data_VT8
#
_chem_comp.id VT8
_chem_comp.name "5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 Cl2 N2 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 549.086
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VT8
_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 6CTI
_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
VT8 N1 N1 N 0 1 N N N 6.800 7.539 10.183 5.375 -0.462 0.447 N1 VT8 1
VT8 C2 C1 C 0 1 N N N 7.664 7.948 9.246 5.579 -0.373 -0.879 C2 VT8 2
VT8 O2 O1 O 0 1 N N N 7.255 8.251 8.167 5.053 0.525 -1.508 O2 VT8 3
VT8 N3 N2 N 0 1 N N N 8.988 8.000 9.463 6.357 -1.265 -1.521 N3 VT8 4
VT8 C4 C2 C 0 1 N N N 9.509 7.659 10.665 6.947 -2.267 -0.839 C4 VT8 5
VT8 O4 O2 O 0 1 N N N 10.706 7.723 10.856 7.652 -3.073 -1.419 O4 VT8 6
VT8 C5 C3 C 0 1 N N N 8.647 7.220 11.702 6.740 -2.372 0.558 C5 VT8 7
VT8 C7 C4 C 0 1 N N N 9.139 6.805 13.086 7.388 -3.483 1.344 C7 VT8 8
VT8 C6 C5 C 0 1 N N N 7.269 7.188 11.402 5.955 -1.464 1.176 C6 VT8 9
VT8 PA P1 P 0 1 N N N 5.122 5.208 14.603 -0.879 1.656 -0.841 PA VT8 10
VT8 PB P2 P 0 1 N N N 4.060 2.618 13.795 -3.593 0.510 -0.523 PB VT8 11
VT8 PG P3 P 0 1 N N N 4.080 1.311 16.425 -6.023 -1.067 0.164 PG VT8 12
VT8 "C1'" C6 C 0 1 N N R 5.480 7.450 9.914 4.528 0.526 1.119 "C1'" VT8 13
VT8 O1A O3 O 0 1 N N N 4.077 5.287 15.721 -0.555 1.341 -2.386 O1A VT8 14
VT8 O2B O4 O 0 1 N N N 3.964 2.158 12.327 -3.885 0.331 -1.963 O2B VT8 15
VT8 O1G O5 O 0 1 N N N 3.916 2.736 16.793 -6.340 -1.261 -1.402 O1G VT8 16
VT8 "C2'" C7 C 0 1 N N N 5.081 6.025 9.540 5.130 1.941 0.969 "C2'" VT8 17
VT8 O2A O6 O 0 1 N N N 6.546 5.321 15.137 -1.375 3.045 -0.714 O2A VT8 18
VT8 O1B O7 O 0 1 N N N 2.681 2.982 14.268 -4.312 1.849 0.008 O1B VT8 19
VT8 CL1 CL1 CL 0 0 N N N 4.724 -0.307 14.094 -3.417 -2.427 -0.188 CL1 VT8 20
VT8 O2G O8 O 0 1 N N N 4.971 0.663 17.459 -6.578 -2.336 0.985 O2G VT8 21
VT8 "C3'" C8 C 0 1 N N S 4.635 5.503 10.665 3.898 2.857 0.794 "C3'" VT8 22
VT8 "O3'" O9 O 0 1 N N N 3.793 4.301 10.551 3.829 3.811 1.855 "O3'" VT8 23
VT8 O3A O10 O 0 1 N N N 5.040 3.844 13.783 -2.003 0.634 -0.309 O3A VT8 24
VT8 C3B C9 C 0 1 N N N 4.856 1.292 14.805 -4.222 -0.927 0.407 C3B VT8 25
VT8 O3G O11 O 0 1 N N N 2.752 0.590 16.282 -6.684 0.164 0.652 O3G VT8 26
VT8 "C4'" C10 C 0 1 N N R 3.837 6.737 11.338 2.697 1.887 0.859 "C4'" VT8 27
VT8 "O4'" O12 O 0 1 N N N 4.588 7.732 11.157 3.238 0.604 0.475 "O4'" VT8 28
VT8 "C5'" C11 C 0 1 N N N 3.595 6.473 12.871 1.608 2.322 -0.123 "C5'" VT8 29
VT8 "O5'" O13 O 0 1 N N N 4.878 6.383 13.512 0.462 1.484 0.035 "O5'" VT8 30
VT8 CL2 CL2 CL 0 0 N N N 6.536 1.575 15.017 -3.867 -0.710 2.161 CL2 VT8 31
VT8 H1 H1 H 0 1 N N N 9.597 8.295 8.727 6.493 -1.186 -2.478 H1 VT8 32
VT8 H2 H2 H 0 1 N N N 8.281 6.507 13.706 7.978 -4.107 0.672 H2 VT8 33
VT8 H3 H3 H 0 1 N N N 9.834 5.958 12.989 8.038 -3.056 2.108 H3 VT8 34
VT8 H4 H4 H 0 1 N N N 9.657 7.652 13.560 6.617 -4.089 1.819 H4 VT8 35
VT8 H5 H5 H 0 1 N N N 6.571 6.875 12.165 5.787 -1.528 2.241 H5 VT8 36
VT8 H6 H6 H 0 1 N N N 5.183 8.132 9.104 4.411 0.272 2.173 H6 VT8 37
VT8 H7 H7 H 0 1 N N N 4.515 5.394 16.557 -0.224 0.446 -2.544 H7 VT8 38
VT8 H8 H8 H 0 1 N N N 2.991 2.938 16.873 -5.938 -2.050 -1.790 H8 VT8 39
VT8 H9 H9 H 0 1 N N N 4.292 6.030 8.774 5.686 2.216 1.865 H9 VT8 40
VT8 H10 H10 H 0 1 N N N 5.950 5.463 9.168 5.772 1.992 0.090 H10 VT8 41
VT8 H11 H11 H 0 1 N N N 2.059 2.849 13.563 -4.164 2.029 0.947 H11 VT8 42
VT8 H12 H12 H 0 1 N N N 4.527 -0.088 17.834 -7.532 -2.472 0.902 H12 VT8 43
VT8 H13 H13 H 0 1 N N N 5.474 5.271 11.337 3.931 3.360 -0.172 H13 VT8 44
VT8 H14 H14 H 0 1 N N N 4.008 3.695 11.251 4.589 4.408 1.898 H14 VT8 45
VT8 H15 H15 H 0 1 N N N 2.861 6.827 10.838 2.298 1.845 1.872 H15 VT8 46
VT8 H16 H16 H 0 1 N N N 3.017 7.302 13.306 1.331 3.357 0.076 H16 VT8 47
VT8 H17 H17 H 0 1 N N N 3.043 5.531 13.005 1.983 2.237 -1.143 H17 VT8 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
VT8 O2 C2 DOUB N N 1
VT8 C2 N3 SING N N 2
VT8 C2 N1 SING N N 3
VT8 N3 C4 SING N N 4
VT8 "C2'" "C1'" SING N N 5
VT8 "C2'" "C3'" SING N N 6
VT8 "C1'" N1 SING N N 7
VT8 "C1'" "O4'" SING N N 8
VT8 N1 C6 SING N N 9
VT8 "O3'" "C3'" SING N N 10
VT8 "C3'" "C4'" SING N N 11
VT8 C4 O4 DOUB N N 12
VT8 C4 C5 SING N N 13
VT8 "O4'" "C4'" SING N N 14
VT8 "C4'" "C5'" SING N N 15
VT8 C6 C5 DOUB N N 16
VT8 C5 C7 SING N N 17
VT8 O2B PB DOUB N N 18
VT8 "C5'" "O5'" SING N N 19
VT8 "O5'" PA SING N N 20
VT8 O3A PB SING N N 21
VT8 O3A PA SING N N 22
VT8 PB O1B SING N N 23
VT8 PB C3B SING N N 24
VT8 CL1 C3B SING N N 25
VT8 PA O2A DOUB N N 26
VT8 PA O1A SING N N 27
VT8 C3B CL2 SING N N 28
VT8 C3B PG SING N N 29
VT8 O3G PG DOUB N N 30
VT8 PG O1G SING N N 31
VT8 PG O2G SING N N 32
VT8 N3 H1 SING N N 33
VT8 C7 H2 SING N N 34
VT8 C7 H3 SING N N 35
VT8 C7 H4 SING N N 36
VT8 C6 H5 SING N N 37
VT8 "C1'" H6 SING N N 38
VT8 O1A H7 SING N N 39
VT8 O1G H8 SING N N 40
VT8 "C2'" H9 SING N N 41
VT8 "C2'" H10 SING N N 42
VT8 O1B H11 SING N N 43
VT8 O2G H12 SING N N 44
VT8 "C3'" H13 SING N N 45
VT8 "O3'" H14 SING N N 46
VT8 "C4'" H15 SING N N 47
VT8 "C5'" H16 SING N N 48
VT8 "C5'" H17 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
VT8 SMILES ACDLabs 12.01 "N1(C=C(C(NC1=O)=O)C)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)(Cl)Cl)=O"
VT8 InChI InChI 1.03 "InChI=1S/C11H17Cl2N2O13P3/c1-5-3-15(10(18)14-9(5)17)8-2-6(16)7(27-8)4-26-31(24,25)28-30(22,23)11(12,13)29(19,20)21/h3,6-8,16H,2,4H2,1H3,(H,22,23)(H,24,25)(H,14,17,18)(H2,19,20,21)/t6-,7+,8+/m0/s1"
VT8 InChIKey InChI 1.03 SHEBHODIZXGBLE-XLPZGREQSA-N
VT8 SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
VT8 SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
VT8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O"
VT8 SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)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
VT8 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
VT8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[bis(chloranyl)-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]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
VT8 "Create component" 2018-03-26 RCSB
VT8 "Initial release" 2018-06-20 RCSB
#