data_6D2 # _chem_comp.id 6D2 _chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl](3-carbamimidamidopropyl)amino}-5'-deoxyadenosine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H30 N10 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 466.495 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 6D2 _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 5ISE _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 6D2 C11 C1 C 0 1 N N N 52.559 32.412 131.120 3.806 -0.985 0.347 C11 6D2 1 6D2 C10 C2 C 0 1 N N N 51.272 33.270 131.264 2.970 -0.841 -0.926 C10 6D2 2 6D2 C2 C3 C 0 1 Y N N 50.478 42.393 127.611 -5.981 -2.417 0.947 C2 6D2 3 6D2 C6 C4 C 0 1 Y N N 50.723 41.251 125.590 -6.193 -0.295 1.830 C6 6D2 4 6D2 C5 C5 C 0 1 Y N N 50.539 40.025 126.234 -4.937 0.032 1.291 C5 6D2 5 6D2 C4 C6 C 0 1 Y N N 50.327 40.057 127.581 -4.249 -0.956 0.565 C4 6D2 6 6D2 C14 C7 C 0 1 N N N 52.405 29.585 129.909 6.425 -3.371 1.558 C14 6D2 7 6D2 C12 C8 C 0 1 N N N 52.917 32.081 129.676 4.723 -2.203 0.221 C12 6D2 8 6D2 C8 C9 C 0 1 Y N N 50.303 37.965 126.927 -3.065 0.903 0.629 C8 6D2 9 6D2 N6 N1 N 0 1 N N N 50.917 41.249 124.213 -6.917 0.636 2.554 N6 6D2 10 6D2 N1 N2 N 0 1 Y N N 50.690 42.403 126.312 -6.667 -1.521 1.633 N1 6D2 11 6D2 N3 N3 N 0 1 Y N N 50.300 41.231 128.267 -4.802 -2.156 0.424 N3 6D2 12 6D2 ND N4 N 0 1 N N N 51.443 34.577 131.841 2.090 0.329 -0.805 ND 6D2 13 6D2 CG C10 C 0 1 N N N 52.469 34.699 132.903 2.870 1.572 -0.757 CG 6D2 14 6D2 CB C11 C 0 1 N N N 51.997 35.692 133.982 1.990 2.707 -0.231 CB 6D2 15 6D2 CA C12 C 0 1 N N S 53.088 36.139 134.991 2.790 4.011 -0.219 CA 6D2 16 6D2 C C13 C 0 1 N N N 53.781 35.004 135.676 1.890 5.150 0.186 C 6D2 17 6D2 O O1 O 0 1 N N N 55.024 34.710 135.402 1.929 5.579 1.315 O 6D2 18 6D2 N N5 N 0 1 N N N 54.130 36.878 134.400 3.897 3.897 0.740 N 6D2 19 6D2 "C5'" C14 C 0 1 N N N 51.641 35.551 130.756 1.109 0.365 -1.897 "C5'" 6D2 20 6D2 "C4'" C15 C 0 1 N N R 50.710 36.821 130.904 0.016 -0.674 -1.636 "C4'" 6D2 21 6D2 "C3'" C16 C 0 1 N N S 49.248 36.621 130.756 -0.984 -0.710 -2.813 "C3'" 6D2 22 6D2 "C2'" C17 C 0 1 N N R 48.773 37.362 129.559 -2.353 -0.941 -2.135 "C2'" 6D2 23 6D2 "O2'" O2 O 0 1 N N N 47.511 37.968 129.799 -2.932 -2.169 -2.582 "O2'" 6D2 24 6D2 "C1'" C18 C 0 1 N N R 49.952 38.359 129.349 -2.018 -1.017 -0.629 "C1'" 6D2 25 6D2 N9 N6 N 0 1 Y N N 50.131 38.756 127.977 -3.073 -0.377 0.161 N9 6D2 26 6D2 N7 N7 N 0 1 Y N N 50.510 38.713 125.824 -4.161 1.142 1.288 N7 6D2 27 6D2 "O4'" O3 O 0 1 N N N 51.122 37.605 129.773 -0.774 -0.295 -0.488 "O4'" 6D2 28 6D2 "O3'" O4 O 0 1 N N N 48.711 37.178 131.963 -0.676 -1.788 -3.699 "O3'" 6D2 29 6D2 N10 N8 N 0 1 N N N 52.845 29.402 131.301 6.569 -4.226 0.584 N10 6D2 30 6D2 N11 N9 N 0 1 N N N 51.930 28.487 129.277 7.176 -3.500 2.702 N11 6D2 31 6D2 N12 N10 N 0 1 N N N 52.442 30.806 129.189 5.523 -2.340 1.441 N12 6D2 32 6D2 OXT O5 O 0 1 N N N 53.128 34.378 136.533 1.046 5.688 -0.708 OXT 6D2 33 6D2 H112 H1 H 0 0 N N N 52.410 31.469 131.666 4.410 -0.088 0.489 H112 6D2 34 6D2 H111 H2 H 0 0 N N N 53.397 32.966 131.567 3.144 -1.115 1.204 H111 6D2 35 6D2 H102 H3 H 0 0 N N N 50.841 33.400 130.260 3.632 -0.710 -1.782 H102 6D2 36 6D2 H101 H4 H 0 0 N N N 50.566 32.713 131.897 2.366 -1.737 -1.067 H101 6D2 37 6D2 H21 H5 H 0 1 N N N 50.447 43.325 128.155 -6.402 -3.403 0.814 H21 6D2 38 6D2 H122 H6 H 0 0 N N N 54.014 32.089 129.589 4.119 -3.099 0.080 H122 6D2 39 6D2 H121 H7 H 0 0 N N N 52.493 32.867 129.034 5.385 -2.072 -0.635 H121 6D2 40 6D2 H81 H8 H 0 1 N N N 50.281 36.886 126.951 -2.268 1.615 0.473 H81 6D2 41 6D2 H61 H9 H 0 1 N N N 51.019 42.190 123.889 -6.558 1.526 2.694 H61 6D2 42 6D2 H62 H10 H 0 1 N N N 51.743 40.730 123.994 -7.783 0.398 2.921 H62 6D2 43 6D2 HG3 H12 H 0 1 N N N 52.636 33.714 133.363 3.726 1.439 -0.094 HG3 6D2 44 6D2 HG2 H13 H 0 1 N N N 53.409 35.061 132.461 3.222 1.819 -1.758 HG2 6D2 45 6D2 HB2 H14 H 0 1 N N N 51.615 36.590 133.474 1.119 2.821 -0.877 HB2 6D2 46 6D2 HB3 H15 H 0 1 N N N 51.183 35.217 134.549 1.662 2.473 0.782 HB3 6D2 47 6D2 HA H16 H 0 1 N N N 52.596 36.754 135.759 3.191 4.200 -1.215 HA 6D2 48 6D2 H H17 H 0 1 N N N 54.796 37.134 135.100 3.552 3.721 1.672 H 6D2 49 6D2 H2 H18 H 0 1 N N N 54.579 36.321 133.701 4.550 3.182 0.456 H2 6D2 50 6D2 "H5'1" H20 H 0 0 N N N 51.419 35.061 129.797 0.661 1.357 -1.951 "H5'1" 6D2 51 6D2 "H5'2" H21 H 0 0 N N N 52.691 35.880 130.765 1.607 0.139 -2.840 "H5'2" 6D2 52 6D2 "H4'1" H22 H 0 0 N N N 50.938 37.332 131.851 0.459 -1.659 -1.484 "H4'1" 6D2 53 6D2 "H3'1" H23 H 0 0 N N N 49.010 35.551 130.668 -0.976 0.238 -3.350 "H3'1" 6D2 54 6D2 "H2'1" H24 H 0 0 N N N 48.722 36.683 128.695 -3.025 -0.107 -2.338 "H2'1" 6D2 55 6D2 "H2'2" H25 H 0 0 N N N 46.852 37.293 129.915 -3.107 -2.198 -3.533 "H2'2" 6D2 56 6D2 "H1'1" H26 H 0 0 N N N 49.802 39.237 129.994 -1.889 -2.055 -0.321 "H1'1" 6D2 57 6D2 "H3'2" H27 H 0 0 N N N 49.031 36.685 132.709 -1.273 -1.858 -4.457 "H3'2" 6D2 58 6D2 H104 H28 H 0 0 N N N 52.732 28.457 131.609 7.206 -4.953 0.667 H104 6D2 59 6D2 H113 H29 H 0 0 N N N 51.892 27.611 129.757 7.813 -4.227 2.785 H113 6D2 60 6D2 H4 H30 H 0 1 N N N 51.617 28.552 128.330 7.070 -2.864 3.427 H4 6D2 61 6D2 H123 H31 H 0 0 N N N 52.105 30.782 128.248 5.416 -1.704 2.165 H123 6D2 62 6D2 H5 H32 H 0 1 N N N 53.673 33.700 136.914 0.543 6.464 -0.425 H5 6D2 63 # 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 6D2 N6 C6 SING N N 1 6D2 C6 C5 DOUB Y N 2 6D2 C6 N1 SING Y N 3 6D2 N7 C5 SING Y N 4 6D2 N7 C8 DOUB Y N 5 6D2 C5 C4 SING Y N 6 6D2 N1 C2 DOUB Y N 7 6D2 C8 N9 SING Y N 8 6D2 C4 N9 SING Y N 9 6D2 C4 N3 DOUB Y N 10 6D2 C2 N3 SING Y N 11 6D2 N9 "C1'" SING N N 12 6D2 N12 C12 SING N N 13 6D2 N12 C14 SING N N 14 6D2 N11 C14 SING N N 15 6D2 "C1'" "C2'" SING N N 16 6D2 "C1'" "O4'" SING N N 17 6D2 "C2'" "O2'" SING N N 18 6D2 "C2'" "C3'" SING N N 19 6D2 C12 C11 SING N N 20 6D2 "O4'" "C4'" SING N N 21 6D2 C14 N10 DOUB N N 22 6D2 "C3'" "C4'" SING N N 23 6D2 "C3'" "O3'" SING N N 24 6D2 "C5'" "C4'" SING N N 25 6D2 "C5'" ND SING N N 26 6D2 C11 C10 SING N N 27 6D2 C10 ND SING N N 28 6D2 ND CG SING N N 29 6D2 CG CB SING N N 30 6D2 CB CA SING N N 31 6D2 N CA SING N N 32 6D2 CA C SING N N 33 6D2 O C DOUB N N 34 6D2 C OXT SING N N 35 6D2 C11 H112 SING N N 36 6D2 C11 H111 SING N N 37 6D2 C10 H102 SING N N 38 6D2 C10 H101 SING N N 39 6D2 C2 H21 SING N N 40 6D2 C12 H122 SING N N 41 6D2 C12 H121 SING N N 42 6D2 C8 H81 SING N N 43 6D2 N6 H61 SING N N 44 6D2 N6 H62 SING N N 45 6D2 CG HG3 SING N N 46 6D2 CG HG2 SING N N 47 6D2 CB HB2 SING N N 48 6D2 CB HB3 SING N N 49 6D2 CA HA SING N N 50 6D2 N H SING N N 51 6D2 N H2 SING N N 52 6D2 "C5'" "H5'1" SING N N 53 6D2 "C5'" "H5'2" SING N N 54 6D2 "C4'" "H4'1" SING N N 55 6D2 "C3'" "H3'1" SING N N 56 6D2 "C2'" "H2'1" SING N N 57 6D2 "O2'" "H2'2" SING N N 58 6D2 "C1'" "H1'1" SING N N 59 6D2 "O3'" "H3'2" SING N N 60 6D2 N10 H104 SING N N 61 6D2 N11 H113 SING N N 62 6D2 N11 H4 SING N N 63 6D2 N12 H123 SING N N 64 6D2 OXT H5 SING N N 65 # 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 6D2 SMILES ACDLabs 12.01 "C(CN(CCC(C(O)=O)N)CC1C(O)C(O)C(O1)n3c2c(c(ncn2)N)nc3)CNC(=N)\N" 6D2 InChI InChI 1.03 "InChI=1S/C18H30N10O5/c19-9(17(31)32)2-5-27(4-1-3-23-18(21)22)6-10-12(29)13(30)16(33-10)28-8-26-11-14(20)24-7-25-15(11)28/h7-10,12-13,16,29-30H,1-6,19H2,(H,31,32)(H2,20,24,25)(H4,21,22,23)/t9-,10+,12+,13+,16+/m0/s1" 6D2 InChIKey InChI 1.03 XBMZCXWGTKEJNB-UOYPZJKHSA-N 6D2 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCN(CCCNC(N)=N)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O" 6D2 SMILES CACTVS 3.385 "N[CH](CCN(CCCNC(N)=N)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O" 6D2 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C(/N)\NCCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O" 6D2 SMILES "OpenEye OEToolkits" 2.0.4 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCNC(=N)N)CCC(C(=O)O)N)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 6D2 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl](3-carbamimidamidopropyl)amino}-5'-deoxyadenosine" 6D2 "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-(3-carbamimidamidopropyl)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 6D2 "Create component" 2016-03-16 EBI 6D2 "Initial release" 2017-03-15 RCSB #