data_RP1
#
_chem_comp.id RP1
_chem_comp.name "6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2-D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H12 N5 O5 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "RP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-12-13
_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 345.272
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RP1
_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 1NE4
_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
RP1 P P P 0 1 N N R 38.974 46.920 84.298 -3.849 0.110 0.375 P RP1 1
RP1 S1P S1P S 0 1 N N N 38.362 48.345 83.474 -5.446 -0.826 0.593 S1P RP1 2
RP1 O2P O2P O 0 1 N N N 38.784 45.593 83.667 -3.706 1.195 1.556 O2P RP1 3
RP1 "O5'" O5* O 0 1 N N N 38.358 46.856 85.772 -3.871 0.869 -1.041 "O5'" RP1 4
RP1 "C5'" C5* C 0 1 N N N 39.074 46.196 86.828 -2.597 1.497 -1.242 "C5'" RP1 5
RP1 "C4'" C4* C 0 1 N N R 40.486 46.691 86.816 -1.537 0.411 -1.211 "C4'" RP1 6
RP1 "O4'" O4* O 0 1 N N N 41.341 46.072 87.793 -0.200 0.842 -1.464 "O4'" RP1 7
RP1 "C3'" C3* C 0 1 N N S 41.194 46.368 85.528 -1.455 -0.145 0.235 "C3'" RP1 8
RP1 "O3'" O3* O 0 1 N N N 40.544 47.166 84.555 -2.612 -0.927 0.453 "O3'" RP1 9
RP1 "C2'" C2* C 0 1 N N R 42.643 46.686 85.893 -0.130 -0.926 0.179 "C2'" RP1 10
RP1 "O2'" O2* O 0 1 N N N 42.961 48.068 85.874 -0.367 -2.298 -0.143 "O2'" RP1 11
RP1 "C1'" C1* C 0 1 N N R 42.683 46.205 87.350 0.652 -0.211 -0.951 "C1'" RP1 12
RP1 N9 N9 N 0 1 Y N N 43.364 44.935 87.570 1.888 0.365 -0.415 N9 RP1 13
RP1 C8 C8 C 0 1 Y N N 44.292 44.670 88.545 2.059 1.645 0.022 C8 RP1 14
RP1 N7 N7 N 0 1 Y N N 44.757 43.448 88.507 3.282 1.815 0.431 N7 RP1 15
RP1 C5 C5 C 0 1 Y N N 44.093 42.869 87.438 3.971 0.657 0.289 C5 RP1 16
RP1 C6 C6 C 0 1 Y N N 44.164 41.599 86.874 5.292 0.255 0.547 C6 RP1 17
RP1 N6 N6 N 0 1 N N N 44.995 40.652 87.314 6.210 1.142 1.083 N6 RP1 18
RP1 N1 N1 N 0 1 Y N N 43.360 41.329 85.821 5.639 -0.997 0.269 N1 RP1 19
RP1 C2 C2 C 0 1 Y N N 42.557 42.295 85.368 4.770 -1.850 -0.243 C2 RP1 20
RP1 N3 N3 N 0 1 Y N N 42.415 43.537 85.806 3.524 -1.516 -0.506 N3 RP1 21
RP1 C4 C4 C 0 1 Y N N 43.223 43.766 86.856 3.086 -0.286 -0.262 C4 RP1 22
RP1 HOP2 2HOP H 0 0 N N N 38.743 45.694 82.723 -4.472 1.781 1.491 HOP2 RP1 23
RP1 "H5'1" 1H5* H 0 0 N N N 39.053 45.107 86.678 -2.410 2.218 -0.446 "H5'1" RP1 24
RP1 "H5'2" 2H5* H 0 0 N N N 38.606 46.424 87.797 -2.582 2.000 -2.209 "H5'2" RP1 25
RP1 "H4'" H4* H 0 1 N N N 40.352 47.767 87.002 -1.806 -0.388 -1.901 "H4'" RP1 26
RP1 "H3'" H3* H 0 1 N N N 41.174 45.352 85.108 -1.402 0.674 0.953 "H3'" RP1 27
RP1 "H2'" H2* H 0 1 N N N 43.351 46.227 85.187 0.407 -0.841 1.124 "H2'" RP1 28
RP1 "HO2'" *HO2 H 0 0 N N N 43.032 48.389 86.765 0.496 -2.733 -0.164 "HO2'" RP1 29
RP1 "H1'" H1* H 0 1 N N N 43.263 46.954 87.909 0.886 -0.919 -1.746 "H1'" RP1 30
RP1 H8 H8 H 0 1 N N N 44.609 45.401 89.274 1.292 2.405 0.027 H8 RP1 31
RP1 HN61 1HN6 H 0 0 N N N 45.841 41.075 87.637 7.118 0.851 1.260 HN61 RP1 32
RP1 HN62 2HN6 H 0 0 N N N 45.203 40.018 86.569 5.946 2.055 1.277 HN62 RP1 33
RP1 H2 H2 H 0 1 N N N 41.936 42.026 84.526 5.094 -2.858 -0.453 H2 RP1 34
# #
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
RP1 P S1P DOUB N N 1
RP1 P O2P SING N N 2
RP1 P "O5'" SING N N 3
RP1 P "O3'" SING N N 4
RP1 O2P HOP2 SING N N 5
RP1 "O5'" "C5'" SING N N 6
RP1 "C5'" "C4'" SING N N 7
RP1 "C5'" "H5'1" SING N N 8
RP1 "C5'" "H5'2" SING N N 9
RP1 "C4'" "O4'" SING N N 10
RP1 "C4'" "C3'" SING N N 11
RP1 "C4'" "H4'" SING N N 12
RP1 "O4'" "C1'" SING N N 13
RP1 "C3'" "O3'" SING N N 14
RP1 "C3'" "C2'" SING N N 15
RP1 "C3'" "H3'" SING N N 16
RP1 "C2'" "O2'" SING N N 17
RP1 "C2'" "C1'" SING N N 18
RP1 "C2'" "H2'" SING N N 19
RP1 "O2'" "HO2'" SING N N 20
RP1 "C1'" N9 SING N N 21
RP1 "C1'" "H1'" SING N N 22
RP1 N9 C8 SING Y N 23
RP1 N9 C4 SING Y N 24
RP1 C8 N7 DOUB Y N 25
RP1 C8 H8 SING N N 26
RP1 N7 C5 SING Y N 27
RP1 C5 C6 DOUB Y N 28
RP1 C5 C4 SING Y N 29
RP1 C6 N6 SING N N 30
RP1 C6 N1 SING Y N 31
RP1 N6 HN61 SING N N 32
RP1 N6 HN62 SING N N 33
RP1 N1 C2 DOUB Y N 34
RP1 C2 N3 SING Y N 35
RP1 C2 H2 SING N N 36
RP1 N3 C4 DOUB Y N 37
# #
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
RP1 SMILES ACDLabs 10.04 "S=P3(OCC4OC(n1c2ncnc(N)c2nc1)C(O)C4O3)O"
RP1 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@@](O)(=S)O[C@H]4[C@H]3O"
RP1 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=S)O[CH]4[CH]3O"
RP1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=S)(O4)O)O)N"
RP1 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=S)(O4)O)O)N"
RP1 InChI InChI 1.03 "InChI=1S/C10H12N5O5PS/c11-8-5-9(13-2-12-8)15(3-14-5)10-6(16)7-4(19-10)1-18-21(17,22)20-7/h2-4,6-7,10,16H,1H2,(H,17,22)(H2,11,12,13)/t4-,6-,7-,10-,21-/m1/s1"
RP1 InChIKey InChI 1.03 SMPNJFHAPJOHPP-PUHOFUEYSA-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
RP1 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,4aR,6R,7R,7aS)-6-(6-amino-9H-purin-9-yl)tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-sulfide"
RP1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,4R,6S,7R,8R)-8-(6-aminopurin-9-yl)-4-hydroxy-4-sulfanylidene-3,5,9-trioxa-4$l^{5}-phosphabicyclo[4.3.0]nonan-7-ol"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
RP1 "Create component" 2002-12-13 RCSB
RP1 "Modify descriptor" 2011-06-04 RCSB
RP1 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id RP1
_pdbx_chem_comp_synonyms.name "RP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##