data_VC8
#
_chem_comp.id VC8
_chem_comp.name "4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 Cl2 N3 O12 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 534.074
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VC8
_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 6CTW
_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
VC8 C4 C1 C 0 1 N N N 9.363 7.537 10.928 -6.561 -3.057 -0.243 C4 VC8 1
VC8 N4 N1 N 0 1 N N N 10.794 7.560 11.151 -7.172 -4.285 -0.144 N4 VC8 2
VC8 C5 C2 C 0 1 N N N 8.556 7.153 11.969 -6.481 -2.403 -1.489 C5 VC8 3
VC8 C6 C3 C 0 1 N N N 7.195 7.138 11.718 -5.874 -1.194 -1.559 C6 VC8 4
VC8 N3 N2 N 0 1 N N N 8.823 7.874 9.764 -6.050 -2.477 0.836 N3 VC8 5
VC8 C2 C4 C 0 1 N N N 7.507 7.838 9.587 -5.456 -1.288 0.752 C2 VC8 6
VC8 O2 O1 O 0 1 N N N 7.028 8.138 8.534 -4.993 -0.776 1.758 O2 VC8 7
VC8 N1 N3 N 0 1 N N N 6.680 7.473 10.542 -5.359 -0.642 -0.425 N1 VC8 8
VC8 "C1'" C5 C 0 1 N N R 5.237 7.423 10.188 -4.700 0.665 -0.486 "C1'" VC8 9
VC8 "C2'" C6 C 0 1 N N N 4.906 6.225 9.724 -5.465 1.694 0.384 "C2'" VC8 10
VC8 "C3'" C7 C 0 1 N N S 4.491 5.347 10.924 -4.335 2.711 0.701 "C3'" VC8 11
VC8 "O3'" O2 O 0 1 N N N 3.498 4.398 10.735 -4.189 3.657 -0.360 "O3'" VC8 12
VC8 "O4'" O3 O 0 1 N N N 4.198 7.640 11.383 -3.387 0.589 0.092 "O4'" VC8 13
VC8 "C4'" C8 C 0 1 N N S 4.246 6.490 11.946 -3.093 1.799 0.800 "C4'" VC8 14
VC8 "C5'" C9 C 0 1 N N N 3.422 6.280 13.225 -1.888 2.494 0.162 "C5'" VC8 15
VC8 "O5'" O4 O 0 1 N N N 4.635 6.221 13.933 -0.719 1.696 0.360 "O5'" VC8 16
VC8 PA P1 P 0 1 N N N 4.899 4.921 14.888 0.736 2.123 -0.182 PA VC8 17
VC8 O1A O5 O 0 1 N N N 3.830 4.946 15.934 1.220 3.459 0.575 O1A VC8 18
VC8 O2A O6 O 0 1 N N N 6.286 5.014 15.444 0.665 2.378 -1.638 O2A VC8 19
VC8 O3A O7 O 0 1 N N N 4.865 3.632 13.887 1.785 0.935 0.104 O3A VC8 20
VC8 PB P2 P 0 1 N N N 3.828 2.388 13.872 3.264 0.596 -0.434 PB VC8 21
VC8 O1B O8 O 0 1 N N N 2.483 2.804 14.392 3.224 0.411 -2.033 O1B VC8 22
VC8 O2B O9 O 0 1 N N N 3.719 1.922 12.436 4.181 1.704 -0.088 O2B VC8 23
VC8 C3B C10 C 0 1 N N N 4.553 1.055 14.951 3.854 -0.945 0.341 C3B VC8 24
VC8 CL1 CL1 CL 0 0 N N N 6.259 1.421 15.278 3.898 -0.738 2.132 CL1 VC8 25
VC8 CL2 CL2 CL 0 0 N N N 4.509 -0.532 14.160 2.736 -2.296 -0.080 CL2 VC8 26
VC8 PG P3 P 0 1 N N N 3.713 0.965 16.600 5.529 -1.329 -0.267 PG VC8 27
VC8 O2G O10 O 0 1 N N N 3.539 2.372 17.109 6.526 -0.123 0.109 O2G VC8 28
VC8 O1G O11 O 0 1 N N N 4.602 0.204 17.535 6.049 -2.690 0.417 O1G VC8 29
VC8 O3G O12 O 0 1 N N N 2.402 0.249 16.453 5.492 -1.499 -1.737 O3G VC8 30
VC8 H1 H1 H 0 1 N N N 11.411 7.837 10.414 -7.549 -4.705 -0.933 H1 VC8 31
VC8 H2 H2 H 0 1 N N N 11.165 7.299 12.042 -7.226 -4.733 0.715 H2 VC8 32
VC8 H3 H3 H 0 1 N N N 8.961 6.877 12.932 -6.896 -2.860 -2.376 H3 VC8 33
VC8 H4 H4 H 0 1 N N N 6.525 6.842 12.512 -5.800 -0.674 -2.502 H4 VC8 34
VC8 H5 H5 H 0 1 N N N 5.035 8.202 9.438 -4.639 1.010 -1.518 H5 VC8 35
VC8 H6 H6 H 0 1 N N N 4.066 6.316 9.020 -6.269 2.165 -0.182 H6 VC8 36
VC8 H7 H7 H 0 1 N N N 5.767 5.773 9.210 -5.846 1.233 1.295 H7 VC8 37
VC8 H8 H8 H 0 1 N N N 5.402 4.829 11.257 -4.522 3.216 1.649 H8 VC8 38
VC8 H9 H9 H 0 1 N N N 3.344 3.933 11.549 -4.977 4.194 -0.519 H9 VC8 39
VC8 H10 H10 H 0 1 N N N 5.249 6.528 12.396 -2.881 1.575 1.845 H10 VC8 40
VC8 H11 H11 H 0 1 N N N 2.775 7.127 13.496 -2.065 2.620 -0.906 H11 VC8 41
VC8 H12 H12 H 0 1 N N N 2.836 5.350 13.244 -1.744 3.470 0.625 H12 VC8 42
VC8 H13 H13 H 0 1 N N N 4.229 5.019 16.793 1.289 3.365 1.535 H13 VC8 43
VC8 H14 H14 H 0 1 N N N 1.831 2.690 13.711 2.642 -0.300 -2.332 H14 VC8 44
VC8 H15 H15 H 0 1 N N N 2.615 2.548 17.245 6.600 0.045 1.058 H15 VC8 45
VC8 H16 H16 H 0 1 N N N 4.150 -0.574 17.840 6.936 -2.956 0.139 H16 VC8 46
#
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
VC8 O2 C2 DOUB N N 1
VC8 C2 N3 SING N N 2
VC8 C2 N1 SING N N 3
VC8 "C2'" "C1'" SING N N 4
VC8 "C2'" "C3'" SING N N 5
VC8 N3 C4 DOUB N N 6
VC8 "C1'" N1 SING N N 7
VC8 "C1'" "O4'" SING N N 8
VC8 N1 C6 SING N N 9
VC8 "O3'" "C3'" SING N N 10
VC8 "C3'" "C4'" SING N N 11
VC8 C4 N4 SING N N 12
VC8 C4 C5 SING N N 13
VC8 "O4'" "C4'" SING N N 14
VC8 C6 C5 DOUB N N 15
VC8 "C4'" "C5'" SING N N 16
VC8 O2B PB DOUB N N 17
VC8 "C5'" "O5'" SING N N 18
VC8 PB O3A SING N N 19
VC8 PB O1B SING N N 20
VC8 PB C3B SING N N 21
VC8 O3A PA SING N N 22
VC8 "O5'" PA SING N N 23
VC8 CL2 C3B SING N N 24
VC8 PA O2A DOUB N N 25
VC8 PA O1A SING N N 26
VC8 C3B CL1 SING N N 27
VC8 C3B PG SING N N 28
VC8 O3G PG DOUB N N 29
VC8 PG O2G SING N N 30
VC8 PG O1G SING N N 31
VC8 N4 H1 SING N N 32
VC8 N4 H2 SING N N 33
VC8 C5 H3 SING N N 34
VC8 C6 H4 SING N N 35
VC8 "C1'" H5 SING N N 36
VC8 "C2'" H6 SING N N 37
VC8 "C2'" H7 SING N N 38
VC8 "C3'" H8 SING N N 39
VC8 "O3'" H9 SING N N 40
VC8 "C4'" H10 SING N N 41
VC8 "C5'" H11 SING N N 42
VC8 "C5'" H12 SING N N 43
VC8 O1A H13 SING N N 44
VC8 O1B H14 SING N N 45
VC8 O2G H15 SING N N 46
VC8 O1G H16 SING N N 47
#
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
VC8 SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)(P(O)(O)=O)Cl)=O"
VC8 InChI InChI 1.03 "InChI=1S/C10H16Cl2N3O12P3/c11-10(12,28(18,19)20)29(21,22)27-30(23,24)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,21,22)(H,23,24)(H2,13,14,17)(H2,18,19,20)/t5-,6-,8+/m0/s1"
VC8 InChIKey InChI 1.03 UVMWAJJREHNIPG-VMHSAVOQSA-N
VC8 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@H](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2"
VC8 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Cl)(Cl)[P](O)(O)=O)O2"
VC8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Cl)Cl)O)O"
VC8 SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)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
VC8 "SYSTEMATIC NAME" ACDLabs 12.01 "4-amino-1-{2-deoxy-5-O-[(R)-{[(R)-[dichloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-L-threo-pentofuranosyl}pyrimidin-2(1H)-one"
VC8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{S},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(chloranyl)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
VC8 "Create component" 2018-03-26 RCSB
VC8 "Initial release" 2018-06-20 RCSB
#