data_VA6
#
_chem_comp.id VA6
_chem_comp.name "9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 F2 N5 O11 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-22
_chem_comp.pdbx_modified_date 2018-07-13
_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 525.190
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VA6
_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 6CRB
_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
VA6 N1 N1 N 0 1 Y N N -14.977 -8.706 66.599 -7.880 2.280 -1.163 N1 VA6 1
VA6 C2 C1 C 0 1 Y N N -14.968 -8.267 65.340 -7.506 1.198 -1.822 C2 VA6 2
VA6 N3 N2 N 0 1 Y N N -13.886 -7.721 64.758 -6.472 0.470 -1.456 N3 VA6 3
VA6 C4 C2 C 0 1 Y N N -12.677 -7.583 65.474 -5.752 0.804 -0.389 C4 VA6 4
VA6 C5 C3 C 0 1 Y N N -12.643 -8.033 66.821 -6.109 1.947 0.345 C5 VA6 5
VA6 C6 C4 C 0 1 Y N N -13.827 -8.604 67.391 -7.221 2.692 -0.085 C6 VA6 6
VA6 N6 N3 N 0 1 N N N -13.797 -9.034 68.702 -7.620 3.827 0.598 N6 VA6 7
VA6 N7 N4 N 0 1 Y N N -11.390 -7.803 67.291 -5.226 2.058 1.366 N7 VA6 8
VA6 C8 C5 C 0 1 Y N N -10.684 -7.249 66.317 -4.370 1.080 1.306 C8 VA6 9
VA6 N9 N5 N 0 1 Y N N -11.434 -7.129 65.207 -4.653 0.278 0.240 N9 VA6 10
VA6 PA P1 P 0 1 N N N -7.277 -4.618 65.033 1.604 -2.005 -0.426 PA VA6 11
VA6 PB P2 P 0 1 N N N -7.728 -1.942 64.164 3.959 -0.206 -0.465 PB VA6 12
VA6 PG P3 P 0 1 N N N -5.253 -0.477 65.065 6.076 1.826 0.035 PG VA6 13
VA6 "C1'" C6 C 0 1 N N S -10.910 -6.521 64.089 -3.917 -0.924 -0.160 "C1'" VA6 14
VA6 O1A O1 O 0 1 N N N -5.950 -4.542 64.261 1.468 -1.920 -1.897 O1A VA6 15
VA6 O2B O2 O 0 1 N N N -9.005 -1.410 63.541 3.708 0.416 -1.929 O2B VA6 16
VA6 O1G O3 O 0 1 N N N -4.559 -1.757 64.678 6.574 2.987 1.034 O1G VA6 17
VA6 "C2'" C7 C 0 1 N N N -11.711 -5.302 63.404 -4.570 -2.185 0.460 "C2'" VA6 18
VA6 O2A O4 O 0 1 N N N -6.945 -5.020 66.553 2.215 -3.440 -0.026 O2A VA6 19
VA6 O1B O5 O 0 1 N N N -6.720 -2.165 63.050 4.993 -1.262 -0.549 O1B VA6 20
VA6 O2G O6 O 0 1 N N N -4.683 -0.031 66.335 7.201 0.677 -0.055 O2G VA6 21
VA6 "C3'" C8 C 0 1 N N S -10.553 -4.661 63.185 -3.362 -3.162 0.481 "C3'" VA6 22
VA6 "O3'" O7 O 0 1 N N N -10.773 -3.432 62.379 -3.503 -4.122 1.530 "O3'" VA6 23
VA6 O3A O8 O 0 1 N N N -8.065 -3.329 64.969 2.588 -0.840 0.091 O3A VA6 24
VA6 C3B C9 C 0 1 N N N -7.045 -0.718 65.305 4.523 1.108 0.665 C3B VA6 25
VA6 F1B F1 F 0 1 N N N -7.576 0.480 65.093 3.546 2.106 0.744 F1B VA6 26
VA6 F2B F2 F 0 1 N N N -7.273 -1.122 66.635 4.742 0.567 1.937 F2B VA6 27
VA6 O3G O9 O 0 1 N N N -5.051 0.676 64.036 5.845 2.398 -1.310 O3G VA6 28
VA6 "C4'" C10 C 0 1 N N R -9.695 -5.761 62.549 -2.177 -2.212 0.754 "C4'" VA6 29
VA6 "O4'" O10 O 0 1 N N N -10.338 -7.118 63.099 -2.582 -0.891 0.370 "O4'" VA6 30
VA6 "C5'" C11 C 0 1 N N N -8.334 -5.674 62.902 -0.967 -2.645 -0.077 "C5'" VA6 31
VA6 "O5'" O11 O 0 1 N N N -8.116 -5.727 64.334 0.157 -1.828 0.258 "O5'" VA6 32
VA6 H1 H1 H 0 1 N N N -15.874 -8.354 64.759 -8.069 0.900 -2.693 H1 VA6 33
VA6 H2 H2 H 0 1 N N N -14.692 -9.404 68.953 -8.389 4.333 0.291 H2 VA6 34
VA6 H3 H3 H 0 1 N N N -13.102 -9.746 68.803 -7.131 4.117 1.384 H3 VA6 35
VA6 H4 H4 H 0 1 N N N -9.653 -6.938 66.402 -3.556 0.925 1.999 H4 VA6 36
VA6 H5 H5 H 0 1 N N N -10.071 -5.961 64.528 -3.891 -1.006 -1.246 H5 VA6 37
VA6 H6 H6 H 0 1 N N N -8.892 -1.335 62.601 3.041 1.115 -1.950 H6 VA6 38
VA6 H7 H7 H 0 1 N N N -4.107 -1.635 63.852 7.398 3.414 0.760 H7 VA6 39
VA6 H8 H8 H 0 1 N N N -12.394 -4.774 64.086 -4.931 -1.985 1.469 H8 VA6 40
VA6 H9 H9 H 0 1 N N N -12.251 -5.579 62.487 -5.372 -2.564 -0.174 H9 VA6 41
VA6 H10 H10 H 0 1 N N N -6.006 -5.126 66.655 2.331 -3.567 0.926 H10 VA6 42
VA6 H11 H11 H 0 1 N N N -4.329 0.845 66.234 7.403 0.257 0.792 H11 VA6 43
VA6 H12 H12 H 0 1 N N N -10.084 -4.374 64.138 -3.248 -3.658 -0.484 H12 VA6 44
VA6 H13 H13 H 0 1 N N N -11.314 -2.824 62.869 -4.284 -4.685 1.446 H13 VA6 45
VA6 H14 H14 H 0 1 N N N -9.822 -5.734 61.457 -1.923 -2.228 1.813 H14 VA6 46
VA6 H15 H15 H 0 1 N N N -7.796 -6.512 62.434 -0.734 -3.688 0.136 H15 VA6 47
VA6 H16 H16 H 0 1 N N N -7.933 -4.723 62.521 -1.195 -2.532 -1.137 H16 VA6 48
#
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
VA6 "O3'" "C3'" SING N N 1
VA6 "C4'" "C5'" SING N N 2
VA6 "C4'" "O4'" SING N N 3
VA6 "C4'" "C3'" SING N N 4
VA6 "C5'" "O5'" SING N N 5
VA6 O1B PB DOUB N N 6
VA6 "O4'" "C1'" SING N N 7
VA6 "C3'" "C2'" SING N N 8
VA6 "C2'" "C1'" SING N N 9
VA6 O2B PB SING N N 10
VA6 O3G PG DOUB N N 11
VA6 "C1'" N9 SING N N 12
VA6 PB O3A SING N N 13
VA6 PB C3B SING N N 14
VA6 O1A PA DOUB N N 15
VA6 "O5'" PA SING N N 16
VA6 O1G PG SING N N 17
VA6 N3 C2 DOUB Y N 18
VA6 N3 C4 SING Y N 19
VA6 O3A PA SING N N 20
VA6 PA O2A SING N N 21
VA6 PG C3B SING N N 22
VA6 PG O2G SING N N 23
VA6 F1B C3B SING N N 24
VA6 N9 C4 SING Y N 25
VA6 N9 C8 SING Y N 26
VA6 C3B F2B SING N N 27
VA6 C2 N1 SING Y N 28
VA6 C4 C5 DOUB Y N 29
VA6 C8 N7 DOUB Y N 30
VA6 N1 C6 DOUB Y N 31
VA6 C5 N7 SING Y N 32
VA6 C5 C6 SING Y N 33
VA6 C6 N6 SING N N 34
VA6 C2 H1 SING N N 35
VA6 N6 H2 SING N N 36
VA6 N6 H3 SING N N 37
VA6 C8 H4 SING N N 38
VA6 "C1'" H5 SING N N 39
VA6 O2B H6 SING N N 40
VA6 O1G H7 SING N N 41
VA6 "C2'" H8 SING N N 42
VA6 "C2'" H9 SING N N 43
VA6 O2A H10 SING N N 44
VA6 O2G H11 SING N N 45
VA6 "C3'" H12 SING N N 46
VA6 "O3'" H13 SING N N 47
VA6 "C4'" H14 SING N N 48
VA6 "C5'" H15 SING N N 49
VA6 "C5'" H16 SING N N 50
#
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
VA6 SMILES ACDLabs 12.01 "n1c(c2c(nc1)n(cn2)C3CC(O)C(COP(O)(=O)OP(C(P(O)(O)=O)(F)F)(O)=O)O3)N"
VA6 InChI InChI 1.03 "InChI=1S/C11H16F2N5O11P3/c12-11(13,30(20,21)22)31(23,24)29-32(25,26)27-2-6-5(19)1-7(28-6)18-4-17-8-9(14)15-3-16-10(8)18/h3-7,19H,1-2H2,(H,23,24)(H,25,26)(H2,14,15,16)(H2,20,21,22)/t5-,6+,7-/m0/s1"
VA6 InChIKey InChI 1.03 QVHRTXWVFSLQPZ-XVMARJQXSA-N
VA6 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O3"
VA6 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O3"
VA6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O)N"
VA6 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O)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
VA6 "SYSTEMATIC NAME" ACDLabs 12.01 "9-{2-deoxy-5-O-[(S)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"
VA6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(fluoranyl)methyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VA6 "Create component" 2018-03-22 RCSB
VA6 "Initial release" 2018-07-18 RCSB
#