M N2 C6 SING N N 6
C8M N2 "C5'" SING N N 7
C8M "C5'" "C4'" SING N N 8
C8M "C4'" "O4'" SING N N 9
C8M "C4'" "C3'" SING N N 10
C8M "O4'" "C1'" SING N N 11
C8M "C1'" N5 SING N N 12
C8M "C1'" "C2'" SING N N 13
C8M N5 C11 SING Y N 14
C8M N5 C7 SING Y N 15
C8M C11 N4 DOUB Y N 16
C8M C11 C12 SING Y N 17
C8M N4 C10 SING Y N 18
C8M C10 N3 DOUB Y N 19
C8M N3 C9 SING Y N 20
C8M C9 N7 SING N N 21
C8M C9 C12 DOUB Y N 22
C8M C12 N6 SING Y N 23
C8M N6 C7 DOUB Y N 24
C8M C7 C8 SING N N 25
C8M "C2'" "O2'" SING N N 26
C8M "C2'" "C3'" SING N N 27
C8M "C3'" "O3'" SING N N 28
C8M N1 HN1 SING N N 29
C8M N1 HN1A SING N N 30
C8M C4 H4 SING N N 31
C8M C4 H4A SING N N 32
C8M C5 H5 SING N N 33
C8M C5 H5A SING N N 34
C8M C6 H6 SING N N 35
C8M C6 H6A SING N N 36
C8M C6 H6B SING N N 37
C8M "C5'" "H5'" SING N N 38
C8M "C5'" "H5'A" SING N N 39
C8M "C4'" "H4'" SING N N 40
C8M "C1'" "H1'" SING N N 41
C8M C10 H10 SING N N 42
C8M N7 HN7 SING N N 43
C8M N7 HN7A SING N N 44
C8M "C2'" "H2'" SING N N 45
C8M "O2'" "HO2'" SING N N 46
C8M "C3'" "H3'" SING N N 47
C8M "O3'" "HO3'" SING N N 48
C8M C8 H8 SING N N 49
C8M C8 H8A SING N N 50
C8M C8 H8B SING N N 51
# #
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
C8M SMILES ACDLabs 10.04 "O=C(N)CCN(C)CC3OC(n2c(nc1c(ncnc12)N)C)C(O)C3O"
C8M SMILES_CANONICAL CACTVS 3.341 "CN(CCC(N)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2c(C)nc3c(N)ncnc23"
C8M SMILES CACTVS 3.341 "CN(CCC(N)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2c(C)nc3c(N)ncnc23"
C8M SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)C[N@@](C)CCC(=O)N)O)O)N"
C8M SMILES "OpenEye OEToolkits" 1.5.0 "Cc1nc2c(ncnc2n1C3C(C(C(O3)CN(C)CCC(=O)N)O)O)N"
C8M InChI InChI 1.03 "InChI=1S/C15H23N7O4/c1-7-20-10-13(17)18-6-19-14(10)22(7)15-12(25)11(24)8(26-15)5-21(2)4-3-9(16)23/h6,8,11-12,15,24-25H,3-5H2,1-2H3,(H2,16,23)(H2,17,18,19)/t8-,11-,12-,15-/m1/s1"
C8M InChIKey InChI 1.03 MAQWABZHWBDHHD-PMXXHBEXSA-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
C8M "SYSTEMATIC NAME" ACDLabs 10.04 "3-[{[(2R,3S,4R,5R)-5-(6-amino-8-methyl-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}(methyl)amino]propanamide (non-preferred name)"
C8M "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "3-[[(2R,3S,4R,5R)-5-(6-amino-8-methyl-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl-methyl-amino]propanamide"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
C8M "Create component" 2008-07-31 RCSB
C8M "Modify aromatic_flag" 2011-06-04 RCSB
C8M "Modify descriptor" 2011-06-04 RCSB
C8M "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id C8M
_pdbx_chem_comp_synonyms.name "5'-[(2-carboxamidomethyl)methylamino]-5'-deoxy-8-methyladenosine"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##