data_A1EFN
# 
_chem_comp.id                                    A1EFN 
_chem_comp.name                                  "[(2R,3S,5R)-5-[6-azanylidene-1-(phenylmethyl)purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C17 H20 N5 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-12 
_chem_comp.pdbx_modified_date                    2025-09-12 
_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                        421.344 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     A1EFN 
_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        9KFV 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1EFN C7     C1  C 0 1 Y N N N N N 5.689  -22.057 -6.786 -6.004 1.404  -0.431 C7    A1EFN 1  
A1EFN C9     C2  C 0 1 Y N N N N N 4.970  -22.368 -7.957 -6.315 2.395  0.481  C9    A1EFN 2  
A1EFN N1     N1  N 0 1 N N N N N N 7.935  -19.991 -5.318 -4.101 -1.145 -1.092 N1    A1EFN 3  
A1EFN C2     C3  C 0 1 N N N N N N 8.473  -20.058 -6.563 -3.376 -0.414 -1.986 C2    A1EFN 4  
A1EFN C10    C4  C 0 1 Y N N N N N 4.354  -21.327 -8.694 -6.509 2.074  1.812  C10   A1EFN 5  
A1EFN C4     C5  C 0 1 Y N N N N N 10.464 -19.213 -5.668 -1.441 -0.668 -0.787 C4    A1EFN 6  
A1EFN N3     N2  N 0 1 N N N N N N 9.758  -19.657 -6.724 -2.104 -0.146 -1.835 N3    A1EFN 7  
A1EFN C6     C6  C 0 1 N N N N N N 8.612  -19.558 -4.274 -3.432 -2.042 -0.254 C6    A1EFN 8  
A1EFN C1     C7  C 0 1 N N N N N N 6.551  -20.400 -5.058 -5.555 -0.990 -1.008 C1    A1EFN 9  
A1EFN "C1'"  C8  C 0 1 N N R N N N 12.467 -18.753 -6.653 0.827  0.422  -0.821 "C1'" A1EFN 10 
A1EFN C11    C9  C 0 1 Y N N N N N 4.451  -19.982 -8.260 -6.393 0.761  2.230  C11   A1EFN 11 
A1EFN C12    C10 C 0 1 Y N N N N N 5.155  -19.673 -7.084 -6.083 -0.230 1.318  C12   A1EFN 12 
A1EFN "C2'"  C11 C 0 1 N N N N N N 13.202 -17.434 -6.740 0.675  1.829  -0.203 "C2'" A1EFN 13 
A1EFN C3     C12 C 0 1 Y N N N N N 5.783  -20.721 -6.356 -5.888 0.091  -0.013 C3    A1EFN 14 
A1EFN "C3'"  C13 C 0 1 N N S N N N 14.582 -17.809 -7.103 2.129  2.319  -0.021 "C3'" A1EFN 15 
A1EFN "C4'"  C14 C 0 1 N N R N N N 14.787 -19.132 -6.543 2.988  1.148  -0.550 "C4'" A1EFN 16 
A1EFN C5     C15 C 0 1 Y N N N N N 9.902  -19.156 -4.422 -2.051 -1.622 0.043  C5    A1EFN 17 
A1EFN "C5'"  C16 C 0 1 N N N N N N 15.096 -18.887 -5.108 4.251  0.988  0.299  "C5'" A1EFN 18 
A1EFN C8     C17 C 0 1 Y N N N N N 12.001 -18.458 -4.386 -0.062 -1.297 0.798  C8    A1EFN 19 
A1EFN N6     N3  N 0 1 N N N N N N 7.934  -19.534 -2.973 -3.976 -3.138 0.219  N6    A1EFN 20 
A1EFN N7     N4  N 0 1 Y N N N N N 10.932 -18.650 -3.542 -1.171 -1.965 0.985  N7    A1EFN 21 
A1EFN N9     N5  N 0 1 Y N N N N N 11.605 -18.806 -5.497 -0.195 -0.482 -0.287 N9    A1EFN 22 
A1EFN "O3'"  O1  O 0 1 N N N N N N 14.673 -17.940 -8.533 2.361  3.499  -0.792 "O3'" A1EFN 23 
A1EFN "O4'"  O2  O 0 1 N N N N N N 13.490 -19.847 -6.651 2.144  -0.016 -0.421 "O4'" A1EFN 24 
A1EFN "O5'"  O3  O 0 1 N N N N N N 15.587 -20.073 -4.579 5.085  -0.020 -0.275 "O5'" A1EFN 25 
A1EFN OP3    O4  O 0 1 N Y N N N N 17.984 -19.484 -3.667 7.223  -1.513 -0.614 OP1   A1EFN 26 
A1EFN OP1    O5  O 0 1 N N N N N N 17.793 -20.055 -6.231 7.359  0.744  0.510  OP2   A1EFN 27 
A1EFN P      P1  P 0 1 N N N N N N 17.218 -20.230 -4.692 6.501  -0.452 0.359  P     A1EFN 28 
A1EFN OP2    O6  O 0 1 N N N N N N 17.454 -21.781 -4.359 6.259  -1.125 1.801  O1    A1EFN 29 
A1EFN H1     H1  H 0 1 N N N N N N 6.167  -22.843 -6.220 -5.856 1.654  -1.471 H1    A1EFN 30 
A1EFN H3     H2  H 0 1 N N N N N N 4.889  -23.392 -8.290 -6.405 3.420  0.155  H2    A1EFN 31 
A1EFN H2     H3  H 0 1 N N N N N N 7.894  -20.420 -7.400 -3.878 -0.037 -2.865 H3    A1EFN 32 
A1EFN H4     H4  H 0 1 N N N N N N 3.806  -21.561 -9.595 -6.751 2.848  2.524  H4    A1EFN 33 
A1EFN H5     H5  H 0 1 N N N N N N 6.033  -19.584 -4.533 -5.949 -0.716 -1.987 H5    A1EFN 34 
A1EFN H6     H6  H 0 1 N N N N N N 6.561  -21.297 -4.421 -6.003 -1.930 -0.686 H6    A1EFN 35 
A1EFN "H1'"  H7  H 0 1 N N N N N N 11.853 -18.860 -7.560 0.757  0.473  -1.907 H7    A1EFN 36 
A1EFN H7     H8  H 0 1 N N N N N N 3.984  -19.194 -8.833 -6.544 0.510  3.270  H8    A1EFN 37 
A1EFN H9     H9  H 0 1 N N N N N N 5.218  -18.652 -6.737 -5.992 -1.255 1.645  H9    A1EFN 38 
A1EFN "H2'"  H10 H 0 1 N N N N N N 13.182 -16.912 -5.772 0.133  2.488  -0.881 H10   A1EFN 39 
A1EFN "H2''" H11 H 0 1 N N N N N N 12.757 -16.790 -7.513 0.166  1.771  0.760  H11   A1EFN 40 
A1EFN "H3'"  H12 H 0 1 N N N N N N 15.310 -17.084 -6.710 2.342  2.502  1.033  H12   A1EFN 41 
A1EFN "H4'"  H13 H 0 1 N N N N N N 15.598 -19.678 -7.047 3.252  1.314  -1.594 H13   A1EFN 42 
A1EFN "H5'"  H14 H 0 1 N N N N N N 15.852 -18.093 -5.017 4.791  1.934  0.328  H14   A1EFN 43 
A1EFN "H5''" H15 H 0 1 N N N N N N 14.183 -18.587 -4.573 3.973  0.696  1.312  H15   A1EFN 44 
A1EFN H8     H16 H 0 1 N N N N N N 12.980 -18.082 -4.128 0.823  -1.377 1.412  H16   A1EFN 45 
A1EFN H61    H17 H 0 1 N N N N N N 8.531  -19.195 -2.246 -3.463 -3.724 0.798  H17   A1EFN 46 
A1EFN "HO3'" H19 H 0 1 N N N N N N 15.560 -18.182 -8.774 1.804  4.248  -0.541 H19   A1EFN 47 
A1EFN HOP3   H20 H 0 1 N Y N N N N 18.699 -19.017 -4.083 8.083  -1.817 -0.294 H20   A1EFN 48 
A1EFN HOP2   H21 H 0 1 N N N N N N 17.855 -22.208 -5.107 5.704  -1.916 1.778  H21   A1EFN 49 
# 
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 
A1EFN C10   C11    DOUB Y N 1  
A1EFN C10   C9     SING Y N 2  
A1EFN "O3'" "C3'"  SING N N 3  
A1EFN C11   C12    SING Y N 4  
A1EFN C9    C7     DOUB Y N 5  
A1EFN "C3'" "C2'"  SING N N 6  
A1EFN "C3'" "C4'"  SING N N 7  
A1EFN C12   C3     DOUB Y N 8  
A1EFN C7    C3     SING Y N 9  
A1EFN "C2'" "C1'"  SING N N 10 
A1EFN N3    C2     DOUB N N 11 
A1EFN N3    C4     SING N N 12 
A1EFN "C1'" "O4'"  SING N N 13 
A1EFN "C1'" N9     SING N N 14 
A1EFN "O4'" "C4'"  SING N N 15 
A1EFN C2    N1     SING N N 16 
A1EFN "C4'" "C5'"  SING N N 17 
A1EFN C3    C1     SING N N 18 
A1EFN OP1   P      DOUB N N 19 
A1EFN C4    N9     SING Y N 20 
A1EFN C4    C5     DOUB Y N 21 
A1EFN N9    C8     SING Y N 22 
A1EFN N1    C1     SING N N 23 
A1EFN N1    C6     SING N N 24 
A1EFN "C5'" "O5'"  SING N N 25 
A1EFN P     "O5'"  SING N N 26 
A1EFN P     OP3    SING N N 27 
A1EFN C5    C6     SING N N 28 
A1EFN C5    N7     SING Y N 29 
A1EFN C8    N7     DOUB Y N 30 
A1EFN C6    N6     DOUB N N 31 
A1EFN P     OP2    SING N N 32 
A1EFN C7    H1     SING N N 33 
A1EFN C9    H3     SING N N 34 
A1EFN C2    H2     SING N N 35 
A1EFN C10   H4     SING N N 36 
A1EFN C1    H5     SING N N 37 
A1EFN C1    H6     SING N N 38 
A1EFN "C1'" "H1'"  SING N N 39 
A1EFN C11   H7     SING N N 40 
A1EFN C12   H9     SING N N 41 
A1EFN "C2'" "H2'"  SING N N 42 
A1EFN "C2'" "H2''" SING N N 43 
A1EFN "C3'" "H3'"  SING N N 44 
A1EFN "C4'" "H4'"  SING N N 45 
A1EFN "C5'" "H5'"  SING N N 46 
A1EFN "C5'" "H5''" SING N N 47 
A1EFN C8    H8     SING N N 48 
A1EFN N6    H61    SING N N 49 
A1EFN "O3'" "HO3'" SING N N 50 
A1EFN OP3   HOP3   SING N N 51 
A1EFN OP2   HOP2   SING N N 52 
# 
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 
A1EFN InChI            InChI                1.06  "InChI=1S/C17H20N5O6P/c18-16-15-17(20-9-21(16)7-11-4-2-1-3-5-11)22(10-19-15)14-6-12(23)13(28-14)8-27-29(24,25)26/h1-5,9-10,12-14,18,23H,6-8H2,(H2,24,25,26)/b18-16-/t12-,13+,14+/m0/s1" 
A1EFN InChIKey         InChI                1.06  VOTNTSLRIQPLTA-IFMMWNIESA-N                                                                                                                                                             
A1EFN SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=N)N(Cc4ccccc4)C=Nc23"                                                                                                                    
A1EFN SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=N)N(Cc4ccccc4)C=Nc23"                                                                                                                         
A1EFN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C\1/c2c(n(cn2)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=CN1Cc4ccccc4"                                                                                                               
A1EFN SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)CN2C=Nc3c(ncn3C4CC(C(O4)COP(=O)(O)O)O)C2=N"                                                                                                                                  
# 
_pdbx_chem_comp_identifier.comp_id           A1EFN 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[(2~{R},3~{S},5~{R})-5-[6-azanylidene-1-(phenylmethyl)purin-9-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 
A1EFN "Create component"   2024-11-12 PDBC 
A1EFN "Other modification" 2024-11-29 PDBC 
A1EFN "Initial release"    2025-09-17 RCSB 
# 
