data_VA5
#
_chem_comp.id VA5
_chem_comp.name "9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 Cl F 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 2018-06-29
_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 541.644
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VA5
_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 6CR9
_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
VA5 PA P1 P 0 1 N N N 5.011 5.096 14.702 1.356 -1.793 -0.485 PA VA5 1
VA5 O1A O1 O 0 1 N N N 4.000 5.112 15.827 1.054 -1.907 -2.062 O1A VA5 2
VA5 O2A O2 O 0 1 N N N 6.364 5.225 15.259 1.934 -3.066 -0.000 O2A VA5 3
VA5 O3A O3 O 0 1 N N N 4.948 3.724 13.873 2.401 -0.596 -0.225 O3A VA5 4
VA5 "O5'" O4 O 0 1 N N N 4.754 6.290 13.646 -0.014 -1.490 0.304 "O5'" VA5 5
VA5 PB P2 P 0 1 N N N 3.756 2.653 13.833 3.987 -0.427 -0.449 PB VA5 6
VA5 O2B O5 O 0 1 N N N 3.659 2.195 12.370 4.303 -0.605 -1.884 O2B VA5 7
VA5 O1B O6 O 0 1 N N N 2.420 3.256 14.299 4.773 -1.534 0.416 O1B VA5 8
VA5 C3B C1 C 0 1 N N S 4.229 1.187 14.816 4.501 1.239 0.084 C3B VA5 9
VA5 F3B F1 F 0 1 N N N 4.048 0.029 14.102 3.819 2.201 -0.667 F3B VA5 10
VA5 CL1 CL1 CL 0 0 N N N 5.923 1.289 15.118 4.115 1.456 1.832 F3CL VA5 11
VA5 PG P3 P 0 1 N N N 3.377 1.141 16.420 6.296 1.431 -0.170 PG VA5 12
VA5 O1G O7 O 0 1 N N N 3.429 2.529 17.027 6.751 2.901 0.301 O1G VA5 13
VA5 O2G O8 O 0 1 N N N 4.070 0.158 17.275 7.082 0.323 0.695 O2G VA5 14
VA5 O3G O9 O 0 1 N N N 1.929 0.712 16.215 6.613 1.252 -1.605 O3G VA5 15
VA5 "C5'" C2 C 0 1 N N N 3.490 6.360 12.971 -1.102 -2.415 0.357 "C5'" VA5 16
VA5 "C4'" C3 C 0 1 N N R 3.456 6.988 11.524 -2.241 -1.815 1.184 "C4'" VA5 17
VA5 "O4'" O10 O 0 1 N N N 4.247 7.958 11.302 -2.789 -0.680 0.505 "O4'" VA5 18
VA5 "C1'" C4 C 0 1 N N S 5.322 7.130 10.655 -4.168 -0.919 0.183 "C1'" VA5 19
VA5 N9 N1 N 0 1 Y N N 6.608 7.480 10.566 -4.945 0.315 0.320 N9 VA5 20
VA5 C4 C5 C 0 1 Y N N 7.436 7.853 9.556 -6.135 0.599 -0.299 C4 VA5 21
VA5 N3 N2 N 0 1 Y N N 7.327 8.190 8.226 -6.930 -0.047 -1.146 N3 VA5 22
VA5 C2 C6 C 0 1 Y N N 8.434 8.546 7.557 -8.044 0.506 -1.577 C2 VA5 23
VA5 N1 N3 N 0 1 Y N N 9.645 8.583 8.114 -8.427 1.713 -1.201 N1 VA5 24
VA5 C6 C7 C 0 1 Y N N 9.836 8.260 9.411 -7.697 2.435 -0.357 C6 VA5 25
VA5 N6 N4 N 0 1 N N N 11.084 8.273 10.067 -8.107 3.699 0.032 N6 VA5 26
VA5 C5 C8 C 0 1 Y N N 8.708 7.878 10.163 -6.499 1.886 0.131 C5 VA5 27
VA5 N7 N5 N 0 1 Y N N 8.592 7.510 11.468 -5.530 2.313 0.976 N7 VA5 28
VA5 C8 C9 C 0 1 Y N N 7.320 7.248 11.667 -4.620 1.391 1.092 C8 VA5 29
VA5 "C2'" C10 C 0 1 N N N 4.694 6.246 9.619 -4.647 -1.975 1.212 "C2'" VA5 30
VA5 "C3'" C11 C 0 1 N N R 3.656 5.887 10.327 -3.372 -2.854 1.349 "C3'" VA5 31
VA5 "O3'" O11 O 0 1 N N N 3.682 4.492 10.875 -3.315 -3.834 0.311 "O3'" VA5 32
VA5 H1 H1 H 0 1 N N N 4.452 5.202 16.658 0.673 -1.106 -2.448 H1 VA5 33
VA5 H2 H2 H 0 1 N N N 1.793 3.227 13.586 4.611 -1.477 1.367 H2 VA5 34
VA5 H3 H3 H 0 1 N N N 2.545 2.852 17.157 7.696 3.074 0.194 H3 VA5 35
VA5 H4 H4 H 0 1 N N N 3.466 -0.534 17.516 6.921 0.380 1.647 H4 VA5 36
VA5 H5 H5 H 0 1 N N N 2.815 6.956 13.602 -1.455 -2.619 -0.654 H5 VA5 37
VA5 H6 H6 H 0 1 N N N 3.105 5.333 12.891 -0.767 -3.344 0.819 H6 VA5 38
VA5 H7 H7 H 0 1 N N N 2.423 7.343 11.396 -1.868 -1.516 2.164 H7 VA5 39
VA5 H8 H8 H 0 1 N N N 5.416 6.374 11.449 -4.258 -1.311 -0.830 H8 VA5 40
VA5 H9 H9 H 0 1 N N N 8.340 8.816 6.516 -8.667 -0.046 -2.264 H9 VA5 41
VA5 H10 H10 H 0 1 N N N 11.796 8.557 9.425 -8.936 4.067 -0.312 H10 VA5 42
VA5 H11 H11 H 0 1 N N N 11.051 8.915 10.833 -7.565 4.216 0.648 H11 VA5 43
VA5 H12 H12 H 0 1 N N N 6.907 6.892 12.599 -3.736 1.467 1.708 H12 VA5 44
VA5 H13 H13 H 0 1 N N N 5.334 5.394 9.348 -4.905 -1.507 2.161 H13 VA5 45
VA5 H14 H14 H 0 1 N N N 4.413 6.797 8.709 -5.483 -2.555 0.821 H14 VA5 46
VA5 H15 H15 H 0 1 N N N 2.750 5.966 9.708 -3.330 -3.327 2.330 H15 VA5 47
VA5 H16 H16 H 0 1 N N N 3.575 4.520 11.819 -4.055 -4.456 0.317 H16 VA5 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
VA5 C2 N1 DOUB Y N 1
VA5 C2 N3 SING Y N 2
VA5 N1 C6 SING Y N 3
VA5 N3 C4 DOUB Y N 4
VA5 C6 N6 SING N N 5
VA5 C6 C5 DOUB Y N 6
VA5 C4 C5 SING Y N 7
VA5 C4 N9 SING Y N 8
VA5 "C2'" "C3'" SING N N 9
VA5 "C2'" "C1'" SING N N 10
VA5 C5 N7 SING Y N 11
VA5 "C3'" "O3'" SING N N 12
VA5 "C3'" "C4'" SING N N 13
VA5 N9 "C1'" SING N N 14
VA5 N9 C8 SING Y N 15
VA5 "C1'" "O4'" SING N N 16
VA5 "O4'" "C4'" SING N N 17
VA5 N7 C8 DOUB Y N 18
VA5 "C4'" "C5'" SING N N 19
VA5 O2B PB DOUB N N 20
VA5 "C5'" "O5'" SING N N 21
VA5 "O5'" PA SING N N 22
VA5 PB O3A SING N N 23
VA5 PB O1B SING N N 24
VA5 PB C3B SING N N 25
VA5 O3A PA SING N N 26
VA5 F3B C3B SING N N 27
VA5 PA O2A DOUB N N 28
VA5 PA O1A SING N N 29
VA5 C3B CL1 SING N N 30
VA5 C3B PG SING N N 31
VA5 O3G PG DOUB N N 32
VA5 PG O1G SING N N 33
VA5 PG O2G SING N N 34
VA5 O1A H1 SING N N 35
VA5 O1B H2 SING N N 36
VA5 O1G H3 SING N N 37
VA5 O2G H4 SING N N 38
VA5 "C5'" H5 SING N N 39
VA5 "C5'" H6 SING N N 40
VA5 "C4'" H7 SING N N 41
VA5 "C1'" H8 SING N N 42
VA5 C2 H9 SING N N 43
VA5 N6 H10 SING N N 44
VA5 N6 H11 SING N N 45
VA5 C8 H12 SING N N 46
VA5 "C2'" H13 SING N N 47
VA5 "C2'" H14 SING N N 48
VA5 "C3'" H15 SING N N 49
VA5 "O3'" 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
VA5 SMILES ACDLabs 12.01 "P(=O)(O)(OP(O)(C(Cl)(P(O)(O)=O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O"
VA5 InChI InChI 1.03 "InChI=1S/C11H16ClFN5O11P3/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+,11-/m1/s1"
VA5 InChIKey InChI 1.03 MGXOAMBWOAGILL-FHZUQPTBSA-N
VA5 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)(Cl)[P](O)(O)=O)O3"
VA5 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[C](F)(Cl)[P](O)(O)=O)O3"
VA5 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)(P(=O)(O)O)Cl)O)O)N"
VA5 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)(P(=O)(O)O)Cl)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
VA5 "SYSTEMATIC NAME" ACDLabs 12.01 "9-{5-O-[(R)-{[(R)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-deoxy-alpha-D-threo-pentofuranosyl}-9H-purin-6-amine"
VA5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(2~{R},3~{R},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-chloranyl-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
VA5 "Create component" 2018-03-22 RCSB
VA5 "Initial release" 2018-07-04 RCSB
#