data_6D1 # _chem_comp.id 6D1 _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H24 Cl N7 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-03-16 _chem_comp.pdbx_modified_date 2017-03-10 _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 429.859 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6D1 _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 5IS8 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 6D1 N1 N N 0 1 N N N 53.837 36.350 135.447 -4.300 -3.019 -0.452 N1 6D1 1 6D1 C1 CA C 0 1 N N S 52.813 35.382 135.765 -5.038 -1.753 -0.543 C1 6D1 2 6D1 C2 CB C 0 1 N N N 52.623 34.383 134.607 -4.048 -0.587 -0.586 C2 6D1 3 6D1 C3 CG C 0 1 N N N 51.402 34.761 133.818 -3.286 -0.517 0.739 C3 6D1 4 6D1 N2 NA* N 0 1 N N N 51.527 34.486 132.414 -2.335 0.602 0.699 N2 6D1 5 6D1 C4 CB* C 0 1 N N N 51.716 33.015 132.225 -3.039 1.889 0.632 C4 6D1 6 6D1 C5 CG* C 0 1 N N N 51.680 32.541 130.719 -2.062 2.983 0.195 C5 6D1 7 6D1 CL1 CLD* CL 0 0 N N N 51.857 30.800 130.601 -2.920 4.568 0.140 CL1 6D1 8 6D1 C6 C5* C 0 1 N N N 50.297 34.936 131.705 -1.423 0.560 1.850 C6 6D1 9 6D1 C7 C4* C 0 1 N N R 49.824 36.384 132.053 -0.376 -0.534 1.631 C7 6D1 10 6D1 O1 O4* O 0 1 N N N 50.534 37.354 131.238 0.408 -0.234 0.464 O1 6D1 11 6D1 C8 C1* C 0 1 N N R 49.547 38.141 130.523 1.747 -0.709 0.722 C8 6D1 12 6D1 C9 C2* C 0 1 N N R 48.286 37.297 130.479 1.984 -0.333 2.207 C9 6D1 13 6D1 O2 O2* O 0 1 N N N 47.109 38.057 130.507 2.967 -1.186 2.798 O2 6D1 14 6D1 C10 C3* C 0 1 N N S 48.372 36.513 131.742 0.587 -0.585 2.833 C10 6D1 15 6D1 O3 O3* O 0 1 N N N 47.748 37.175 132.843 0.544 -1.869 3.459 O3 6D1 16 6D1 N3 N9 N 0 1 Y N N 49.700 38.502 129.128 2.712 -0.029 -0.146 N3 6D1 17 6D1 C11 C8 C 0 1 Y N N 49.851 37.764 128.007 2.547 1.188 -0.737 C11 6D1 18 6D1 N4 N7 N 0 1 Y N N 50.023 38.613 126.977 3.601 1.488 -1.439 N4 6D1 19 6D1 C12 C5 C 0 1 Y N N 50.011 39.892 127.456 4.507 0.485 -1.343 C12 6D1 20 6D1 C13 C6 C 0 1 Y N N 50.146 41.160 126.848 5.790 0.258 -1.870 C13 6D1 21 6D1 N5 N6 N 0 1 N N N 50.348 41.212 125.405 6.392 1.193 -2.694 N5 6D1 22 6D1 N6 N1 N 0 1 Y N N 50.090 42.270 127.596 6.411 -0.875 -1.559 N6 6D1 23 6D1 C14 C2 C 0 1 Y N N 49.904 42.178 128.945 5.844 -1.772 -0.773 C14 6D1 24 6D1 N7 N3 N 0 1 Y N N 49.772 40.983 129.558 4.644 -1.602 -0.258 N7 6D1 25 6D1 C15 C4 C 0 1 Y N N 49.828 39.825 128.826 3.949 -0.498 -0.509 C15 6D1 26 6D1 C16 C C 0 1 N N N 53.179 34.638 137.007 -5.873 -1.747 -1.798 C16 6D1 27 6D1 O4 OXT O 0 1 N N N 52.345 34.522 137.932 -6.916 -0.909 -1.906 O4 6D1 28 6D1 O5 O O 0 1 N N N 54.321 34.120 137.097 -5.605 -2.498 -2.705 O5 6D1 29 6D1 H1 H2 H 0 1 N N N 53.943 36.987 136.211 -4.932 -3.800 -0.357 H1 6D1 30 6D1 H2 H H 0 1 N N N 54.703 35.878 135.284 -3.691 -3.141 -1.247 H2 6D1 31 6D1 H4 HA H 0 1 N N N 51.857 35.901 135.931 -5.687 -1.646 0.326 H4 6D1 32 6D1 H5 HB3 H 0 1 N N N 52.498 33.369 135.014 -3.342 -0.739 -1.403 H5 6D1 33 6D1 H6 HB2 H 0 1 N N N 53.506 34.409 133.952 -4.590 0.345 -0.743 H6 6D1 34 6D1 H7 HG3 H 0 1 N N N 51.221 35.838 133.948 -3.991 -0.365 1.556 H7 6D1 35 6D1 H8 HG2 H 0 1 N N N 50.544 34.195 134.210 -2.743 -1.449 0.896 H8 6D1 36 6D1 H10 HB*2 H 0 1 N N N 50.916 32.493 132.769 -3.853 1.821 -0.090 H10 6D1 37 6D1 H11 HB*1 H 0 1 N N N 52.691 32.736 132.650 -3.443 2.134 1.614 H11 6D1 38 6D1 H12 HG*2 H 0 1 N N N 52.502 33.024 130.171 -1.239 3.040 0.907 H12 6D1 39 6D1 H13 HG*1 H 0 1 N N N 50.719 32.836 130.272 -1.671 2.747 -0.794 H13 6D1 40 6D1 H14 H5*2 H 0 1 N N N 49.483 34.241 131.960 -0.925 1.524 1.954 H14 6D1 41 6D1 H15 H5*1 H 0 1 N N N 50.492 34.892 130.623 -1.990 0.344 2.755 H15 6D1 42 6D1 H16 H4*1 H 0 1 N N N 50.000 36.573 133.122 -0.868 -1.499 1.509 H16 6D1 43 6D1 H17 H1*1 H 0 1 N N N 49.328 39.049 131.104 1.804 -1.789 0.585 H17 6D1 44 6D1 H18 H2*1 H 0 1 N N N 48.315 36.625 129.609 2.272 0.714 2.302 H18 6D1 45 6D1 H19 H2*2 H 0 1 N N N 46.357 37.478 130.477 3.151 -0.990 3.727 H19 6D1 46 6D1 H20 H3*1 H 0 1 N N N 47.934 35.515 131.591 0.344 0.199 3.550 H20 6D1 47 6D1 H21 H3*2 H 0 1 N N N 47.828 36.638 133.623 1.174 -1.974 4.184 H21 6D1 48 6D1 H22 H81 H 0 1 N N N 49.836 36.686 127.948 1.671 1.812 -0.637 H22 6D1 49 6D1 H23 H61 H 0 1 N N N 50.429 42.165 125.113 5.929 2.016 -2.914 H23 6D1 50 6D1 H24 H62 H 0 1 N N N 51.185 40.719 125.168 7.278 1.025 -3.051 H24 6D1 51 6D1 H25 H21 H 0 1 N N N 49.862 43.082 129.535 6.384 -2.679 -0.546 H25 6D1 52 6D1 H26 H4 H 0 1 N N N 52.724 34.012 138.639 -7.422 -0.942 -2.729 H26 6D1 53 # 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 6D1 N5 C13 SING N N 1 6D1 C13 C12 DOUB Y N 2 6D1 C13 N6 SING Y N 3 6D1 N4 C12 SING Y N 4 6D1 N4 C11 DOUB Y N 5 6D1 C12 C15 SING Y N 6 6D1 N6 C14 DOUB Y N 7 6D1 C11 N3 SING Y N 8 6D1 C15 N3 SING Y N 9 6D1 C15 N7 DOUB Y N 10 6D1 C14 N7 SING Y N 11 6D1 N3 C8 SING N N 12 6D1 C9 O2 SING N N 13 6D1 C9 C8 SING N N 14 6D1 C9 C10 SING N N 15 6D1 C8 O1 SING N N 16 6D1 CL1 C5 SING N N 17 6D1 C5 C4 SING N N 18 6D1 O1 C7 SING N N 19 6D1 C6 C7 SING N N 20 6D1 C6 N2 SING N N 21 6D1 C10 C7 SING N N 22 6D1 C10 O3 SING N N 23 6D1 C4 N2 SING N N 24 6D1 N2 C3 SING N N 25 6D1 C3 C2 SING N N 26 6D1 C2 C1 SING N N 27 6D1 N1 C1 SING N N 28 6D1 C1 C16 SING N N 29 6D1 C16 O5 DOUB N N 30 6D1 C16 O4 SING N N 31 6D1 N1 H1 SING N N 32 6D1 N1 H2 SING N N 33 6D1 C1 H4 SING N N 34 6D1 C2 H5 SING N N 35 6D1 C2 H6 SING N N 36 6D1 C3 H7 SING N N 37 6D1 C3 H8 SING N N 38 6D1 C4 H10 SING N N 39 6D1 C4 H11 SING N N 40 6D1 C5 H12 SING N N 41 6D1 C5 H13 SING N N 42 6D1 C6 H14 SING N N 43 6D1 C6 H15 SING N N 44 6D1 C7 H16 SING N N 45 6D1 C8 H17 SING N N 46 6D1 C9 H18 SING N N 47 6D1 O2 H19 SING N N 48 6D1 C10 H20 SING N N 49 6D1 O3 H21 SING N N 50 6D1 C11 H22 SING N N 51 6D1 N5 H23 SING N N 52 6D1 N5 H24 SING N N 53 6D1 C14 H25 SING N N 54 6D1 O4 H26 SING N N 55 # 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 6D1 SMILES ACDLabs 12.01 "NC(C(=O)O)CCN(CCCl)CC1OC(C(O)C1O)n2cnc3c2ncnc3N" 6D1 InChI InChI 1.03 "InChI=1S/C16H24ClN7O5/c17-2-4-23(3-1-8(18)16(27)28)5-9-11(25)12(26)15(29-9)24-7-22-10-13(19)20-6-21-14(10)24/h6-9,11-12,15,25-26H,1-5,18H2,(H,27,28)(H2,19,20,21)/t8-,9+,11+,12+,15+/m0/s1" 6D1 InChIKey InChI 1.03 HTQOMKNFDALONB-OPYVMVOTSA-N 6D1 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(CCCl)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O" 6D1 SMILES CACTVS 3.385 "N[CH](CCN(CCCl)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O" 6D1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)O)N)CCCl)O)O)N" 6D1 SMILES "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)O)N)CCCl)O)O)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 6D1 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl](2-chloroethyl)amino}-5'-deoxyadenosine" 6D1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-chloroethyl)amino]-2-azanyl-butanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 6D1 "Create component" 2016-03-16 EBI 6D1 "Initial release" 2017-03-15 RCSB #