data_8PI
# 
_chem_comp.id                                    8PI 
_chem_comp.name                                  "1-{[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]amino}-1,2-dideoxy-5-O-phosphono-D-erythro-pentitol" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C10 H18 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-09-23 
_chem_comp.pdbx_modified_date                    2022-07-29 
_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                        367.252 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     8PI 
_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        7S9L 
_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 
8PI "C1'" C1  C 0 1 N N N 19.546 27.959 22.007 -0.983 -0.425 -0.055 "C1'" 8PI 1  
8PI C2    C2  C 0 1 N N N 17.786 29.488 18.948 -4.707 -2.139 -0.092 C2    8PI 2  
8PI "C2'" C3  C 0 1 N N N 20.688 27.338 22.770 0.241  0.494  -0.064 "C2'" 8PI 3  
8PI "C3'" C4  C 0 1 N N S 20.879 27.976 24.103 1.513  -0.350 0.034  "C3'" 8PI 4  
8PI C4    C5  C 0 1 N N N 17.638 28.726 21.354 -3.410 -0.218 -0.157 C4    8PI 5  
8PI "C4'" C6  C 0 1 N N R 20.298 27.010 25.125 2.738  0.557  -0.101 "C4'" 8PI 6  
8PI C5    C7  C 0 1 N N S 16.208 29.078 21.435 -4.691 0.591  -0.253 C5    8PI 7  
8PI "C5'" C8  C 0 1 N N N 18.783 27.145 25.240 4.011  -0.287 -0.004 "C5'" 8PI 8  
8PI C6    C9  C 0 1 N N N 15.587 29.658 20.217 -5.982 -0.207 -0.254 C6    8PI 9  
8PI C8    C10 C 0 1 N N N 15.122 29.981 23.486 -5.444 2.661  0.789  C8    8PI 10 
8PI N1    N1  N 0 1 N N N 16.353 29.856 19.004 -5.878 -1.533 -0.171 N1    8PI 11 
8PI N2    N2  N 0 1 N N N 18.602 29.678 17.770 -4.708 -3.505 -0.017 N2    8PI 12 
8PI N3    N3  N 0 1 N N N 18.392 28.932 20.150 -3.524 -1.525 -0.084 N3    8PI 13 
8PI N7    N4  N 0 1 N N N 15.461 28.856 22.651 -4.729 1.521  0.878  N7    8PI 14 
8PI N9    N5  N 0 1 N N N 18.395 28.146 22.428 -2.201 0.383  -0.148 N9    8PI 15 
8PI "O3'" O1  O 0 1 N N N 22.264 28.133 24.250 1.549  -1.014 1.298  "O3'" 8PI 16 
8PI "O4'" O2  O 0 1 N N N 20.562 25.731 24.608 2.703  1.221  -1.366 "O4'" 8PI 17 
8PI "O5'" O3  O 0 1 N N N 18.300 26.669 26.444 5.153  0.571  -0.012 "O5'" 8PI 18 
8PI O6    O4  O 0 1 N N N 14.452 29.968 20.222 -7.065 0.340  -0.326 O6    8PI 19 
8PI O8    O5  O 0 1 N N N 15.462 31.063 23.142 -6.054 2.916  -0.228 O8    8PI 20 
8PI OP1   O6  O 0 1 N N N 19.494 24.376 26.785 6.809  -0.831 1.278  OP1   8PI 21 
8PI OP2   O7  O 0 1 N N N 17.341 24.816 27.869 6.997  -0.846 -1.239 OP2   8PI 22 
8PI P     P1  P 0 1 N N N 18.152 25.054 26.628 6.664  0.021  0.076  P     8PI 23 
8PI H1    H1  H 0 1 N N N 19.425 27.331 21.112 -0.932 -1.106 -0.904 H1    8PI 24 
8PI H2    H2  H 0 1 N N N 19.908 28.955 21.711 -0.998 -1.000 0.871  H2    8PI 25 
8PI H3    H3  H 0 1 N N N 20.478 26.268 22.915 0.256  1.069  -0.990 H3    8PI 26 
8PI H4    H4  H 0 1 N N N 21.612 27.455 22.184 0.190  1.174  0.786  H4    8PI 27 
8PI H5    H5  H 0 1 N N N 20.350 28.939 24.149 1.520  -1.091 -0.766 H5    8PI 28 
8PI H6    H6  H 0 1 N N N 20.769 27.164 26.107 2.731  1.297  0.698  H6    8PI 29 
8PI H7    H7  H 0 1 N N N 16.475 30.087 21.781 -4.656 1.176  -1.171 H7    8PI 30 
8PI H8    H8  H 0 1 N N N 18.515 28.208 25.148 3.995  -0.862 0.922  H8    8PI 31 
8PI H9    H9  H 0 1 N N N 18.315 26.577 24.423 4.061  -0.968 -0.853 H9    8PI 32 
8PI H10   H10 H 0 1 N N N 14.571 29.841 24.404 -5.472 3.347  1.622  H10   8PI 33 
8PI H11   H11 H 0 1 N N N 18.202 30.074 16.943 -5.548 -3.990 -0.024 H11   8PI 34 
8PI H12   H12 H 0 1 N N N 19.566 29.413 17.782 -3.869 -3.988 0.043  H12   8PI 35 
8PI H13   H13 H 0 1 N N N 15.182 27.932 22.911 -4.241 1.317  1.691  H13   8PI 36 
8PI H14   H14 H 0 1 N N N 18.057 27.933 23.345 -2.139 1.349  -0.203 H14   8PI 37 
8PI H15   H15 H 0 1 N Y N 22.450 28.539 25.089 1.545  -0.415 2.057  H15   8PI 38 
8PI H16   H16 H 0 1 N N N 20.262 25.072 25.223 2.707  0.621  -2.125 H16   8PI 39 
8PI H18   H18 H 0 1 N N N 17.845 24.293 28.482 6.922  -0.350 -2.066 H18   8PI 40 
8PI OP3   O8  O 0 1 N Y N 17.493 24.381 25.391 7.683  1.264  0.173  O1    8PI 41 
8PI H17   H17 H 0 1 N N N 18.079 23.721 25.040 8.613  1.006  0.229  H17   8PI 42 
# 
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 
8PI N2    C2    SING N N 1  
8PI C2    N1    DOUB N N 2  
8PI C2    N3    SING N N 3  
8PI N1    C6    SING N N 4  
8PI N3    C4    DOUB N N 5  
8PI C6    O6    DOUB N N 6  
8PI C6    C5    SING N N 7  
8PI C4    C5    SING N N 8  
8PI C4    N9    SING N N 9  
8PI C5    N7    SING N N 10 
8PI "C1'" N9    SING N N 11 
8PI "C1'" "C2'" SING N N 12 
8PI N7    C8    SING N N 13 
8PI "C2'" "C3'" SING N N 14 
8PI O8    C8    DOUB N N 15 
8PI "C3'" "O3'" SING N N 16 
8PI "C3'" "C4'" SING N N 17 
8PI "O4'" "C4'" SING N N 18 
8PI "C4'" "C5'" SING N N 19 
8PI "C5'" "O5'" SING N N 20 
8PI "O5'" P     SING N N 21 
8PI P     OP1   DOUB N N 22 
8PI P     OP2   SING N N 23 
8PI "C1'" H1    SING N N 24 
8PI "C1'" H2    SING N N 25 
8PI "C2'" H3    SING N N 26 
8PI "C2'" H4    SING N N 27 
8PI "C3'" H5    SING N N 28 
8PI "C4'" H6    SING N N 29 
8PI C5    H7    SING N N 30 
8PI "C5'" H8    SING N N 31 
8PI "C5'" H9    SING N N 32 
8PI C8    H10   SING N N 33 
8PI N2    H11   SING N N 34 
8PI N2    H12   SING N N 35 
8PI N7    H13   SING N N 36 
8PI N9    H14   SING N N 37 
8PI "O3'" H15   SING N N 38 
8PI "O4'" H16   SING N N 39 
8PI OP2   H18   SING N N 40 
8PI P     OP3   SING N N 41 
8PI OP3   H17   SING N N 42 
# 
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 
8PI SMILES           ACDLabs              12.01 "O=C1N=C(N)N=C(NCCC(O)C(O)COP(=O)(O)O)C1NC=O"                                                                                                                         
8PI InChI            InChI                1.03  "InChI=1S/C10H18N5O8P/c11-10-14-8(7(13-4-16)9(19)15-10)12-2-1-5(17)6(18)3-23-24(20,21)22/h4-7,17-18H,1-3H2,(H,13,16)(H2,20,21,22)(H3,11,12,14,15,19)/t5-,6+,7-/m0/s1" 
8PI InChIKey         InChI                1.03  UQQLUYQUTNSKKT-XVMARJQXSA-N                                                                                                                                           
8PI SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)[C@@H](NC=O)C(=N1)NCC[C@H](O)[C@H](O)CO[P](O)(O)=O"                                                                                                        
8PI SMILES           CACTVS               3.385 "NC1=NC(=O)[CH](NC=O)C(=N1)NCC[CH](O)[CH](O)CO[P](O)(O)=O"                                                                                                            
8PI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C(CNC1=NC(=NC(=O)C1NC=O)N)[C@@H]([C@@H](COP(=O)(O)O)O)O"                                                                                                             
8PI SMILES           "OpenEye OEToolkits" 2.0.7 "C(CNC1=NC(=NC(=O)C1NC=O)N)C(C(COP(=O)(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 
8PI "SYSTEMATIC NAME" ACDLabs              12.01 "1-{[(5S)-2-amino-5-formamido-6-oxo-5,6-dihydropyrimidin-4-yl]amino}-1,2-dideoxy-5-O-phosphono-D-erythro-pentitol"                  
8PI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S})-5-[(2-azanyl-5-formamido-6-oxidanylidene-5~{H}-pyrimidin-4-yl)amino]-2,3-bis(oxidanyl)pentyl] 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 
8PI "Create component" 2021-09-23 RCSB 
8PI "Initial release"  2022-08-03 RCSB 
# 
