data_SP1
#
_chem_comp.id SP1
_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 "SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-12-13
_chem_comp.pdbx_modified_date 2021-03-13
_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 SP1
_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 1NE6
_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
SP1 P P P 0 1 N N S 39.403 47.444 83.986 -3.739 0.195 0.406 P SP1 1
SP1 S1P S1P S 0 1 N N N 39.316 45.780 83.197 -3.274 1.917 0.946 S1P SP1 2
SP1 O2P O2P O 0 1 N N N 38.765 48.594 83.302 -5.153 -0.202 1.067 O2P SP1 3
SP1 "O5'" O5* O 0 1 N N N 38.751 47.291 85.440 -3.877 0.163 -1.194 "O5'" SP1 4
SP1 "C5'" C5* C 0 1 N N N 39.469 46.643 86.502 -2.587 0.418 -1.768 "C5'" SP1 5
SP1 "C4'" C4* C 0 1 N N R 40.855 47.215 86.562 -1.638 -0.652 -1.266 "C4'" SP1 6
SP1 "O4'" O4* O 0 1 N N N 41.694 46.587 87.556 -0.332 -0.652 -1.822 "O4'" SP1 7
SP1 "C3'" C3* C 0 1 N N S 41.597 46.957 85.279 -1.419 -0.414 0.251 "C3'" SP1 8
SP1 "O3'" O3* O 0 1 N N N 40.945 47.770 84.320 -2.608 -0.842 0.909 "O3'" SP1 9
SP1 "C2'" C2* C 0 1 N N R 43.037 47.233 85.695 -0.204 -1.336 0.491 "C2'" SP1 10
SP1 "O2'" O2* O 0 1 N N N 43.370 48.610 85.798 -0.613 -2.697 0.633 "O2'" SP1 11
SP1 "C1'" C1* C 0 1 N N R 43.040 46.625 87.105 0.592 -1.136 -0.825 "C1'" SP1 12
SP1 N9 N9 N 0 1 Y N N 43.601 45.276 87.231 1.659 -0.154 -0.618 N9 SP1 13
SP1 C8 C8 C 0 1 Y N N 44.626 44.905 88.071 1.589 1.181 -0.881 C8 SP1 14
SP1 N7 N7 N 0 1 Y N N 44.942 43.637 87.990 2.718 1.754 -0.578 N7 SP1 15
SP1 C5 C5 C 0 1 Y N N 44.067 43.136 87.035 3.580 0.826 -0.097 C5 SP1 16
SP1 C6 C6 C 0 1 Y N N 43.887 41.849 86.521 4.906 0.855 0.366 C6 SP1 17
SP1 N6 N6 N 0 1 N N N 44.632 40.808 86.888 5.616 2.042 0.408 N6 SP1 18
SP1 N1 N1 N 0 1 Y N N 42.908 41.663 85.610 5.461 -0.283 0.768 N1 SP1 19
SP1 C2 C2 C 0 1 Y N N 42.163 42.720 85.251 4.792 -1.421 0.732 C2 SP1 20
SP1 N3 N3 N 0 1 Y N N 42.244 43.985 85.661 3.551 -1.497 0.300 N3 SP1 21
SP1 C4 C4 C 0 1 Y N N 43.231 44.129 86.562 2.913 -0.411 -0.122 C4 SP1 22
SP1 HOP2 2HOP H 0 0 N N N 38.629 49.298 83.925 -5.797 0.451 0.763 HOP2 SP1 23
SP1 "H5'1" 1H5* H 0 0 N N N 39.518 45.560 86.316 -2.232 1.401 -1.457 "H5'1" SP1 24
SP1 "H5'2" 2H5* H 0 0 N N N 38.954 46.816 87.458 -2.651 0.375 -2.855 "H5'2" SP1 25
SP1 "H4'" H4* H 0 1 N N N 40.693 48.280 86.783 -2.091 -1.632 -1.413 "H4'" SP1 26
SP1 "H3'" H3* H 0 1 N N N 41.606 45.967 84.800 -1.194 0.627 0.481 "H3'" SP1 27
SP1 "H2'" H2* H 0 1 N N N 43.757 46.834 84.965 0.369 -1.009 1.359 "H2'" SP1 28
SP1 "HO2'" *HO2 H 0 0 N N N 43.444 48.851 86.714 0.189 -3.216 0.780 "HO2'" SP1 29
SP1 "H1'" H1* H 0 1 N N N 43.701 47.267 87.705 1.020 -2.086 -1.147 "H1'" SP1 30
SP1 H8 H8 H 0 1 N N N 45.124 45.596 88.735 0.725 1.689 -1.282 H8 SP1 31
SP1 HN61 1HN6 H 0 0 N N N 45.495 41.135 87.273 6.529 2.050 0.734 HN61 SP1 32
SP1 HN62 2HN6 H 0 0 N N N 44.819 40.234 86.091 5.201 2.866 0.108 HN62 SP1 33
SP1 H2 H2 H 0 1 N N N 41.388 42.516 84.527 5.282 -2.323 1.068 H2 SP1 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
SP1 P S1P DOUB N N 1
SP1 P O2P SING N N 2
SP1 P "O5'" SING N N 3
SP1 P "O3'" SING N N 4
SP1 O2P HOP2 SING N N 5
SP1 "O5'" "C5'" SING N N 6
SP1 "C5'" "C4'" SING N N 7
SP1 "C5'" "H5'1" SING N N 8
SP1 "C5'" "H5'2" SING N N 9
SP1 "C4'" "O4'" SING N N 10
SP1 "C4'" "C3'" SING N N 11
SP1 "C4'" "H4'" SING N N 12
SP1 "O4'" "C1'" SING N N 13
SP1 "C3'" "O3'" SING N N 14
SP1 "C3'" "C2'" SING N N 15
SP1 "C3'" "H3'" SING N N 16
SP1 "C2'" "O2'" SING N N 17
SP1 "C2'" "C1'" SING N N 18
SP1 "C2'" "H2'" SING N N 19
SP1 "O2'" "HO2'" SING N N 20
SP1 "C1'" N9 SING N N 21
SP1 "C1'" "H1'" SING N N 22
SP1 N9 C8 SING Y N 23
SP1 N9 C4 SING Y N 24
SP1 C8 N7 DOUB Y N 25
SP1 C8 H8 SING N N 26
SP1 N7 C5 SING Y N 27
SP1 C5 C6 DOUB Y N 28
SP1 C5 C4 SING Y N 29
SP1 C6 N6 SING N N 30
SP1 C6 N1 SING Y N 31
SP1 N6 HN61 SING N N 32
SP1 N6 HN62 SING N N 33
SP1 N1 C2 DOUB Y N 34
SP1 C2 N3 SING Y N 35
SP1 C2 H2 SING N N 36
SP1 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
SP1 SMILES ACDLabs 10.04 "S=P3(OCC4OC(n1c2ncnc(N)c2nc1)C(O)C4O3)O"
SP1 SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@@H]4CO[P@](O)(=S)O[C@H]4[C@H]3O"
SP1 SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH]4CO[P](O)(=S)O[CH]4[CH]3O"
SP1 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"
SP1 SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C4C(O3)COP(=S)(O4)O)O)N"
SP1 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"
SP1 InChIKey InChI 1.03 SMPNJFHAPJOHPP-LHKKBNDGSA-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
SP1 "SYSTEMATIC NAME" ACDLabs 10.04 "(2S,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"
SP1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1R,4S,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
SP1 "Create component" 2002-12-13 RCSB
SP1 "Modify descriptor" 2011-06-04 RCSB
SP1 "Modify synonyms" 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SP1
_pdbx_chem_comp_synonyms.name "SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
##