data_APW
#
_chem_comp.id APW
_chem_comp.name "{5'-O-[(R)-{[(S)-AMINO(HYDROXY-KAPPAO)PHOSPHORYL]OXY}(HYDROXY-KAPPAO)PHOSPHORYL]ADENOSINATO(2-)}MAGNESIUM"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H14 Mg N6 O9 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "MAGNESIUM-5'-ADENYLY-BETA-AMIDO-DIPHOSPHATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-02-19
_chem_comp.pdbx_modified_date 2020-06-17
_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 448.505
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code APW
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_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
APW MG MG MG 0 0 N N N 29.717 29.386 18.759 -5.845 -0.950 0.038 MG APW 1
APW O2A O2A O 0 1 N N N 28.749 31.125 19.304 -4.103 -1.713 0.039 O2A APW 2
APW PA PA P 0 1 N N R 29.072 31.992 20.626 -3.273 -0.302 -0.087 PA APW 3
APW O1A O1A O 0 1 N N N 28.872 33.540 20.320 -3.133 0.318 1.250 O1A APW 4
APW O3A O3A O 0 1 N N N 30.541 31.675 21.324 -4.107 0.677 -1.058 O3A APW 5
APW PB PB P 0 1 N N S 31.542 30.367 21.265 -5.133 1.595 -0.222 PB APW 6
APW O1B O1B O 0 1 N N N 32.137 30.159 22.606 -5.318 2.893 -0.909 O1B APW 7
APW O2B O2B O 0 1 N N N 30.561 29.366 20.662 -6.568 0.800 -0.141 O2B APW 8
APW N3B N3B N 0 1 N N N 32.772 30.789 20.108 -4.534 1.851 1.329 N3B APW 9
APW "O5'" O5* O 0 1 N N N 27.989 31.483 21.700 -1.816 -0.580 -0.714 "O5'" APW 10
APW "C5'" C5* C 0 1 N N N 27.945 32.109 22.975 -1.100 -1.368 0.239 "C5'" APW 11
APW "C4'" C4* C 0 1 N N R 26.496 32.415 23.266 0.301 -1.669 -0.298 "C4'" APW 12
APW "C3'" C3* C 0 1 N N S 26.364 33.211 24.545 1.080 -2.560 0.694 "C3'" APW 13
APW "O3'" O3* O 0 1 N N N 26.605 34.593 24.300 1.020 -3.930 0.290 "O3'" APW 14
APW "C2'" C2* C 0 1 N N R 24.934 32.914 24.931 2.532 -2.033 0.614 "C2'" APW 15
APW "O2'" O2* O 0 1 N N N 24.034 33.738 24.188 3.414 -3.062 0.160 "O2'" APW 16
APW "C1'" C1* C 0 1 N N R 24.772 31.454 24.525 2.455 -0.884 -0.416 "C1'" APW 17
APW "O4'" O4* O 0 1 N N N 25.717 31.226 23.468 1.076 -0.454 -0.391 "O4'" APW 18
APW N9 N9 N 0 1 Y N N 25.131 30.642 25.709 3.339 0.215 -0.020 N9 APW 19
APW C4 C4 C 0 1 Y N N 24.567 30.740 26.918 4.673 0.332 -0.320 C4 APW 20
APW C5 C5 C 0 1 Y N N 25.249 29.764 27.776 5.098 1.535 0.270 C5 APW 21
APW N7 N7 N 0 1 Y N N 26.168 29.151 27.009 4.019 2.084 0.879 N7 APW 22
APW C8 C8 C 0 1 Y N N 26.088 29.696 25.766 2.987 1.309 0.713 C8 APW 23
APW N3 N3 N 0 1 Y N N 23.579 31.490 27.452 5.552 -0.404 -0.990 N3 APW 24
APW C2 C2 C 0 1 Y N N 23.229 31.339 28.745 6.804 -0.014 -1.108 C2 APW 25
APW N1 N1 N 0 1 Y N N 23.806 30.467 29.590 7.248 1.111 -0.577 N1 APW 26
APW C6 C6 C 0 1 Y N N 24.805 29.654 29.182 6.442 1.912 0.111 C6 APW 27
APW N6 N6 N 0 1 N N N 25.400 28.773 30.025 6.917 3.089 0.664 N6 APW 28
APW H3B1 1H3B H 0 0 N N N 33.186 31.662 20.366 -3.718 2.436 1.232 H3B1 APW 29
APW H3B2 2H3B H 0 0 N N N 32.362 30.870 19.200 -5.226 2.398 1.821 H3B2 APW 30
APW "H5'1" 1H5* H 0 0 N N N 28.548 33.029 22.981 -1.632 -2.303 0.411 "H5'1" APW 31
APW "H5'2" 2H5* H 0 0 N N N 28.355 31.438 23.744 -1.019 -0.818 1.177 "H5'2" APW 32
APW "H4'" H4* H 0 1 N N N 26.132 32.972 22.390 0.236 -2.153 -1.273 "H4'" APW 33
APW "H3'" H3* H 0 1 N N N 27.082 32.954 25.338 0.685 -2.443 1.703 "H3'" APW 34
APW H2 H2 H 0 1 N N N 26.659 35.057 25.127 1.522 -4.436 0.944 H2 APW 35
APW H1 H1 H 0 1 N N N 24.720 33.102 25.993 2.855 -1.655 1.583 H1 APW 36
APW "H2'" H2* H 0 1 N N N 23.264 33.921 24.714 3.371 -3.774 0.813 "H2'" APW 37
APW "H1'" H1* H 0 1 N N N 23.755 31.201 24.191 2.721 -1.246 -1.409 "H1'" APW 38
APW H8 H8 H 0 1 N N N 26.711 29.408 24.932 1.997 1.505 1.099 H8 APW 39
APW H3 H3 H 0 1 N N N 22.432 31.960 29.127 7.493 -0.636 -1.660 H3 APW 40
APW HN61 1HN6 H 0 0 N N N 26.280 29.141 30.325 7.848 3.337 0.551 HN61 APW 41
APW HN62 2HN6 H 0 0 N N N 25.546 27.905 29.551 6.318 3.668 1.161 HN62 APW 42
# #
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
APW MG O2A SING N N 1
APW MG O2B SING N N 2
APW O2A PA SING N N 3
APW PA O1A DOUB N N 4
APW PA O3A SING N N 5
APW PA "O5'" SING N N 6
APW O3A PB SING N N 7
APW PB O1B DOUB N N 8
APW PB O2B SING N N 9
APW PB N3B SING N N 10
APW N3B H3B1 SING N N 11
APW N3B H3B2 SING N N 12
APW "O5'" "C5'" SING N N 13
APW "C5'" "C4'" SING N N 14
APW "C5'" "H5'1" SING N N 15
APW "C5'" "H5'2" SING N N 16
APW "C4'" "C3'" SING N N 17
APW "C4'" "O4'" SING N N 18
APW "C4'" "H4'" SING N N 19
APW "C3'" "O3'" SING N N 20
APW "C3'" "C2'" SING N N 21
APW "C3'" "H3'" SING N N 22
APW "O3'" H2 SING N N 23
APW "C2'" "O2'" SING N N 24
APW "C2'" "C1'" SING N N 25
APW "C2'" H1 SING N N 26
APW "O2'" "H2'" SING N N 27
APW "C1'" "O4'" SING N N 28
APW "C1'" N9 SING N N 29
APW "C1'" "H1'" SING N N 30
APW N9 C4 SING Y N 31
APW N9 C8 SING Y N 32
APW C4 C5 SING Y N 33
APW C4 N3 DOUB Y N 34
APW C5 N7 SING Y N 35
APW C5 C6 DOUB Y N 36
APW N7 C8 DOUB Y N 37
APW C8 H8 SING N N 38
APW N3 C2 SING Y N 39
APW C2 N1 DOUB Y N 40
APW C2 H3 SING N N 41
APW N1 C6 SING Y N 42
APW C6 N6 SING N N 43
APW N6 HN61 SING N N 44
APW N6 HN62 SING N N 45
# #
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
APW SMILES ACDLabs 10.04 "O=P4(O[Mg]OP(=O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)O4)N"
APW SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@]4(=O)O[Mg]O[P@](N)(=O)O4)[C@@H](O)[C@H]3O"
APW SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P]4(=O)O[Mg]O[P](N)(=O)O4)[CH](O)[CH]3O"
APW SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@]4(=O)O[Mg]O[P@](=O)(O4)N)O)O)N"
APW SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP4(=O)O[Mg]OP(=O)(O4)N)O)O)N"
APW InChI InChI 1.03 "InChI=1S/C10H16N6O9P2.Mg/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(24-10)1-23-27(21,22)25-26(12,19)20;/h2-4,6-7,10,17-18H,1H2,(H,21,22)(H2,11,13,14)(H3,12,19,20);/q;+2/p-2/t4-,6-,7-,10-;/m1./s1"
APW InChIKey InChI 1.03 XFWUVFOBMRZZRT-MCDZGGTQSA-L
# #
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
APW "SYSTEMATIC NAME" ACDLabs 10.04 "{5'-O-[(R)-{[(S)-amino(hydroxy-kappaO)phosphoryl]oxy}(hydroxy-kappaO)phosphoryl]adenosinato(2-)}magnesium"
APW "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4R,5R)-2-[[(2R,4S)-4-amino-2,4-dioxo-1,3,5-trioxa-2$l^{5},4$l^{5}-diphospha-6$l^{2}-magnesacyclohex-2-yl]oxymethyl]-5-(6-aminopurin-9-yl)oxolane-3,4-diol"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
APW "Create component" 2006-02-19 RCSB
APW "Modify descriptor" 2011-06-04 RCSB
APW "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id APW
_pdbx_chem_comp_synonyms.name "MAGNESIUM-5'-ADENYLY-BETA-AMIDO-DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##