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 ?
##