data_NKM # _chem_comp.id NKM _chem_comp.name "(2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C23 H31 N5 O12" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-05-16 _chem_comp.pdbx_modified_date 2019-07-05 _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 569.519 _chem_comp.one_letter_code ? _chem_comp.three_letter_code NKM _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 6OYZ _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 NKM C13 C1 C 0 1 N N S -306.992 -3.059 277.889 -0.760 2.102 -0.195 C13 NKM 1 NKM C15 C2 C 0 1 N N S -307.172 -3.049 280.426 -1.784 3.976 1.075 C15 NKM 2 NKM C17 C3 C 0 1 N N N -307.023 -1.170 278.987 -2.803 1.719 0.969 C17 NKM 3 NKM C22 C4 C 0 1 N N S -306.004 1.903 277.139 -5.030 -1.351 1.125 C22 NKM 4 NKM C24 C5 C 0 1 N N N -303.819 3.158 276.812 -5.612 -0.256 -1.056 C24 NKM 5 NKM C26 C6 C 0 1 N N N -305.909 4.420 275.966 -3.691 -1.848 -1.332 C26 NKM 6 NKM C28 C7 C 0 1 N N N -306.058 2.092 275.751 -4.684 -2.762 0.697 C28 NKM 7 NKM C01 C8 C 0 1 N N N -308.374 -0.896 273.725 -0.618 -2.753 1.215 C01 NKM 8 NKM C03 C9 C 0 1 N N S -309.544 -1.993 275.599 1.017 -1.338 0.181 C03 NKM 9 NKM C04 C10 C 0 1 N N R -310.882 -1.933 276.339 2.425 -1.678 0.720 C04 NKM 10 NKM C05 C11 C 0 1 N N R -311.348 -3.403 276.407 3.376 -1.247 -0.419 C05 NKM 11 NKM C07 C12 C 0 1 N N S -309.346 -3.496 275.379 1.284 -0.742 -1.219 C07 NKM 12 NKM C08 C13 C 0 1 N N R -307.973 -3.946 275.910 0.312 0.404 -1.504 C08 NKM 13 NKM C09 C14 C 0 1 N N N -307.711 -5.383 275.429 0.617 0.997 -2.856 C09 NKM 14 NKM C14 C15 C 0 1 N N S -306.509 -3.710 279.205 -0.478 3.216 0.823 C14 NKM 15 NKM C16 C16 C 0 1 N N N -307.010 -1.671 280.290 -2.898 2.993 1.314 C16 NKM 16 NKM C19 C17 C 0 1 N N N -306.510 0.101 278.710 -3.950 0.830 1.235 C19 NKM 17 NKM C23 C18 C 0 1 N N N -304.537 2.038 277.594 -6.163 -0.837 0.234 C23 NKM 18 NKM C25 C19 C 0 1 N N N -304.635 4.468 276.842 -4.966 -1.285 -1.965 C25 NKM 19 NKM C33 C20 C 0 1 N N N -310.860 -4.065 278.555 4.545 0.496 0.845 C33 NKM 20 NKM C34 C21 C 0 1 N N N -311.245 -4.394 279.791 5.678 1.027 1.355 C34 NKM 21 NKM C35 C22 C 0 1 N N N -312.601 -4.374 280.108 6.909 0.363 1.136 C35 NKM 22 NKM C38 C23 C 0 1 N N N -313.074 -3.701 277.934 5.780 -1.294 -0.063 C38 NKM 23 NKM N11 N1 N 0 1 N N N -306.794 -5.628 274.310 0.449 0.256 -3.970 N11 NKM 24 NKM N21 N2 N 0 1 N N N -306.532 0.567 277.451 -3.856 -0.489 0.974 N21 NKM 25 NKM N27 N3 N 0 1 N N N -305.993 3.316 275.206 -4.058 -2.977 -0.461 N27 NKM 26 NKM N32 N4 N 0 1 N N N -311.764 -3.715 277.627 4.605 -0.671 0.134 N32 NKM 27 NKM N37 N5 N 0 1 N N N -313.491 -4.027 279.168 6.926 -0.782 0.425 N37 NKM 28 NKM O02 O1 O 0 1 N N N -309.596 -1.311 274.341 0.221 -2.520 0.081 O02 NKM 29 NKM O06 O2 O 0 1 N N N -310.386 -4.174 276.101 2.640 -0.247 -1.157 O06 NKM 30 NKM O10 O3 O 0 1 N N N -308.267 -6.309 275.972 1.012 2.140 -2.942 O10 NKM 31 NKM O12 O4 O 0 1 N N N -307.980 -3.933 277.337 0.453 1.411 -0.500 O12 NKM 32 NKM O18 O5 O 0 1 N N N -307.532 -1.888 278.042 -1.700 1.192 0.383 O18 NKM 33 NKM O20 O6 O 0 1 N N N -306.044 0.767 279.607 -4.981 1.288 1.690 O20 NKM 34 NKM O29 O7 O 0 1 N N N -306.134 1.132 275.021 -4.977 -3.698 1.409 O29 NKM 35 NKM O30 O8 O 0 1 N N N -306.537 -3.511 281.620 -2.095 4.780 -0.064 O30 NKM 36 NKM O31 O9 O 0 1 N N N -305.089 -3.562 279.303 0.507 4.109 0.299 O31 NKM 37 NKM O36 O10 O 0 1 N N N -312.946 -4.663 281.205 7.943 0.823 1.585 O36 NKM 38 NKM O39 O11 O 0 1 N N N -313.877 -3.397 277.119 5.811 -2.328 -0.702 O39 NKM 39 NKM O40 O12 O 0 1 N N N -311.866 -1.110 275.581 2.542 -3.080 0.966 O40 NKM 40 NKM H131 H1 H 0 0 N N N -306.131 -3.012 277.206 -1.177 2.532 -1.105 H131 NKM 41 NKM H151 H2 H 0 0 N N N -308.239 -3.316 280.436 -1.669 4.615 1.951 H151 NKM 42 NKM H221 H4 H 0 0 N N N -306.604 2.666 277.656 -5.354 -1.350 2.166 H221 NKM 43 NKM H242 H5 H 0 0 N N N -303.689 2.840 275.767 -6.427 0.224 -1.597 H242 NKM 44 NKM H241 H6 H 0 0 N N N -302.833 3.338 277.266 -4.870 0.503 -0.806 H241 NKM 45 NKM H261 H7 H 0 0 N N N -305.911 5.299 275.305 -3.016 -2.194 -2.114 H261 NKM 46 NKM H262 H8 H 0 0 N N N -306.788 4.456 276.627 -3.201 -1.073 -0.743 H262 NKM 47 NKM H013 H9 H 0 0 N N N -308.596 -0.392 272.773 0.001 -2.945 2.091 H013 NKM 48 NKM H012 H10 H 0 0 N N N -307.844 -0.201 274.393 -1.240 -1.876 1.393 H012 NKM 49 NKM H011 H11 H 0 0 N N N -307.742 -1.776 273.535 -1.255 -3.617 1.024 H011 NKM 50 NKM H031 H12 H 0 0 N N N -308.741 -1.597 276.239 0.530 -0.603 0.822 H031 NKM 51 NKM H041 H13 H 0 0 N N N -310.738 -1.535 277.354 2.634 -1.111 1.627 H041 NKM 52 NKM H051 H14 H 0 0 N N N -312.176 -3.510 275.691 3.611 -2.097 -1.059 H051 NKM 53 NKM H071 H15 H 0 0 N N N -309.410 -3.719 274.304 1.195 -1.514 -1.983 H071 NKM 54 NKM H081 H16 H 0 0 N N N -307.192 -3.280 275.514 -0.710 0.024 -1.496 H081 NKM 55 NKM H141 H17 H 0 0 N N N -306.780 -4.776 279.190 -0.120 2.780 1.755 H141 NKM 56 NKM H2 H18 H 0 1 N N N -306.881 -1.026 281.147 -3.807 3.339 1.784 H2 NKM 57 NKM H232 H20 H 0 0 N N N -304.016 1.085 277.418 -6.836 -1.662 -0.003 H232 NKM 58 NKM H231 H21 H 0 0 N N N -304.513 2.276 278.668 -6.718 -0.065 0.767 H231 NKM 59 NKM H251 H22 H 0 0 N N N -303.994 5.286 276.481 -5.669 -2.099 -2.141 H251 NKM 60 NKM H252 H23 H 0 0 N N N -304.934 4.668 277.881 -4.716 -0.816 -2.916 H252 NKM 61 NKM H331 H24 H 0 0 N N N -309.811 -4.081 278.300 3.597 0.988 1.003 H331 NKM 62 NKM H341 H25 H 0 0 N N N -310.514 -4.672 280.535 5.645 1.946 1.922 H341 NKM 63 NKM H112 H26 H 0 0 N N N -306.628 -6.562 273.995 0.133 -0.658 -3.901 H112 NKM 64 NKM H111 H27 H 0 0 N N N -306.335 -4.861 273.862 0.646 0.637 -4.840 H111 NKM 65 NKM H211 H28 H 0 0 N N N -306.911 0.000 276.719 -3.010 -0.867 0.686 H211 NKM 66 NKM H271 H29 H 0 0 N N N -306.007 3.409 274.210 -3.843 -3.884 -0.731 H271 NKM 67 NKM H371 H30 H 0 0 N N N -314.467 -4.011 279.386 7.765 -1.245 0.273 H371 NKM 68 NKM H301 H31 H 0 0 N N N -306.946 -3.103 282.375 -2.911 5.291 0.026 H301 NKM 69 NKM H311 H32 H 0 0 N N N -304.784 -3.960 280.110 0.732 4.838 0.893 H311 NKM 70 NKM H401 H33 H 0 0 N N N -312.689 -1.084 276.055 3.407 -3.349 1.305 H401 NKM 71 # # 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 NKM C01 O02 SING N N 1 NKM N11 C09 SING N N 2 NKM O02 C03 SING N N 3 NKM O29 C28 DOUB N N 4 NKM N27 C28 SING N N 5 NKM N27 C26 SING N N 6 NKM C07 C03 SING N N 7 NKM C07 C08 SING N N 8 NKM C07 O06 SING N N 9 NKM C09 C08 SING N N 10 NKM C09 O10 DOUB N N 11 NKM O40 C04 SING N N 12 NKM C03 C04 SING N N 13 NKM C28 C22 SING N N 14 NKM C08 O12 SING N N 15 NKM C26 C25 SING N N 16 NKM O06 C05 SING N N 17 NKM C04 C05 SING N N 18 NKM C05 N32 SING N N 19 NKM C24 C25 SING N N 20 NKM C24 C23 SING N N 21 NKM O39 C38 DOUB N N 22 NKM C22 N21 SING N N 23 NKM C22 C23 SING N N 24 NKM O12 C13 SING N N 25 NKM N21 C19 SING N N 26 NKM N32 C38 SING N N 27 NKM N32 C33 SING N N 28 NKM C13 O18 SING N N 29 NKM C13 C14 SING N N 30 NKM C38 N37 SING N N 31 NKM O18 C17 SING N N 32 NKM C33 C34 DOUB N N 33 NKM C19 C17 SING N N 34 NKM C19 O20 DOUB N N 35 NKM C17 C16 DOUB N N 36 NKM N37 C35 SING N N 37 NKM C14 O31 SING N N 38 NKM C14 C15 SING N N 39 NKM C34 C35 SING N N 40 NKM C35 O36 DOUB N N 41 NKM C16 C15 SING N N 42 NKM C15 O30 SING N N 43 NKM C13 H131 SING N N 44 NKM C15 H151 SING N N 45 NKM C22 H221 SING N N 46 NKM C24 H242 SING N N 47 NKM C24 H241 SING N N 48 NKM C26 H261 SING N N 49 NKM C26 H262 SING N N 50 NKM C01 H013 SING N N 51 NKM C01 H012 SING N N 52 NKM C01 H011 SING N N 53 NKM C03 H031 SING N N 54 NKM C04 H041 SING N N 55 NKM C05 H051 SING N N 56 NKM C07 H071 SING N N 57 NKM C08 H081 SING N N 58 NKM C14 H141 SING N N 59 NKM C16 H2 SING N N 60 NKM C23 H232 SING N N 61 NKM C23 H231 SING N N 62 NKM C25 H251 SING N N 63 NKM C25 H252 SING N N 64 NKM C33 H331 SING N N 65 NKM C34 H341 SING N N 66 NKM N11 H112 SING N N 67 NKM N11 H111 SING N N 68 NKM N21 H211 SING N N 69 NKM N27 H271 SING N N 70 NKM N37 H371 SING N N 71 NKM O30 H301 SING N N 72 NKM O31 H311 SING N N 73 NKM O40 H401 SING N N 74 # # 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 NKM SMILES ACDLabs 12.01 "C1(OC(=CC(O)C1O)C(=O)NC2CCCCNC2=O)OC(C4C(C(C(N3C=CC(=O)NC3=O)O4)O)OC)C(=O)N" NKM InChI InChI 1.03 "InChI=1S/C23H31N5O12/c1-37-15-14(32)21(28-7-5-12(30)27-23(28)36)39-16(15)17(18(24)33)40-22-13(31)10(29)8-11(38-22)20(35)26-9-4-2-3-6-25-19(9)34/h5,7-10,13-17,21-22,29,31-32H,2-4,6H2,1H3,(H2,24,33)(H,25,34)(H,26,35)(H,27,30,36)/t9-,10-,13-,14+,15-,16-,17+,21+,22+/m0/s1" NKM InChIKey InChI 1.03 BISOEENGZHMDEO-RLXIHFJVSA-N NKM SMILES_CANONICAL CACTVS 3.385 "CO[C@H]1[C@@H](O)[C@@H](O[C@@H]1[C@@H](O[C@H]2OC(=C[C@H](O)[C@@H]2O)C(=O)N[C@H]3CCCCNC3=O)C(N)=O)N4C=CC(=O)NC4=O" NKM SMILES CACTVS 3.385 "CO[CH]1[CH](O)[CH](O[CH]1[CH](O[CH]2OC(=C[CH](O)[CH]2O)C(=O)N[CH]3CCCCNC3=O)C(N)=O)N4C=CC(=O)NC4=O" NKM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@H]1[C@H]([C@@H](O[C@@H]1[C@H](C(=O)N)O[C@@H]2[C@H]([C@H](C=C(O2)C(=O)N[C@H]3CCCCNC3=O)O)O)N4C=CC(=O)NC4=O)O" NKM SMILES "OpenEye OEToolkits" 2.0.7 "COC1C(C(OC1C(C(=O)N)OC2C(C(C=C(O2)C(=O)NC3CCCCNC3=O)O)O)N4C=CC(=O)NC4=O)O" # # 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 NKM "SYSTEMATIC NAME" ACDLabs 12.01 "(2S,3S,4S)-2-{(1R)-2-amino-1-[(2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-3-methoxytetrahydrofuran-2-yl]-2-oxoethoxy}-3,4-dihydroxy-N-[(3S)-2-oxoazepan-3-yl]-3,4-dihydro-2H-pyran-6-carboxamide (non-preferred name)" NKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site NKM "Create component" 2019-05-16 RCSB NKM "Other modification" 2019-06-04 RCSB NKM "Initial release" 2019-07-10 RCSB ##