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 
# 
