data_HF4
#
_chem_comp.id HF4
_chem_comp.name "4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H16 N3 O14 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Cytarabine-TRIPHOSPHATE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-06-27
_chem_comp.pdbx_modified_date 2021-03-01
_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 483.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HF4
_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 6DW3
_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
HF4 C6 C1 C 0 1 N N N 25.488 5.822 133.126 -5.186 1.795 1.364 C6 HF4 1
HF4 N4 N1 N 0 1 N N N 23.561 3.161 135.075 -5.627 4.545 -0.977 N4 HF4 2
HF4 C5 C2 C 0 1 N N N 24.349 5.147 133.692 -5.588 2.990 0.870 C5 HF4 3
HF4 C2 C3 C 0 1 N N N 27.010 4.143 134.097 -4.127 1.322 -0.679 C2 HF4 4
HF4 O3G O1 O 0 1 N N N 24.033 9.012 127.139 6.680 1.431 -0.197 O3G HF4 5
HF4 PG P1 P 0 1 N N N 23.512 9.946 128.127 5.497 1.888 0.565 PG HF4 6
HF4 O1G O2 O 0 1 N N N 22.156 9.436 128.470 5.953 2.353 2.037 O1G HF4 7
HF4 O2G O3 O 0 1 N N N 23.405 11.320 127.454 4.811 3.127 -0.201 O2G HF4 8
HF4 O3B O4 O 0 1 N N N 24.411 10.088 129.567 4.438 0.681 0.687 O3B HF4 9
HF4 PB P2 P 0 1 N N N 24.435 11.519 130.410 3.926 -0.464 -0.323 PB HF4 10
HF4 O1B O5 O 0 1 N N N 23.562 11.610 131.603 5.004 -1.658 -0.371 O1B HF4 11
HF4 O2B O6 O 0 1 N N N 24.265 12.667 129.470 3.765 0.110 -1.678 O2B HF4 12
HF4 O3A O7 O 0 1 N N N 25.948 11.719 130.848 2.512 -1.038 0.189 O3A HF4 13
HF4 PA P3 P 0 1 N N N 26.586 10.797 132.038 1.356 -1.932 -0.488 PA HF4 14
HF4 O1A O8 O 0 1 N N N 26.113 11.224 133.343 1.789 -3.482 -0.455 O1A HF4 15
HF4 O2A O9 O 0 1 N N N 28.091 11.062 131.904 1.160 -1.504 -1.891 O2A HF4 16
HF4 "O5'" O10 O 0 1 N N N 26.264 9.173 131.782 -0.018 -1.740 0.329 "O5'" HF4 17
HF4 "C5'" C4 C 0 1 N N N 27.045 8.378 130.877 -1.256 -2.321 -0.085 "C5'" HF4 18
HF4 "C4'" C5 C 0 1 N N R 28.320 7.825 131.500 -2.355 -1.943 0.911 "C4'" HF4 19
HF4 "C3'" C6 C 0 1 N N S 28.902 6.642 130.762 -3.670 -2.651 0.534 "C3'" HF4 20
HF4 "O3'" O11 O 0 1 N N N 30.318 6.472 130.961 -4.106 -3.498 1.599 "O3'" HF4 21
HF4 "C2'" C7 C 0 1 N N S 28.279 5.509 131.375 -4.675 -1.494 0.316 "C2'" HF4 22
HF4 "O2'" O12 O 0 1 N N N 27.097 5.257 130.633 -4.790 -1.173 -1.072 "O2'" HF4 23
HF4 "O4'" O13 O 0 1 N N N 27.975 7.394 132.856 -2.600 -0.528 0.854 "O4'" HF4 24
HF4 "C1'" C8 C 0 1 N N R 28.004 5.909 132.796 -4.010 -0.334 1.099 "C1'" HF4 25
HF4 N1 N2 N 0 1 N N N 26.822 5.300 133.319 -4.451 0.961 0.576 N1 HF4 26
HF4 C4 C9 C 0 1 N N N 24.584 3.935 134.442 -5.232 3.338 -0.450 C4 HF4 27
HF4 N3 N3 N 0 1 N N N 25.856 3.456 134.653 -4.515 2.493 -1.180 N3 HF4 28
HF4 O2 O14 O 0 1 N N N 28.296 3.565 134.277 -3.468 0.563 -1.370 O2 HF4 29
HF4 H1 H1 H 0 1 N N N 25.344 6.726 132.553 -5.442 1.508 2.373 H1 HF4 30
HF4 H2 H2 H 0 1 N N N 23.805 2.353 135.611 -6.152 5.160 -0.441 H2 HF4 31
HF4 H3 H3 H 0 1 N N N 22.602 3.428 134.981 -5.381 4.781 -1.885 H3 HF4 32
HF4 H4 H4 H 0 1 N N N 23.350 5.535 133.560 -6.172 3.666 1.476 H4 HF4 33
HF4 H5 H5 H 0 1 N N N 21.977 8.649 127.969 6.591 3.078 2.040 H5 HF4 34
HF4 H6 H6 H 0 1 N N N 23.699 11.256 126.553 4.028 3.479 0.243 H6 HF4 35
HF4 H7 H7 H 0 1 N N N 23.039 12.401 131.554 5.161 -2.082 0.484 H7 HF4 36
HF4 H8 H8 H 0 1 N N N 26.839 11.580 133.843 1.935 -3.831 0.435 H8 HF4 37
HF4 H9 H9 H 0 1 N N N 27.321 9.002 130.015 -1.520 -1.948 -1.075 H9 HF4 38
HF4 H10 H10 H 0 1 N N N 26.429 7.533 130.536 -1.155 -3.406 -0.120 H10 HF4 39
HF4 H11 H11 H 0 1 N N N 29.072 8.626 131.545 -2.054 -2.227 1.919 H11 HF4 40
HF4 H12 H12 H 0 1 N N N 28.655 6.704 129.692 -3.544 -3.228 -0.383 H12 HF4 41
HF4 H13 H13 H 0 1 N N N 30.783 7.202 130.570 -4.959 -3.924 1.439 H13 HF4 42
HF4 H14 H14 H 0 1 N N N 28.949 4.637 131.357 -5.649 -1.740 0.739 H14 HF4 43
HF4 H15 H15 H 0 1 N N N 26.644 4.508 131.003 -5.118 -1.900 -1.618 H15 HF4 44
HF4 H16 H16 H 0 1 N N N 28.859 5.572 133.401 -4.229 -0.414 2.164 H16 HF4 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
HF4 O3G PG DOUB N N 1
HF4 O2G PG SING N N 2
HF4 PG O1G SING N N 3
HF4 PG O3B SING N N 4
HF4 O2B PB DOUB N N 5
HF4 O3B PB SING N N 6
HF4 PB O3A SING N N 7
HF4 PB O1B SING N N 8
HF4 "O2'" "C2'" SING N N 9
HF4 "C3'" "O3'" SING N N 10
HF4 "C3'" "C2'" SING N N 11
HF4 "C3'" "C4'" SING N N 12
HF4 O3A PA SING N N 13
HF4 "C5'" "C4'" SING N N 14
HF4 "C5'" "O5'" SING N N 15
HF4 "C2'" "C1'" SING N N 16
HF4 "C4'" "O4'" SING N N 17
HF4 "O5'" PA SING N N 18
HF4 O2A PA DOUB N N 19
HF4 PA O1A SING N N 20
HF4 "C1'" "O4'" SING N N 21
HF4 "C1'" N1 SING N N 22
HF4 C6 N1 SING N N 23
HF4 C6 C5 DOUB N N 24
HF4 N1 C2 SING N N 25
HF4 C5 C4 SING N N 26
HF4 C2 O2 DOUB N N 27
HF4 C2 N3 SING N N 28
HF4 C4 N3 DOUB N N 29
HF4 C4 N4 SING N N 30
HF4 C6 H1 SING N N 31
HF4 N4 H2 SING N N 32
HF4 N4 H3 SING N N 33
HF4 C5 H4 SING N N 34
HF4 O1G H5 SING N N 35
HF4 O2G H6 SING N N 36
HF4 O1B H7 SING N N 37
HF4 O1A H8 SING N N 38
HF4 "C5'" H9 SING N N 39
HF4 "C5'" H10 SING N N 40
HF4 "C4'" H11 SING N N 41
HF4 "C3'" H12 SING N N 42
HF4 "O3'" H13 SING N N 43
HF4 "C2'" H14 SING N N 44
HF4 "O2'" H15 SING N N 45
HF4 "C1'" H16 SING N N 46
# #
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
HF4 SMILES ACDLabs 12.01 "C=1N(C(=O)N=C(N)C=1)C2C(C(C(COP(OP(OP(=O)(O)O)(O)=O)(O)=O)O2)O)O"
HF4 InChI InChI 1.03 "InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7+,8-/m1/s1"
HF4 InChIKey InChI 1.03 PCDQPRRSZKQHHS-CCXZUQQUSA-N
HF4 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]2O"
HF4 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"
HF4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"
HF4 SMILES "OpenEye OEToolkits" 2.0.6 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"
# #
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
HF4 "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one"
HF4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[(2~{R},3~{S},4~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-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
HF4 "Create component" 2018-06-27 RCSB
HF4 "Modify synonyms" 2018-06-27 RCSB
HF4 "Initial release" 2018-10-10 RCSB
HF4 "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id HF4
_pdbx_chem_comp_synonyms.name Cytarabine-TRIPHOSPHATE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##