data_VA4
#
_chem_comp.id VA4
_chem_comp.name "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 Cl 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 523.654
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VA4
_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 6CR8
_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
VA4 N1 N1 N 0 1 Y N N 9.737 8.481 8.240 -8.240 -2.235 -0.773 N1 VA4 1
VA4 C2 C1 C 0 1 Y N N 8.574 8.562 7.641 -7.774 -1.451 -1.727 C2 VA4 2
VA4 N3 N2 N 0 1 Y N N 7.434 8.260 8.240 -6.682 -0.730 -1.579 N3 VA4 3
VA4 C4 C2 C 0 1 Y N N 7.455 7.887 9.521 -5.996 -0.766 -0.442 C4 VA4 4
VA4 C5 C3 C 0 1 Y N N 8.666 7.795 10.234 -6.452 -1.586 0.605 C5 VA4 5
VA4 C6 C4 C 0 1 Y N N 9.835 8.108 9.512 -7.622 -2.336 0.399 C6 VA4 6
VA4 N6 N3 N 0 1 N N N 11.163 8.007 10.166 -8.118 -3.161 1.393 N6 VA4 7
VA4 N7 N4 N 0 1 Y N N 8.373 7.362 11.525 -5.583 -1.439 1.634 N7 VA4 8
VA4 C8 C5 C 0 1 Y N N 7.066 7.230 11.602 -4.646 -0.603 1.294 C8 VA4 9
VA4 N9 N5 N 0 1 Y N N 6.484 7.541 10.395 -4.856 -0.160 0.022 N9 VA4 10
VA4 PA P1 P 0 1 N N N 4.909 5.345 14.703 1.584 1.626 0.788 PA VA4 11
VA4 PB P2 P 0 1 N N N 3.850 2.708 13.872 4.200 0.345 0.238 PB VA4 12
VA4 PG P3 P 0 1 N N N 3.963 1.321 16.588 6.479 -1.348 -0.658 PG VA4 13
VA4 "C1'" C6 C 0 1 N N R 5.056 7.476 10.061 -4.019 0.790 -0.714 "C1'" VA4 14
VA4 O1A O1 O 0 1 N N N 3.918 5.448 15.862 1.375 1.314 2.354 O1A VA4 15
VA4 O2B O2 O 0 1 N N N 3.765 2.203 12.398 4.601 0.140 1.648 O2B VA4 16
VA4 O1G O3 O 0 1 N N N 3.576 2.738 17.003 6.915 -1.571 0.876 O1G VA4 17
VA4 "C2'" C7 C 0 1 N N N 4.767 6.262 9.698 -4.533 2.233 -0.508 "C2'" VA4 18
VA4 O2A O4 O 0 1 N N N 6.286 5.505 15.212 2.139 2.988 0.626 O2A VA4 19
VA4 O1B O5 O 0 1 N N N 2.414 3.047 14.380 4.940 1.650 -0.346 O1B VA4 20
VA4 O2G O6 O 0 1 N N N 5.069 0.803 17.602 6.897 -2.637 -1.528 O2G VA4 21
VA4 "C3'" C8 C 0 1 N N S 4.250 5.582 10.914 -3.245 3.083 -0.434 "C3'" VA4 22
VA4 "O3'" O7 O 0 1 N N N 3.448 4.483 10.659 -3.216 4.041 -1.493 "O3'" VA4 23
VA4 O3A O8 O 0 1 N N N 4.858 3.938 13.888 2.605 0.552 0.159 O3A VA4 24
VA4 C3B C9 C 0 1 N N R 4.681 1.401 14.936 4.673 -1.114 -0.747 C3B VA4 25
VA4 CL1 CL1 CL 0 0 N N N 4.632 -0.196 14.210 3.844 -2.576 -0.093 CL3B VA4 26
VA4 O3G O9 O 0 1 N N N 2.819 0.413 16.632 7.159 -0.148 -1.195 O3G VA4 27
VA4 "C4'" C10 C 0 1 N N R 3.439 6.773 11.576 -2.105 2.054 -0.604 "C4'" VA4 28
VA4 "O4'" O10 O 0 1 N N N 4.160 7.750 11.383 -2.677 0.797 -0.181 "O4'" VA4 29
VA4 "C5'" C11 C 0 1 N N N 3.297 6.523 13.073 -0.916 2.424 0.285 "C5'" VA4 30
VA4 "O5'" O11 O 0 1 N N N 4.589 6.461 13.598 0.168 1.529 0.028 "O5'" VA4 31
VA4 H1 H1 H 0 1 N N N 8.545 8.890 6.612 -8.308 -1.398 -2.665 H1 VA4 32
VA4 H2 H2 H 0 1 N N N 11.877 8.253 9.511 -8.927 -3.674 1.238 H2 VA4 33
VA4 H3 H3 H 0 1 N N N 11.198 8.630 10.947 -7.658 -3.227 2.244 H3 VA4 34
VA4 H4 H4 H 0 1 N N N 6.528 6.922 12.486 -3.823 -0.303 1.926 H4 VA4 35
VA4 H5 H5 H 0 1 N N N 4.801 8.231 9.303 -4.004 0.539 -1.775 H5 VA4 36
VA4 H6 H6 H 0 1 N N N 4.392 5.594 16.672 1.013 0.436 2.535 H6 VA4 37
VA4 H7 H7 H 0 1 N N N 2.650 2.765 17.215 6.507 -2.342 1.293 H7 VA4 38
VA4 H8 H8 H 0 1 N N N 4.000 6.271 8.910 -5.147 2.543 -1.353 H8 VA4 39
VA4 H9 H9 H 0 1 N N N 5.667 5.750 9.327 -5.095 2.308 0.422 H9 VA4 40
VA4 H10 H10 H 0 1 N N N 1.785 2.877 13.689 4.723 1.846 -1.268 H10 VA4 41
VA4 H11 H11 H 0 1 N N N 4.762 0.012 18.029 7.846 -2.822 -1.526 H11 VA4 42
VA4 H12 H12 H 0 1 N N N 5.087 5.320 11.577 -3.170 3.579 0.534 H12 VA4 43
VA4 H13 H13 H 0 1 N N N 3.638 3.799 11.290 -3.945 4.676 -1.469 H13 VA4 44
VA4 H14 H14 H 0 1 N N N 5.735 1.697 15.043 4.377 -0.963 -1.785 H14 VA4 45
VA4 H15 H15 H 0 1 N N N 2.444 6.832 11.111 -1.795 1.999 -1.647 H15 VA4 46
VA4 H16 H16 H 0 1 N N N 2.737 7.345 13.542 -0.604 3.445 0.068 H16 VA4 47
VA4 H17 H17 H 0 1 N N N 2.771 5.573 13.250 -1.208 2.349 1.333 H17 VA4 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
VA4 C2 N1 DOUB Y N 1
VA4 C2 N3 SING Y N 2
VA4 N1 C6 SING Y N 3
VA4 N3 C4 DOUB Y N 4
VA4 C6 N6 SING N N 5
VA4 C6 C5 DOUB Y N 6
VA4 C4 C5 SING Y N 7
VA4 C4 N9 SING Y N 8
VA4 "C2'" "C1'" SING N N 9
VA4 "C2'" "C3'" SING N N 10
VA4 "C1'" N9 SING N N 11
VA4 "C1'" "O4'" SING N N 12
VA4 C5 N7 SING Y N 13
VA4 N9 C8 SING Y N 14
VA4 "O3'" "C3'" SING N N 15
VA4 "C3'" "C4'" SING N N 16
VA4 "O4'" "C4'" SING N N 17
VA4 N7 C8 DOUB Y N 18
VA4 "C4'" "C5'" SING N N 19
VA4 O2B PB DOUB N N 20
VA4 "C5'" "O5'" SING N N 21
VA4 "O5'" PA SING N N 22
VA4 PB O3A SING N N 23
VA4 PB O1B SING N N 24
VA4 PB C3B SING N N 25
VA4 O3A PA SING N N 26
VA4 CL1 C3B SING N N 27
VA4 PA O2A DOUB N N 28
VA4 PA O1A SING N N 29
VA4 C3B PG SING N N 30
VA4 PG O3G DOUB N N 31
VA4 PG O1G SING N N 32
VA4 PG O2G SING N N 33
VA4 C2 H1 SING N N 34
VA4 N6 H2 SING N N 35
VA4 N6 H3 SING N N 36
VA4 C8 H4 SING N N 37
VA4 "C1'" H5 SING N N 38
VA4 O1A H6 SING N N 39
VA4 O1G H7 SING N N 40
VA4 "C2'" H8 SING N N 41
VA4 "C2'" H9 SING N N 42
VA4 O1B H10 SING N N 43
VA4 O2G H11 SING N N 44
VA4 "C3'" H12 SING N N 45
VA4 "O3'" H13 SING N N 46
VA4 C3B H14 SING N N 47
VA4 "C4'" H15 SING N N 48
VA4 "C5'" H16 SING N N 49
VA4 "C5'" H17 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
VA4 SMILES ACDLabs 12.01 "n1c(c2c(nc1)n(cn2)C3OC(C(C3)O)COP(=O)(O)OP(O)(C(P(=O)(O)O)Cl)=O)N"
VA4 InChI InChI 1.03 "InChI=1S/C11H17ClN5O11P3/c12-11(29(19,20)21)30(22,23)28-31(24,25)26-2-6-5(18)1-7(27-6)17-4-16-8-9(13)14-3-15-10(8)17/h3-7,11,18H,1-2H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t5-,6+,7+,11+/m0/s1"
VA4 InChIKey InChI 1.03 VNWJWEHIFBMHOO-ZSJKCOSDSA-N
VA4 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](Cl)[P](O)(O)=O)O3"
VA4 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O3"
VA4 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@@H](P(=O)(O)O)Cl)O)O)N"
VA4 SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(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
VA4 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyadenosine"
VA4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-[[[(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-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
VA4 "Create component" 2018-03-22 RCSB
VA4 "Initial release" 2018-07-04 RCSB
#