data_HDV
#

_chem_comp.id                                   HDV
_chem_comp.name                                 
;9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-me
thyl-9H-purin-6-amine
;

_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C11 H17 F N5 O12 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        Clofarabine-TRIPHOSPHATE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-06-27
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       523.199
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    HDV
_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       6DWD
_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
HDV  O2A    O1   O  0  1  N  N  N  -38.910   7.766  57.568  -2.925  -2.660   0.483  O2A    HDV   1  
HDV  PA     P1   P  0  1  N  N  N  -37.916   8.778  57.740  -2.305  -1.359   0.819  PA     HDV   2  
HDV  O1A    O2   O  0  1  N  N  N  -38.099   9.736  58.820  -1.995  -1.304   2.398  O1A    HDV   3  
HDV  O3A    O3   O  0  1  N  N  N  -37.604   9.655  56.410  -3.313  -0.166   0.428  O3A    HDV   4  
HDV  PB     P2   P  0  1  N  N  N  -38.369   9.668  55.038  -4.891   0.078   0.637  PB     HDV   5  
HDV  O1B    O4   O  0  1  N  N  N  -38.819   8.354  54.621  -5.160   0.590   2.139  O1B    HDV   6  
HDV  O2B    O5   O  0  1  N  N  N  -37.319  10.301  54.204  -5.620  -1.189   0.409  O2B    HDV   7  
HDV  O3B    O6   O  0  1  N  N  N  -39.622  10.572  55.291  -5.404   1.189  -0.409  O3B    HDV   8  
HDV  PG     P3   P  0  1  N  N  N  -39.958  12.074  54.744  -6.858   1.653  -0.925  PG     HDV   9  
HDV  O3G    O7   O  0  1  N  N  N  -39.209  12.362  53.484  -7.718   0.463  -1.110  O3G    HDV  10  
HDV  O2G    O8   O  0  1  N  N  N  -39.549  13.011  55.753  -7.525   2.633   0.163  O2G    HDV  11  
HDV  O1G    O9   O  0  1  N  N  N  -41.443  11.994  54.617  -6.707   2.429  -2.327  O1G    HDV  12  
HDV  "O5'"  O10  O  0  1  N  N  N  -36.489   7.983  57.764  -0.930  -1.191  -0.003  "O5'"  HDV  13  
HDV  "C5'"  C1   C  0  1  N  N  N  -35.372   8.716  58.221   0.127  -2.151   0.045  "C5'"  HDV  14  
HDV  "C4'"  C2   C  0  1  N  N  R  -34.393   7.711  58.856   1.280  -1.685  -0.848  "C4'"  HDV  15  
HDV  "C3'"  C3   C  0  1  N  N  R  -34.050   6.455  58.084   2.438  -2.714  -0.825  "C3'"  HDV  16  
HDV  "O3'"  O11  O  0  1  N  N  N  -32.650   6.153  58.327   2.229  -3.739  -1.799  "O3'"  HDV  17  
HDV  "C2'"  C4   C  0  1  N  N  S  -34.899   5.336  58.609   3.658  -1.838  -1.199  "C2'"  HDV  18  
HDV  "F2'"  F1   F  0  1  N  N  N  -36.149   5.245  57.898   4.770  -2.192  -0.428  "F2'"  HDV  19  
HDV  "C1'"  C5   C  0  1  N  N  R  -35.172   5.697  60.031   3.207  -0.402  -0.868  "C1'"  HDV  20  
HDV  "O4'"  O12  O  0  1  N  N  N  -35.116   7.165  60.013   1.883  -0.486  -0.315  "O4'"  HDV  21  
HDV  N9     N1   N  0  1  Y  N  N  -36.483   5.492  60.614   4.120   0.193   0.111  N9     HDV  22  
HDV  C4     C6   C  0  1  Y  N  N  -36.623   5.164  61.904   5.305   0.828  -0.164  C4     HDV  23  
HDV  C5     C7   C  0  1  Y  N  N  -38.025   5.096  62.140   5.826   1.229   1.077  C5     HDV  24  
HDV  N7     N2   N  0  1  Y  N  N  -38.719   5.383  60.920   4.949   0.827   2.028  N7     HDV  25  
HDV  C8     C8   C  0  1  Y  N  N  -37.726   5.639  60.030   3.944   0.224   1.463  C8     HDV  26  
HDV  N3     N3   N  0  1  Y  N  N  -35.792   4.927  62.886   5.985   1.106  -1.271  N3     HDV  27  
HDV  C2     C9   C  0  1  Y  N  N  -36.411   4.635  64.059   7.132   1.749  -1.210  C2     HDV  28  
HDV  CL2    C10  C  0  1  N  N  N  -35.541   4.380  65.251   7.868   2.043  -2.492  CL2    HDV  29  
HDV  N1     N4   N  0  1  Y  N  N  -37.695   4.570  64.337   7.662   2.147  -0.067  N1     HDV  30  
HDV  C6     C11  C  0  1  Y  N  N  -38.542   4.809  63.409   7.054   1.913   1.091  C6     HDV  31  
HDV  N6     N5   N  0  1  N  N  N  -39.937   4.751  63.632   7.617   2.333   2.283  N6     HDV  32  
HDV  H1     H1   H  0  1  N  N  N  -38.903   9.539  59.285  -1.587  -0.478   2.690  H1     HDV  33  
HDV  H2     H2   H  0  1  N  N  N  -38.347   8.091  53.840  -4.712   1.418   2.359  H2     HDV  34  
HDV  H3     H3   H  0  1  N  N  N  -38.897  13.600  55.393  -7.014   3.436   0.336  H3     HDV  35  
HDV  H4     H4   H  0  1  N  N  N  -41.693  12.146  53.713  -7.545   2.738  -2.697  H4     HDV  36  
HDV  H5     H5   H  0  1  N  N  N  -34.889   9.231  57.377   0.481  -2.250   1.071  H5     HDV  37  
HDV  H6     H6   H  0  1  N  N  N  -35.689   9.457  58.970  -0.239  -3.114  -0.308  H6     HDV  38  
HDV  H7     H7   H  0  1  N  N  N  -33.475   8.228  59.173   0.930  -1.518  -1.867  H7     HDV  39  
HDV  H8     H8   H  0  1  N  N  N  -34.240   6.607  57.011   2.557  -3.144   0.169  H8     HDV  40  
HDV  H9     H9   H  0  1  N  N  N  -32.111   6.861  57.995   2.968  -4.356  -1.885  H9     HDV  41  
HDV  H10    H10  H  0  1  N  N  N  -34.347   4.386  58.557   3.884  -1.931  -2.262  H10    HDV  42  
HDV  H11    H11  H  0  1  N  N  N  -34.386   5.289  60.684   3.194   0.201  -1.776  H11    HDV  43  
HDV  H12    H12  H  0  1  N  N  N  -37.887   5.921  59.000   3.097  -0.194   1.987  H12    HDV  44  
HDV  H13    H13  H  0  1  N  N  N  -34.484   4.477  64.962   7.548   3.009  -2.881  H13    HDV  45  
HDV  H14    H14  H  0  1  N  N  N  -35.774   5.112  66.038   8.941   2.066  -2.298  H14    HDV  46  
HDV  H15    H15  H  0  1  N  N  N  -35.726   3.364  65.629   7.648   1.265  -3.223  H15    HDV  47  
HDV  H16    H16  H  0  1  N  N  N  -40.113   4.505  64.585   7.164   2.156   3.123  H16    HDV  48  
HDV  H17    H17  H  0  1  N  N  N  -40.343   5.644  63.438   8.465   2.805   2.280  H17    HDV  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
HDV  O3G    PG     DOUB  N  N   1  
HDV  O2B    PB     DOUB  N  N   2  
HDV  O1G    PG     SING  N  N   3  
HDV  O1B    PB     SING  N  N   4  
HDV  PG     O3B    SING  N  N   5  
HDV  PG     O2G    SING  N  N   6  
HDV  PB     O3B    SING  N  N   7  
HDV  PB     O3A    SING  N  N   8  
HDV  O3A    PA     SING  N  N   9  
HDV  O2A    PA     DOUB  N  N  10  
HDV  PA     "O5'"  SING  N  N  11  
HDV  PA     O1A    SING  N  N  12  
HDV  "O5'"  "C5'"  SING  N  N  13  
HDV  "F2'"  "C2'"  SING  N  N  14  
HDV  "C3'"  "O3'"  SING  N  N  15  
HDV  "C3'"  "C2'"  SING  N  N  16  
HDV  "C3'"  "C4'"  SING  N  N  17  
HDV  "C5'"  "C4'"  SING  N  N  18  
HDV  "C2'"  "C1'"  SING  N  N  19  
HDV  "C4'"  "O4'"  SING  N  N  20  
HDV  "O4'"  "C1'"  SING  N  N  21  
HDV  C8     N9     SING  Y  N  22  
HDV  C8     N7     DOUB  Y  N  23  
HDV  "C1'"  N9     SING  N  N  24  
HDV  N9     C4     SING  Y  N  25  
HDV  N7     C5     SING  Y  N  26  
HDV  C4     C5     DOUB  Y  N  27  
HDV  C4     N3     SING  Y  N  28  
HDV  C5     C6     SING  Y  N  29  
HDV  N3     C2     DOUB  Y  N  30  
HDV  C6     N6     SING  N  N  31  
HDV  C6     N1     DOUB  Y  N  32  
HDV  C2     N1     SING  Y  N  33  
HDV  C2     CL2    SING  N  N  34  
HDV  O1A    H1     SING  N  N  35  
HDV  O1B    H2     SING  N  N  36  
HDV  O2G    H3     SING  N  N  37  
HDV  O1G    H4     SING  N  N  38  
HDV  "C5'"  H5     SING  N  N  39  
HDV  "C5'"  H6     SING  N  N  40  
HDV  "C4'"  H7     SING  N  N  41  
HDV  "C3'"  H8     SING  N  N  42  
HDV  "O3'"  H9     SING  N  N  43  
HDV  "C2'"  H10    SING  N  N  44  
HDV  "C1'"  H11    SING  N  N  45  
HDV  C8     H12    SING  N  N  46  
HDV  CL2    H13    SING  N  N  47  
HDV  CL2    H14    SING  N  N  48  
HDV  CL2    H15    SING  N  N  49  
HDV  N6     H16    SING  N  N  50  
HDV  N6     H17    SING  N  N  51  
#   #
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
HDV  SMILES            ACDLabs               12.01  "O=P(OCC1OC(C(C1O)F)n3c2c(c(nc(n2)C)N)nc3)(O)OP(OP(O)(=O)O)(O)=O"  
HDV  InChI             InChI                 1.03   "InChI=1S/C11H17FN5O12P3/c1-4-15-9(13)7-10(16-4)17(3-14-7)11-6(12)8(18)5(27-11)2-26-31(22,23)29-32(24,25)28-30(19,20)21/h3,5-6,8,11,18H,2H2,1H3,(H,22,23)(H,24,25)(H2,13,15,16)(H2,19,20,21)/t5-,6+,8-,11-/m1/s1"  
HDV  InChIKey          InChI                 1.03   BGNIGZFVXIGOQD-WCGPTHBMSA-N  
HDV  SMILES_CANONICAL  CACTVS                3.385  "Cc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]3F)c2n1"  
HDV  SMILES            CACTVS                3.385  "Cc1nc(N)c2ncn([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3F)c2n1"  
HDV  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "Cc1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)N"  
HDV  SMILES            "OpenEye OEToolkits"  2.0.6  "Cc1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)F)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
HDV  "SYSTEMATIC NAME"  ACDLabs               12.01  "9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-methyl-9H-purin-6-amine"  
HDV  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[[(2~{R},3~{R},4~{S},5~{R})-5-(6-azanyl-2-methyl-purin-9-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen 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
HDV  "Create component"  2018-06-27  RCSB  
HDV  "Modify synonyms"   2018-06-27  RCSB  
HDV  "Initial release"   2018-10-10  RCSB  
HDV  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     HDV
_pdbx_chem_comp_synonyms.name        Clofarabine-TRIPHOSPHATE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
