data_N4S # _chem_comp.id N4S _chem_comp.name ;N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2'-deoxycytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C19 H37 N6 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-09-09 _chem_comp.pdbx_modified_date 2014-01-17 _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 492.507 _chem_comp.one_letter_code ? _chem_comp.three_letter_code N4S _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2MCJ _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 N4S P P P 0 1 N N N 35.962 -5.359 1.654 -7.620 -3.163 0.480 P N4S 1 N4S OP1 OP1 O 0 1 N N N 37.182 -4.682 2.148 -8.356 -3.438 1.884 OP1 N4S 2 N4S OP2 OP2 O 0 1 N N N 35.000 -4.618 0.806 -8.494 -3.602 -0.631 OP2 N4S 3 N4S "C5'" "C5'" C 0 1 N N N 37.446 -7.533 1.383 -6.762 -1.010 -0.851 "C5'" N4S 4 N4S "O5'" "O5'" O 0 1 N N N 36.412 -6.689 0.861 -7.316 -1.588 0.332 "O5'" N4S 5 N4S "C4'" "C4'" C 0 1 N N R 37.892 -8.586 0.367 -6.603 0.499 -0.655 "C4'" N4S 6 N4S "O4'" "O4'" O 0 1 N N N 36.758 -9.362 -0.047 -5.576 0.780 0.320 "O4'" N4S 7 N4S "C3'" "C3'" C 0 1 N N S 38.524 -8.010 -0.899 -6.070 1.164 -1.949 "C3'" N4S 8 N4S "O3'" "O3'" O 0 1 N N N 39.541 -8.912 -1.368 -7.143 1.492 -2.834 "O3'" N4S 9 N4S "C2'" "C2'" C 0 1 N N N 37.358 -7.966 -1.871 -5.395 2.445 -1.401 "C2'" N4S 10 N4S "C1'" "C1'" C 0 1 N N R 36.550 -9.182 -1.453 -5.133 2.127 0.088 "C1'" N4S 11 N4S N1 N1 N 0 1 N N N 35.100 -9.047 -1.676 -3.701 2.239 0.377 N1 N4S 12 N4S C2 C2 C 0 1 N N N 34.450 -10.090 -2.316 -2.833 1.393 -0.207 C2 N4S 13 N4S O2 O2 O 0 1 N N N 35.075 -11.082 -2.682 -3.249 0.539 -0.972 O2 N4S 14 N4S N3 N3 N 0 1 N N N 33.116 -9.980 -2.525 -1.526 1.472 0.038 N3 N4S 15 N4S C4 C4 C 0 1 N N N 32.438 -8.898 -2.128 -1.046 2.391 0.866 C4 N4S 16 N4S N4 N4 N 0 1 N N N 31.135 -8.847 -2.356 0.305 2.464 1.110 N4 N4S 17 N4S C5 C5 C 0 1 N N N 33.104 -7.816 -1.469 -1.930 3.292 1.494 C5 N4S 18 N4S C6 C6 C 0 1 N N N 34.428 -7.933 -1.264 -3.255 3.202 1.231 C6 N4S 19 N4S CA CA C 0 1 N N N 30.328 -7.668 -1.936 1.220 1.525 0.455 CA N4S 20 N4S CB CB C 0 1 N N N 29.093 -7.531 -2.835 2.655 1.820 0.896 CB N4S 21 N4S CC CC C 0 1 N N N 29.515 -7.034 -4.226 3.610 0.840 0.211 CC N4S 22 N4S CE CE C 0 1 N N N 28.580 -6.367 -6.374 5.935 0.199 -0.004 CE N4S 23 N4S CF CF C 0 1 N N N 27.943 -4.989 -6.094 7.356 0.525 0.459 CF N4S 24 N4S CG CG C 0 1 N N N 26.484 -4.964 -6.588 8.343 -0.437 -0.206 CG N4S 25 N4S CH CH C 0 1 N N N 25.741 -3.738 -6.014 9.764 -0.112 0.258 CH N4S 26 N4S CJ CJ C 0 1 N N N 25.154 -1.420 -6.490 12.089 -0.752 0.042 CJ N4S 27 N4S CK CK C 0 1 N N N 23.742 -1.429 -5.868 13.044 -1.733 -0.642 CK N4S 28 N4S CL CL C 0 1 N N N 23.309 0.004 -5.504 14.479 -1.438 -0.202 CL N4S 29 N4S ND ND N 0 1 N N N 28.422 -7.259 -5.201 4.988 1.123 0.634 ND N4S 30 N4S NI NI N 0 1 N N N 25.473 -2.743 -7.082 10.711 -1.036 -0.380 NI N4S 31 N4S NM NM N 0 1 N N N 22.132 -0.029 -4.612 15.396 -2.379 -0.858 NM N4S 32 N4S H1 H1 H 0 1 N N N 37.196 -3.785 1.834 -8.570 -4.368 2.041 H1 N4S 33 N4S "H5''" "H5''" H 0 0 N N N 37.068 -8.043 2.281 -5.787 -1.455 -1.051 "H5''" N4S 34 N4S "H5'" "H5'" H 0 1 N N N 38.312 -6.910 1.652 -7.428 -1.199 -1.694 "H5'" N4S 35 N4S "H4'" "H4'" H 0 1 N N N 38.629 -9.243 0.852 -7.550 0.948 -0.355 "H4'" N4S 36 N4S "H3'" "H3'" H 0 1 N N N 38.919 -7.000 -0.713 -5.341 0.523 -2.445 "H3'" N4S 37 N4S H3 H3 H 0 1 N N N 40.261 -8.927 -0.749 -6.860 1.911 -3.658 H3 N4S 38 N4S "H2''" "H2''" H 0 0 N N N 37.702 -8.054 -2.912 -4.456 2.635 -1.921 "H2''" N4S 39 N4S "H2'" "H2'" H 0 1 N N N 36.776 -7.040 -1.754 -6.064 3.300 -1.497 "H2'" N4S 40 N4S "H1'" "H1'" H 0 1 N N N 36.923 -10.059 -2.002 -5.695 2.816 0.718 "H1'" N4S 41 N4S H41 H41 H 0 1 N N N 30.686 -9.612 -2.817 0.653 3.136 1.717 H41 N4S 42 N4S H5 H5 H 0 1 N N N 32.563 -6.938 -1.148 -1.555 4.046 2.171 H5 N4S 43 N4S H6 H6 H 0 1 N N N 34.965 -7.138 -0.768 -3.952 3.884 1.696 H6 N4S 44 N4S HA2 HA2 H 0 1 N N N 30.941 -6.759 -2.018 0.956 0.505 0.736 HA2 N4S 45 N4S HA1 HA1 H 0 1 N N N 30.006 -7.800 -0.892 1.141 1.636 -0.626 HA1 N4S 46 N4S HB1 HB1 H 0 1 N N N 28.393 -6.811 -2.387 2.919 2.840 0.615 HB1 N4S 47 N4S HB2 HB2 H 0 1 N N N 28.601 -8.510 -2.931 2.734 1.709 1.977 HB2 N4S 48 N4S HC2 HC2 H 0 1 N N N 30.411 -7.582 -4.552 3.346 -0.180 0.492 HC2 N4S 49 N4S HC1 HC1 H 0 1 N N N 29.741 -5.959 -4.175 3.532 0.951 -0.870 HC1 N4S 50 N4S HE2 HE2 H 0 1 N N N 28.087 -6.823 -7.245 5.873 0.306 -1.087 HE2 N4S 51 N4S HE1 HE1 H 0 1 N N N 29.651 -6.234 -6.586 5.688 -0.825 0.275 HE1 N4S 52 N4S HF2 HF2 H 0 1 N N N 28.517 -4.211 -6.618 7.604 1.549 0.181 HF2 N4S 53 N4S HF1 HF1 H 0 1 N N N 27.963 -4.793 -5.012 7.419 0.418 1.542 HF1 N4S 54 N4S HG1 HG1 H 0 1 N N N 26.474 -4.912 -7.687 8.095 -1.462 0.073 HG1 N4S 55 N4S HG2 HG2 H 0 1 N N N 25.975 -5.882 -6.260 8.280 -0.331 -1.289 HG2 N4S 56 N4S HH1 HH1 H 0 1 N N N 26.361 -3.273 -5.233 10.012 0.912 -0.021 HH1 N4S 57 N4S HH2 HH2 H 0 1 N N N 24.786 -4.066 -5.577 9.826 -0.219 1.341 HH2 N4S 58 N4S HJ2 HJ2 H 0 1 N N N 25.892 -1.186 -5.708 12.167 -0.864 1.124 HJ2 N4S 59 N4S HJ1 HJ1 H 0 1 N N N 25.198 -0.652 -7.276 12.353 0.267 -0.238 HJ1 N4S 60 N4S HK1 HK1 H 0 1 N N N 23.029 -1.851 -6.592 12.780 -2.752 -0.361 HK1 N4S 61 N4S HK2 HK2 H 0 1 N N N 23.750 -2.048 -4.959 12.966 -1.621 -1.723 HK2 N4S 62 N4S HL2 HL2 H 0 1 N N N 24.138 0.515 -4.993 14.743 -0.418 -0.482 HL2 N4S 63 N4S HL1 HL1 H 0 1 N N N 23.053 0.551 -6.424 14.558 -1.549 0.880 HL1 N4S 64 N4S HD1 HD1 H 0 1 N N N 27.544 -7.071 -4.760 5.072 1.090 1.639 HD1 N4S 65 N4S HI1 HI1 H 0 1 N N N 24.698 -3.052 -7.633 10.627 -1.002 -1.385 HI1 N4S 66 N4S HM3 HM3 H 0 1 N N N 21.861 0.906 -4.383 15.296 -2.341 -1.862 HM3 N4S 67 N4S HM2 HM2 H 0 1 N N N 21.376 -0.492 -5.075 16.351 -2.204 -0.584 HM2 N4S 68 N4S OP3 OP3 O 0 1 N Y N ? ? ? -6.235 -3.983 0.430 OP3 N4S 69 N4S H7 H7 H 0 1 N Y N ? ? ? -5.612 -3.746 1.130 H7 N4S 70 # 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 N4S NI CJ SING N N 1 N4S NI CH SING N N 2 N4S CG CF SING N N 3 N4S CG CH SING N N 4 N4S CJ CK SING N N 5 N4S CE CF SING N N 6 N4S CE ND SING N N 7 N4S CK CL SING N N 8 N4S CL NM SING N N 9 N4S ND CC SING N N 10 N4S CC CB SING N N 11 N4S CB CA SING N N 12 N4S O2 C2 DOUB N N 13 N4S N3 C2 SING N N 14 N4S N3 C4 DOUB N N 15 N4S N4 C4 SING N N 16 N4S N4 CA SING N N 17 N4S C2 N1 SING N N 18 N4S C4 C5 SING N N 19 N4S "C2'" "C1'" SING N N 20 N4S "C2'" "C3'" SING N N 21 N4S N1 "C1'" SING N N 22 N4S N1 C6 SING N N 23 N4S C5 C6 DOUB N N 24 N4S "C1'" "O4'" SING N N 25 N4S "O3'" "C3'" SING N N 26 N4S "C3'" "C4'" SING N N 27 N4S "O4'" "C4'" SING N N 28 N4S "C4'" "C5'" SING N N 29 N4S OP2 P DOUB N N 30 N4S "O5'" "C5'" SING N N 31 N4S "O5'" P SING N N 32 N4S P OP1 SING N N 33 N4S OP1 H1 SING N N 34 N4S "C5'" "H5''" SING N N 35 N4S "C5'" "H5'" SING N N 36 N4S "C4'" "H4'" SING N N 37 N4S "C3'" "H3'" SING N N 38 N4S "O3'" H3 SING N N 39 N4S "C2'" "H2''" SING N N 40 N4S "C2'" "H2'" SING N N 41 N4S "C1'" "H1'" SING N N 42 N4S N4 H41 SING N N 43 N4S C5 H5 SING N N 44 N4S C6 H6 SING N N 45 N4S CA HA2 SING N N 46 N4S CA HA1 SING N N 47 N4S CB HB1 SING N N 48 N4S CB HB2 SING N N 49 N4S CC HC2 SING N N 50 N4S CC HC1 SING N N 51 N4S CE HE2 SING N N 52 N4S CE HE1 SING N N 53 N4S CF HF2 SING N N 54 N4S CF HF1 SING N N 55 N4S CG HG1 SING N N 56 N4S CG HG2 SING N N 57 N4S CH HH1 SING N N 58 N4S CH HH2 SING N N 59 N4S CJ HJ2 SING N N 60 N4S CJ HJ1 SING N N 61 N4S CK HK1 SING N N 62 N4S CK HK2 SING N N 63 N4S CL HL2 SING N N 64 N4S CL HL1 SING N N 65 N4S ND HD1 SING N N 66 N4S NI HI1 SING N N 67 N4S NM HM3 SING N N 68 N4S NM HM2 SING N N 69 N4S P OP3 SING N N 70 N4S OP3 H7 SING N N 71 # 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 N4S SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)N=C(NCCCNCCCCNCCCN)C=C1)CC2O" N4S InChI InChI 1.03 "InChI=1S/C19H37N6O7P/c20-6-3-9-21-7-1-2-8-22-10-4-11-23-17-5-12-25(19(27)24-17)18-13-15(26)16(32-18)14-31-33(28,29)30/h5,12,15-16,18,21-22,26H,1-4,6-11,13-14,20H2,(H,23,24,27)(H2,28,29,30)/t15-,16+,18+/m0/s1" N4S InChIKey InChI 1.03 BLNZPBQNKBWMDS-LZLYRXPVSA-N N4S SMILES_CANONICAL CACTVS 3.385 "NCCCNCCCCNCCCNC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2" N4S SMILES CACTVS 3.385 "NCCCNCCCCNCCCNC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2" N4S SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)NCCCNCCCCNCCCN)COP(=O)(O)O)O" N4S SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=NC2=O)NCCCNCCCCNCCCN)COP(=O)(O)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 N4S "SYSTEMATIC NAME" ACDLabs 12.01 ;N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2'-deoxycytidine 5'-(dihydrogen phosphate) ; N4S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[4-[3-[4-(3-azanylpropylamino)butylamino]propylamino]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site N4S "Create component" 2013-09-09 RCSB N4S "Initial release" 2014-01-22 RCSB #