data_L3X
# 
_chem_comp.id                                    L3X 
_chem_comp.name                                  
;3'-deoxy-3'-(glycylamino)adenosine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA OH 3 prime terminus" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H18 N7 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-02-25 
_chem_comp.pdbx_modified_date                    2022-07-08 
_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                        403.288 
_chem_comp.one_letter_code                       A 
_chem_comp.three_letter_code                     L3X 
_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        7U2H 
_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 
L3X P     P1  P 0 1 N N N 90.972 -48.906 0.024  -4.474 -2.275 0.039  P     L3X 1  
L3X OP1   O1  O 0 1 N N N 91.582 -49.569 -1.152 -4.182 -2.885 -1.278 OP1   L3X 2  
L3X OP2   O2  O 0 1 N N N 90.905 -47.429 0.097  -4.760 -3.436 1.117  OP2   L3X 3  
L3X "C1'" C1  C 0 1 N N R 85.980 -48.885 1.025  0.844  0.057  0.505  "C1'" L3X 4  
L3X "C2'" C2  C 0 1 N N R 85.285 -49.171 -0.290 0.562  1.119  -0.589 "C2'" L3X 5  
L3X "O2'" O3  O 0 1 N N N 84.471 -50.297 -0.027 1.401  2.262  -0.417 "O2'" L3X 6  
L3X "C3'" C3  C 0 1 N N S 86.425 -49.560 -1.213 -0.921 1.476  -0.319 "C3'" L3X 7  
L3X "N3'" N1  N 0 1 N N N 86.060 -50.460 -2.328 -1.019 2.699  0.481  "N3'" L3X 8  
L3X "C4'" C4  C 0 1 N N S 87.351 -50.312 -0.292 -1.462 0.269  0.471  "C4'" L3X 9  
L3X "O4'" O4  O 0 1 N N N 87.208 -49.679 1.017  -0.392 -0.686 0.584  "O4'" L3X 10 
L3X "C5'" C5  C 0 1 N N N 88.774 -50.100 -0.772 -2.642 -0.356 -0.277 "C5'" L3X 11 
L3X "O5'" O5  O 0 1 N N N 89.504 -49.492 0.278  -3.211 -1.399 0.517  "O5'" L3X 12 
L3X N9    N2  N 0 1 Y N N 86.295 -47.418 1.184  1.947  -0.819 0.101  N9    L3X 13 
L3X C8    C6  C 0 1 Y N N 87.165 -46.696 0.468  1.834  -2.007 -0.557 C8    L3X 14 
L3X N7    N3  N 0 1 Y N N 87.144 -45.442 0.900  3.014  -2.518 -0.756 N7    L3X 15 
L3X C6    C7  C 0 1 Y N N 85.847 -44.319 2.614  5.359  -1.722 -0.159 C6    L3X 16 
L3X N6    N4  N 0 1 N N N 86.372 -43.108 2.409  6.077  -2.781 -0.688 N6    L3X 17 
L3X C5    C8  C 0 1 Y N N 86.257 -45.355 1.857  3.956  -1.693 -0.239 C5    L3X 18 
L3X C4    C9  C 0 1 Y N N 85.703 -46.555 2.045  3.283  -0.590 0.312  C4    L3X 19 
L3X N3    N5  N 0 1 Y N N 84.757 -46.729 2.970  3.991  0.379  0.883  N3    L3X 20 
L3X C2    C10 C 0 1 Y N N 84.363 -45.699 3.732  5.304  0.312  0.931  C2    L3X 21 
L3X N1    N6  N 0 1 Y N N 84.908 -44.492 3.552  5.981  -0.702 0.424  N1    L3X 22 
L3X C     C11 C 0 1 N N N 86.865 -50.658 -3.409 -1.091 3.899  -0.128 C     L3X 23 
L3X O     O6  O 0 1 N N N 87.919 -50.046 -3.623 -1.075 3.966  -1.339 O     L3X 24 
L3X CA    C12 C 0 1 N N N 86.374 -51.742 -4.385 -1.192 5.157  0.696  CA    L3X 25 
L3X N     N7  N 0 1 N N N 86.675 -51.469 -5.811 -1.258 6.322  -0.196 N     L3X 26 
L3X H2    H2  H 0 1 N N N 91.294 -47.055 -0.685 -5.510 -4.005 0.893  H2    L3X 27 
L3X H3    H3  H 0 1 N N N 85.332 -49.208 1.853  1.065  0.537  1.458  H3    L3X 28 
L3X H4    H4  H 0 1 N N N 84.729 -48.298 -0.664 0.685  0.694  -1.585 H4    L3X 29 
L3X H5    H5  H 0 1 N N N 83.760 -50.046 0.551  2.346  2.071  -0.487 H5    L3X 30 
L3X H6    H6  H 0 1 N N N 86.923 -48.657 -1.595 -1.460 1.590  -1.259 H6    L3X 31 
L3X H7    H7  H 0 1 N N N 85.186 -50.944 -2.287 -1.032 2.645  1.450  H7    L3X 32 
L3X H8    H8  H 0 1 N N N 87.099 -51.382 -0.261 -1.777 0.588  1.465  H8    L3X 33 
L3X H9    H9  H 0 1 N N N 89.229 -51.068 -1.031 -3.396 0.408  -0.468 H9    L3X 34 
L3X H10   H10 H 0 1 N N N 88.776 -49.445 -1.656 -2.295 -0.768 -1.224 H10   L3X 35 
L3X H11   H11 H 0 1 N N N 87.784 -47.073 -0.332 0.903  -2.457 -0.868 H11   L3X 36 
L3X H12   H12 H 0 1 N N N 85.954 -42.452 3.037  7.045  -2.784 -0.635 H12   L3X 37 
L3X H13   H13 H 0 1 N N N 87.358 -43.141 2.570  5.611  -3.519 -1.110 H13   L3X 38 
L3X H14   H14 H 0 1 N N N 83.607 -45.844 4.490  5.849  1.117  1.402  H14   L3X 39 
L3X H15   H15 H 0 1 N N N 85.283 -51.834 -4.276 -2.093 5.118  1.309  H15   L3X 40 
L3X H16   H16 H 0 1 N N N 86.851 -52.694 -4.109 -0.317 5.241  1.340  H16   L3X 41 
L3X H17   H17 H 0 1 N N N 86.325 -52.217 -6.375 -1.326 7.179  0.332  H17   L3X 42 
L3X H18   H18 H 0 1 N N N 86.239 -50.612 -6.085 -0.465 6.345  -0.820 H18   L3X 43 
L3X OP3   OP3 O 0 1 N Y N 90.670 -48.629 1.526  -5.769 -1.326 -0.084 OP3   L3X 44 
L3X H1    H1  H 0 1 N N N 91.157 -49.241 2.065  -6.019 -0.893 0.743  H1    L3X 45 
# 
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 
L3X N     CA    SING N N 1  
L3X CA    C     SING N N 2  
L3X O     C     DOUB N N 3  
L3X C     "N3'" SING N N 4  
L3X "N3'" "C3'" SING N N 5  
L3X "C3'" "C4'" SING N N 6  
L3X "C3'" "C2'" SING N N 7  
L3X OP1   P     DOUB N N 8  
L3X "C5'" "C4'" SING N N 9  
L3X "C5'" "O5'" SING N N 10 
L3X "C4'" "O4'" SING N N 11 
L3X "C2'" "O2'" SING N N 12 
L3X "C2'" "C1'" SING N N 13 
L3X P     OP2   SING N N 14 
L3X P     "O5'" SING N N 15 
L3X C8    N7    DOUB Y N 16 
L3X C8    N9    SING Y N 17 
L3X N7    C5    SING Y N 18 
L3X "O4'" "C1'" SING N N 19 
L3X "C1'" N9    SING N N 20 
L3X N9    C4    SING Y N 21 
L3X C5    C4    DOUB Y N 22 
L3X C5    C6    SING Y N 23 
L3X C4    N3    SING Y N 24 
L3X N6    C6    SING N N 25 
L3X C6    N1    DOUB Y N 26 
L3X N3    C2    DOUB Y N 27 
L3X N1    C2    SING Y N 28 
L3X OP2   H2    SING N N 29 
L3X "C1'" H3    SING N N 30 
L3X "C2'" H4    SING N N 31 
L3X "O2'" H5    SING N N 32 
L3X "C3'" H6    SING N N 33 
L3X "N3'" H7    SING N N 34 
L3X "C4'" H8    SING N N 35 
L3X "C5'" H9    SING N N 36 
L3X "C5'" H10   SING N N 37 
L3X C8    H11   SING N N 38 
L3X N6    H12   SING N N 39 
L3X N6    H13   SING N N 40 
L3X C2    H14   SING N N 41 
L3X CA    H15   SING N N 42 
L3X CA    H16   SING N N 43 
L3X N     H17   SING N N 44 
L3X N     H18   SING N N 45 
L3X P     OP3   SING N N 46 
L3X OP3   H1    SING N N 47 
# 
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 
L3X SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1NC(=O)CN"                                                                                                                                       
L3X InChI            InChI                1.03  "InChI=1S/C12H18N7O7P/c13-1-6(20)18-7-5(2-25-27(22,23)24)26-12(9(7)21)19-4-17-8-10(14)15-3-16-11(8)19/h3-5,7,9,12,21H,1-2,13H2,(H,18,20)(H2,14,15,16)(H2,22,23,24)/t5-,7-,9-,12-/m1/s1" 
L3X InChIKey         InChI                1.03  LEUUMALNMKNMGX-MUIQIWNUSA-N                                                                                                                                                             
L3X SMILES_CANONICAL CACTVS               3.385 "NCC(=O)N[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23"                                                                                                                  
L3X SMILES           CACTVS               3.385 "NCC(=O)N[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23"                                                                                                                         
L3X SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)NC(=O)CN)O)N"                                                                                                               
L3X SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)NC(=O)CN)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 
L3X "SYSTEMATIC NAME" ACDLabs              12.01 
;3'-deoxy-3'-(glycylamino)adenosine 5'-(dihydrogen phosphate)
;
L3X "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-(2-azanylethanoylamino)-4-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 
L3X "Create component"      2022-02-25 RCSB 
L3X "Modify parent residue" 2022-02-28 RCSB 
L3X "Initial release"       2022-07-13 RCSB 
# 
