data_A1CDW
# 
_chem_comp.id                                    A1CDW 
_chem_comp.name                                  
;pentostatin 5'-phosphate
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C11 H17 N4 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         
;(8S)-3-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol; 2'-deoxycoformycin 5'-phosphate
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-05-21 
_chem_comp.pdbx_modified_date                    2025-06-13 
_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                        348.249 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CDW 
_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        9NTH 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_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 
A1CDW C14  C1  C 0 1 Y N N N N N -15.781 -17.514 5.187  -2.974 0.149  -0.110 C14  A1CDW 1  
A1CDW C15  C2  C 0 1 Y N N N N N -16.991 -17.743 5.862  -3.606 -0.912 0.444  C15  A1CDW 2  
A1CDW C17  C3  C 0 1 Y N N N N N -16.710 -19.402 4.550  -1.498 -1.159 0.882  C17  A1CDW 3  
A1CDW C18  C4  C 0 1 N N R N N N -17.617 -16.900 6.929  -5.075 -1.232 0.445  C18  A1CDW 4  
A1CDW C2   C5  C 0 1 N N S N N N -12.982 -20.544 2.748  1.121  2.280  0.903  C2   A1CDW 5  
A1CDW C20  C6  C 0 1 N N N N N N -16.502 -16.337 7.791  -5.757 -0.744 -0.818 C20  A1CDW 6  
A1CDW C22  C7  C 0 1 N N N N N N -14.936 -15.494 6.049  -4.654 1.441  -1.183 C22  A1CDW 7  
A1CDW C3   C8  C 0 1 N N N N N N -13.624 -20.043 4.026  -0.403 2.042  0.813  C3   A1CDW 8  
A1CDW C4   C9  C 0 1 N N R N N N -14.467 -18.902 3.499  -0.543 0.897  -0.215 C4   A1CDW 9  
A1CDW C6   C10 C 0 1 N N R N N N -14.132 -20.410 1.742  1.721  1.252  -0.081 C6   A1CDW 10 
A1CDW C7   C11 C 0 1 N N N N N N -15.009 -21.633 1.603  3.032  0.687  0.471  C7   A1CDW 11 
A1CDW N13  N1  N 0 1 Y N N N N N -15.622 -18.597 4.345  -1.626 -0.009 0.175  N13  A1CDW 12 
A1CDW N16  N2  N 0 1 Y N N N N N -17.550 -18.931 5.445  -2.677 -1.688 1.036  N16  A1CDW 13 
A1CDW N21  N3  N 0 1 N N N N N N -15.757 -15.290 7.101  -5.747 0.703  -0.898 N21  A1CDW 14 
A1CDW N23  N4  N 0 1 N N N N N N -14.859 -16.486 5.234  -3.457 1.195  -0.818 N23  A1CDW 15 
A1CDW O1   O1  O 0 1 N N N N N N -11.905 -19.670 2.375  1.445  3.612  0.499  O1   A1CDW 16 
A1CDW O10  O2  O 0 1 N N N N N N -15.103 -21.945 -1.283 6.211  0.136  -0.119 O10  A1CDW 17 
A1CDW O11  O3  O 0 1 N N N N N N -14.273 -24.288 -0.856 5.323  -1.914 -1.504 O11  A1CDW 18 
A1CDW O12  O4  O 0 1 N N N N N N -12.664 -22.364 -0.930 4.932  -1.740 0.984  O12  A1CDW 19 
A1CDW O19  O5  O 0 1 N N N N N N -18.407 -15.764 6.481  -5.243 -2.648 0.549  O19  A1CDW 20 
A1CDW O5   O6  O 0 1 N N N N N N -14.961 -19.337 2.237  0.726  0.209  -0.178 O5   A1CDW 21 
A1CDW O8   O7  O 0 1 N N N N N N -14.219 -22.675 1.004  3.628  -0.172 -0.503 O8   A1CDW 22 
A1CDW P9   P1  P 0 1 N N N N N N -14.064 -22.810 -0.611 5.022  -0.940 -0.258 P9   A1CDW 23 
A1CDW H17  H1  H 0 1 N N N N N N -16.864 -20.334 4.027  -0.571 -1.568 1.255  H17  A1CDW 24 
A1CDW H18  H2  H 0 1 N N N N N N -18.245 -17.547 7.559  -5.542 -0.755 1.307  H18  A1CDW 25 
A1CDW H2   H3  H 0 1 N N N N N N -12.661 -21.592 2.845  1.478  2.092  1.916  H2   A1CDW 26 
A1CDW H20A H4  H 0 0 N N N N N N -16.940 -15.916 8.708  -5.238 -1.153 -1.684 H20A A1CDW 27 
A1CDW H20B H5  H 0 0 N N N N N N -15.811 -17.151 8.054  -6.789 -1.094 -0.823 H20B A1CDW 28 
A1CDW H22  H6  H 0 1 N N N N N N -14.231 -14.697 5.862  -4.808 2.329  -1.779 H22  A1CDW 29 
A1CDW H3A  H7  H 0 1 N N N N N N -14.245 -20.819 4.497  -0.799 1.736  1.781  H3A  A1CDW 30 
A1CDW H3B  H8  H 0 1 N N N N N N -12.870 -19.690 4.745  -0.909 2.939  0.457  H3B  A1CDW 31 
A1CDW H4   H9  H 0 1 N N N N N N -13.838 -18.007 3.382  -0.726 1.302  -1.211 H4   A1CDW 32 
A1CDW H6   H10 H 0 1 N N N N N N -13.717 -20.147 0.758  1.887  1.711  -1.056 H6   A1CDW 33 
A1CDW H7A  H11 H 0 1 N N N N N N -15.363 -21.954 2.594  3.713  1.507  0.698  H7A  A1CDW 34 
A1CDW H7B  H12 H 0 1 N N N N N N -15.873 -21.403 0.962  2.829  0.121  1.380  H7B  A1CDW 35 
A1CDW H21  H13 H 0 1 N N N N N N -15.862 -14.352 7.432  -6.580 1.172  -0.737 H21  A1CDW 36 
A1CDW H1   H14 H 0 1 N N N N N N -11.504 -19.985 1.574  1.043  4.299  1.049  H1   A1CDW 37 
A1CDW H3   H15 H 0 1 N N N N N N -14.672 -21.268 -1.791 6.327  0.697  -0.898 H3   A1CDW 38 
A1CDW H5   H16 H 0 1 N N N N N N -13.465 -24.674 -1.173 6.149  -2.411 -1.424 H5   A1CDW 39 
A1CDW H19  H17 H 0 1 N N N N N N -18.755 -15.302 7.235  -6.166 -2.934 0.556  H19  A1CDW 40 
# 
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 
A1CDW O1  C2   SING N N 1  
A1CDW C2  C3   SING N N 2  
A1CDW C3  C4   SING N N 3  
A1CDW C4  O5   SING N N 4  
A1CDW O5  C6   SING N N 5  
A1CDW C6  C7   SING N N 6  
A1CDW C7  O8   SING N N 7  
A1CDW O8  P9   SING N N 8  
A1CDW P9  O10  SING N N 9  
A1CDW P9  O11  SING N N 10 
A1CDW P9  O12  DOUB N N 11 
A1CDW C4  N13  SING N N 12 
A1CDW N13 C14  SING Y N 13 
A1CDW C14 C15  DOUB Y N 14 
A1CDW C15 N16  SING Y N 15 
A1CDW N16 C17  DOUB Y N 16 
A1CDW C15 C18  SING N N 17 
A1CDW C18 O19  SING N N 18 
A1CDW C18 C20  SING N N 19 
A1CDW C20 N21  SING N N 20 
A1CDW N21 C22  SING N N 21 
A1CDW C22 N23  DOUB N N 22 
A1CDW C6  C2   SING N N 23 
A1CDW C17 N13  SING Y N 24 
A1CDW N23 C14  SING N N 25 
A1CDW C17 H17  SING N N 26 
A1CDW C18 H18  SING N N 27 
A1CDW C2  H2   SING N N 28 
A1CDW C20 H20A SING N N 29 
A1CDW C20 H20B SING N N 30 
A1CDW C22 H22  SING N N 31 
A1CDW C3  H3A  SING N N 32 
A1CDW C3  H3B  SING N N 33 
A1CDW C4  H4   SING N N 34 
A1CDW C6  H6   SING N N 35 
A1CDW C7  H7A  SING N N 36 
A1CDW C7  H7B  SING N N 37 
A1CDW N21 H21  SING N N 38 
A1CDW O1  H1   SING N N 39 
A1CDW O10 H3   SING N N 40 
A1CDW O11 H5   SING N N 41 
A1CDW O19 H19  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 
A1CDW SMILES           ACDLabs              14.52   "O=P(O)(O)OCC1OC(CC1O)n1cnc2c1N=CNCC2O"                                                                                                                 
A1CDW InChI            InChI                1.06    "InChI=1S/C11H17N4O7P/c16-6-1-9(22-8(6)3-21-23(18,19)20)15-5-14-10-7(17)2-12-4-13-11(10)15/h4-9,16-17H,1-3H2,(H,12,13)(H2,18,19,20)/t6-,7+,8+,9+/m0/s1" 
A1CDW InChIKey         InChI                1.06    NZYBWACXTRESTQ-JQCXWYLXSA-N                                                                                                                             
A1CDW SMILES_CANONICAL CACTVS               3.385   "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3[C@H](O)CNC=Nc23"                                                                                           
A1CDW SMILES           CACTVS               3.385   "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3[CH](O)CNC=Nc23"                                                                                                 
A1CDW SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=CNC[C@H]2O"                                                                                            
A1CDW SMILES           "OpenEye OEToolkits" 3.1.0.0 "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=CNCC2O"                                                                                                             
# 
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 
A1CDW "SYSTEMATIC NAME" ACDLabs              14.52   "(8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol"                                  
A1CDW "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{S},5~{R})-3-oxidanyl-5-[(8~{R})-8-oxidanyl-7,8-dihydro-6~{H}-imidazo[4,5-d][1,3]diazepin-3-yl]oxolan-2-yl]methyl dihydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 A1CDW "(8S)-3-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-3,6,7,8-tetrahydroimidazo[4,5-d][1,3]diazepin-8-ol" PDB "systematic name" 
2 A1CDW 
;2'-deoxycoformycin 5'-phosphate
;
PDB ?                 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1CDW "Create component" 2025-05-21 RCSB 
A1CDW "Initial release"  2025-06-18 RCSB 
# 
