data_HFD
#
_chem_comp.id HFD
_chem_comp.name
;2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-a
mine
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H15 F N5 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Fludarabine-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 525.171
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HFD
_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 6DWK
_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
HFD O2A O1 O 0 1 N N N -1.993 2.239 -4.535 -2.886 -2.875 0.683 O2A HFD 1
HFD PA P1 P 0 1 N N N -1.335 3.426 -3.904 -2.334 -1.502 0.697 PA HFD 2
HFD O1A O2 O 0 1 N N N -2.250 3.892 -2.833 -2.115 -1.028 2.220 O1A HFD 3
HFD O3A O3 O 0 1 N N N -0.937 4.555 -5.090 -3.363 -0.503 -0.034 O3A HFD 4
HFD PB P2 P 0 1 N N N -1.786 5.657 -5.950 -4.957 -0.293 0.034 PB HFD 5
HFD O1B O4 O 0 1 N N N -1.069 6.788 -6.582 -5.690 -1.484 -0.762 O1B HFD 6
HFD O2B O5 O 0 1 N N N -2.286 4.810 -7.024 -5.396 -0.302 1.448 O2B HFD 7
HFD O3B O6 O 0 1 N N N -2.578 6.329 -4.615 -5.342 1.119 -0.638 O3B HFD 8
HFD PG P3 P 0 1 N N N -1.717 7.061 -3.366 -6.622 2.090 -0.543 PG HFD 9
HFD O3G O7 O 0 1 N N N -2.446 7.354 -2.122 -6.245 3.535 -1.144 O3G HFD 10
HFD O2G O8 O 0 1 N N N -0.478 6.417 -2.925 -7.839 1.459 -1.388 O2G HFD 11
HFD O1G O9 O 0 1 N N N -1.159 8.306 -3.888 -7.028 2.235 0.873 O1G HFD 12
HFD "O5'" O10 O 0 1 N N N 0.254 3.070 -3.368 -0.923 -1.482 -0.079 "O5'" HFD 13
HFD "C5'" C1 C 0 1 N N N 1.383 3.940 -3.575 0.165 -2.343 0.263 "C5'" HFD 14
HFD "C4'" C2 C 0 1 N N R 2.618 3.456 -2.939 1.347 -2.065 -0.668 "C4'" HFD 15
HFD "C3'" C3 C 0 1 N N S 3.322 2.321 -3.606 2.488 -3.059 -0.379 "C3'" HFD 16
HFD "O3'" O11 O 0 1 N N N 4.788 2.344 -3.476 2.784 -3.833 -1.543 "O3'" HFD 17
HFD "C2'" C4 C 0 1 N N S 2.779 1.156 -2.921 3.691 -2.159 -0.006 "C2'" HFD 18
HFD "O2'" O12 O 0 1 N N N 1.600 0.755 -3.605 3.822 -2.045 1.413 "O2'" HFD 19
HFD "C1'" C5 C 0 1 N N R 2.374 1.502 -1.579 3.287 -0.801 -0.635 "C1'" HFD 20
HFD "O4'" O13 O 0 1 N N N 2.113 2.971 -1.668 1.860 -0.744 -0.426 "O4'" HFD 21
HFD N9 N1 N 0 1 Y N N 1.221 0.860 -1.044 3.955 0.306 0.055 N9 HFD 22
HFD C4 C6 C 0 1 Y N N 1.297 -0.203 -0.196 5.214 0.783 -0.205 C4 HFD 23
HFD C5 C7 C 0 1 Y N N -0.154 -0.470 0.172 5.423 1.839 0.697 C5 HFD 24
HFD N7 N2 N 0 1 Y N N -0.921 0.515 -0.549 4.300 1.950 1.448 N7 HFD 25
HFD C8 C8 C 0 1 Y N N -0.052 1.271 -1.230 3.435 1.055 1.069 C8 HFD 26
HFD N3 N3 N 0 1 Y N N 2.245 -1.017 0.276 6.179 0.466 -1.064 N3 HFD 27
HFD C2 C9 C 0 1 Y N N 1.840 -2.051 1.089 7.317 1.132 -1.071 C2 HFD 28
HFD F2 F1 F 0 1 N N N 2.651 -2.984 1.655 8.272 0.779 -1.959 F2 HFD 29
HFD N1 N4 N 0 1 Y N N 0.575 -2.315 1.444 7.558 2.133 -0.240 N1 HFD 30
HFD C6 C10 C 0 1 Y N N -0.483 -1.580 1.021 6.652 2.519 0.652 C6 HFD 31
HFD N6 N5 N 0 1 N N N -1.819 -1.947 1.515 6.912 3.567 1.517 N6 HFD 32
HFD H1 H1 H 0 1 N N N -3.018 3.334 -2.807 -1.755 -0.135 2.306 H1 HFD 33
HFD H2 H2 H 0 1 N N N -1.103 6.697 -7.527 -5.449 -1.539 -1.697 H2 HFD 34
HFD H3 H3 H 0 1 N N N -2.393 8.284 -1.935 -6.971 4.174 -1.119 H3 HFD 35
HFD H4 H4 H 0 1 N N N 0.259 6.987 -3.110 -7.643 1.335 -2.327 H4 HFD 36
HFD H5 H5 H 0 1 N N N 1.560 4.030 -4.657 0.465 -2.157 1.295 H5 HFD 37
HFD H6 H6 H 0 1 N N N 1.141 4.929 -3.159 -0.145 -3.382 0.156 H6 HFD 38
HFD H7 H7 H 0 1 N N N 3.317 4.291 -2.783 1.029 -2.154 -1.707 H7 HFD 39
HFD H8 H8 H 0 1 N N N 3.044 2.293 -4.670 2.224 -3.711 0.454 H8 HFD 40
HFD H9 H9 H 0 1 N N N 5.158 1.593 -3.925 3.496 -4.476 -1.417 H9 HFD 41
HFD H10 H10 H 0 1 N N N 3.519 0.342 -2.904 4.611 -2.536 -0.451 H10 HFD 42
HFD H11 H11 H 0 1 N N N 1.227 -0.006 -3.175 3.985 -2.885 1.862 H11 HFD 43
HFD H12 H12 H 0 1 N N N 3.224 1.344 -0.899 3.523 -0.786 -1.699 H12 HFD 44
HFD H13 H13 H 0 1 N N N -0.334 2.107 -1.852 2.452 0.923 1.496 H13 HFD 45
HFD H14 H14 H 0 1 N N N -1.744 -2.734 2.128 6.244 3.840 2.164 H14 HFD 46
HFD H15 H15 H 0 1 N N N -2.215 -1.174 2.011 7.764 4.029 1.476 H15 HFD 47
# #
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
HFD O2B PB DOUB N N 1
HFD O1B PB SING N N 2
HFD PB O3A SING N N 3
HFD PB O3B SING N N 4
HFD O3A PA SING N N 5
HFD O3B PG SING N N 6
HFD O2A PA DOUB N N 7
HFD PA "O5'" SING N N 8
HFD PA O1A SING N N 9
HFD O1G PG DOUB N N 10
HFD "C3'" "O3'" SING N N 11
HFD "C3'" "C4'" SING N N 12
HFD "C3'" "C2'" SING N N 13
HFD "O2'" "C2'" SING N N 14
HFD "C5'" "O5'" SING N N 15
HFD "C5'" "C4'" SING N N 16
HFD PG O2G SING N N 17
HFD PG O3G SING N N 18
HFD "C4'" "O4'" SING N N 19
HFD "C2'" "C1'" SING N N 20
HFD "O4'" "C1'" SING N N 21
HFD "C1'" N9 SING N N 22
HFD C8 N9 SING Y N 23
HFD C8 N7 DOUB Y N 24
HFD N9 C4 SING Y N 25
HFD N7 C5 SING Y N 26
HFD C4 C5 DOUB Y N 27
HFD C4 N3 SING Y N 28
HFD C5 C6 SING Y N 29
HFD N3 C2 DOUB Y N 30
HFD C6 N1 DOUB Y N 31
HFD C6 N6 SING N N 32
HFD C2 N1 SING Y N 33
HFD C2 F2 SING N N 34
HFD O1A H1 SING N N 35
HFD O1B H2 SING N N 36
HFD O3G H3 SING N N 37
HFD O2G H4 SING N N 38
HFD "C5'" H5 SING N N 39
HFD "C5'" H6 SING N N 40
HFD "C4'" H7 SING N N 41
HFD "C3'" H8 SING N N 42
HFD "O3'" H9 SING N N 43
HFD "C2'" H10 SING N N 44
HFD "O2'" H11 SING N N 45
HFD "C1'" H12 SING N N 46
HFD C8 H13 SING N N 47
HFD N6 H14 SING N N 48
HFD N6 H15 SING N N 49
# #
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
HFD SMILES ACDLabs 12.01 "O=P(OCC1OC(C(C1O)O)n3c2c(c(nc(n2)F)N)nc3)(O)OP(OP(O)(O)=O)(O)=O"
HFD InChI InChI 1.03 "InChI=1S/C10H15FN5O13P3/c11-10-14-7(12)4-8(15-10)16(2-13-4)9-6(18)5(17)3(27-9)1-26-31(22,23)29-32(24,25)28-30(19,20)21/h2-3,5-6,9,17-18H,1H2,(H,22,23)(H,24,25)(H2,12,14,15)(H2,19,20,21)/t3-,5-,6+,9-/m1/s1"
HFD InChIKey InChI 1.03 PIOKUWLZUXUBCO-FJFJXFQQSA-N
HFD SMILES_CANONICAL CACTVS 3.385 "Nc1nc(F)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]3O"
HFD SMILES CACTVS 3.385 "Nc1nc(F)nc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O"
HFD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc2c(nc(nc2n1[C@H]3[C@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)F)N"
HFD SMILES "OpenEye OEToolkits" 2.0.6 "c1nc2c(nc(nc2n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(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
HFD "SYSTEMATIC NAME" ACDLabs 12.01 "2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine"
HFD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{S},5~{R})-5-(6-azanyl-2-fluoranyl-purin-9-yl)-3,4-bis(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
HFD "Create component" 2018-06-27 RCSB
HFD "Modify synonyms" 2018-06-27 RCSB
HFD "Initial release" 2018-10-10 RCSB
HFD "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HFD
_pdbx_chem_comp_synonyms.name Fludarabine-TRIPHOSPHATE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##