data_PYP # _chem_comp.id PYP _chem_comp.name "2'-DEOXYRIBOFURANOSYLPYRENE-5'-MONOPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H19 O6 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2000-10-04 _chem_comp.pdbx_modified_date 2011-06-04 _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 398.346 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PYP _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1FZS _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 PYP P P P 0 1 N N N 5.631 6.116 -8.149 -5.787 0.921 -0.337 P PYP 1 PYP O1P O1P O 0 1 N N N 4.711 5.705 -9.234 -6.874 0.068 0.194 O1P PYP 2 PYP O2P O2P O 0 1 N N N 7.079 6.249 -8.429 -5.473 2.103 0.710 O2P PYP 3 PYP "O5'" "O5'" O 0 1 N N N 5.111 7.517 -7.524 -4.463 0.030 -0.553 "O5'" PYP 4 PYP "C5'" "C5'" C 0 1 N N N 4.165 8.407 -8.135 -3.872 -0.751 0.488 "C5'" PYP 5 PYP "C4'" "C4'" C 0 1 N N R 2.794 7.756 -8.350 -2.635 -1.469 -0.054 "C4'" PYP 6 PYP "O4'" "O4'" O 0 1 N N N 2.272 7.311 -7.076 -1.618 -0.509 -0.386 "O4'" PYP 7 PYP "C1'" "C1'" C 0 1 N N R 1.051 8.023 -6.811 -0.345 -1.127 -0.100 "C1'" PYP 8 PYP C1 C1 C 0 1 Y N N 1.808 8.660 -4.450 0.352 1.289 0.489 C1 PYP 9 PYP C2 C2 C 0 1 Y N N 1.563 8.816 -3.073 1.277 2.211 0.658 C2 PYP 10 PYP C3 C3 C 0 1 Y N N 0.041 8.689 -1.147 3.752 2.879 0.626 C3 PYP 11 PYP C4 C4 C 0 1 Y N N -1.230 8.410 -0.612 5.015 2.555 0.430 C4 PYP 12 PYP C5 C5 C 0 1 Y N N -3.578 7.674 -0.937 6.777 0.799 -0.193 C5 PYP 13 PYP C6 C6 C 0 1 Y N N -4.629 7.236 -1.775 7.067 -0.436 -0.549 C6 PYP 14 PYP C7 C7 C 0 1 Y N N -4.383 7.085 -3.155 5.998 -1.436 -0.726 C7 PYP 15 PYP C8 C8 C 0 1 Y N N -2.872 7.207 -5.095 3.651 -2.066 -0.694 C8 PYP 16 PYP C9 C9 C 0 1 Y N N -1.603 7.485 -5.640 2.395 -1.743 -0.501 C9 PYP 17 PYP C10 C10 C 0 1 Y N N 0.734 8.206 -5.318 0.723 -0.081 0.089 C10 PYP 18 PYP C11 C11 C 0 1 Y N N -0.520 7.935 -4.774 1.987 -0.387 -0.102 C11 PYP 19 PYP C12 C12 C 0 1 Y N N 0.247 8.518 -2.566 2.694 1.871 0.445 C12 PYP 20 PYP C13 C13 C 0 1 Y N N -2.274 7.961 -1.508 5.373 1.183 0.031 C13 PYP 21 PYP C14 C14 C 0 1 Y N N -3.066 7.380 -3.680 4.744 -1.095 -0.528 C14 PYP 22 PYP C15 C15 C 0 1 Y N N -0.771 8.086 -3.409 3.016 0.650 0.089 C15 PYP 23 PYP C16 C16 C 0 1 Y N N -2.029 7.812 -2.867 4.427 0.288 -0.129 C16 PYP 24 PYP "C2'" "C2'" C 0 1 N N N 1.196 9.332 -7.585 -0.602 -1.890 1.224 "C2'" PYP 25 PYP "C3'" "C3'" C 0 1 N N S 1.752 8.734 -8.909 -2.052 -2.398 1.030 "C3'" PYP 26 PYP "O3'" "O3'" O 0 1 N N N 0.713 8.019 -9.591 -2.051 -3.754 0.579 "O3'" PYP 27 PYP O3P O3P O 0 1 N N N ? ? ? -6.241 1.556 -1.745 O3P PYP 28 PYP HOP2 HOP2 H 0 0 N N N 7.219 6.277 -9.368 -4.769 2.703 0.426 HOP2 PYP 29 PYP "H5'1" "H5'1" H 0 0 N N N 4.036 9.280 -7.479 -3.582 -0.099 1.311 "H5'1" PYP 30 PYP "H5'2" "H5'2" H 0 0 N N N 4.560 8.688 -9.122 -4.593 -1.487 0.844 "H5'2" PYP 31 PYP "H4'" "H4'" H 0 1 N N N 2.952 6.935 -9.065 -2.900 -2.049 -0.938 "H4'" PYP 32 PYP "H1'" "H1'" H 0 1 N N N 0.173 7.451 -7.145 -0.067 -1.818 -0.896 "H1'" PYP 33 PYP H1 H1 H 0 1 N N N 2.785 8.876 -4.858 -0.687 1.537 0.649 H1 PYP 34 PYP H2 H2 H 0 1 N N N 2.346 9.152 -2.409 0.997 3.213 0.950 H2 PYP 35 PYP H3 H3 H 0 1 N N N 0.846 9.024 -0.510 3.493 3.886 0.918 H3 PYP 36 PYP H4 H4 H 0 1 N N N -1.422 8.528 0.444 5.789 3.297 0.563 H4 PYP 37 PYP H5 H5 H 0 1 N N N -3.744 7.795 0.123 7.565 1.526 -0.065 H5 PYP 38 PYP H6 H6 H 0 1 N N N -5.605 7.021 -1.365 8.096 -0.717 -0.713 H6 PYP 39 PYP H7 H7 H 0 1 N N N -5.170 6.752 -3.815 6.246 -2.445 -1.018 H7 PYP 40 PYP H8 H8 H 0 1 N N N -3.682 6.871 -5.726 3.892 -3.077 -0.986 H8 PYP 41 PYP H9 H9 H 0 1 N N N -1.432 7.365 -6.700 1.634 -2.497 -0.638 H9 PYP 42 PYP "H2'2" "H2'2" H 0 0 N N N 0.248 9.875 -7.712 0.090 -2.725 1.333 "H2'2" PYP 43 PYP "H2'1" "H2'1" H 0 0 N N N 1.816 10.106 -7.109 -0.537 -1.218 2.079 "H2'1" PYP 44 PYP "H3'" "H3'" H 0 1 N N N 2.145 9.466 -9.630 -2.617 -2.303 1.957 "H3'" PYP 45 PYP H3T H3T H 0 1 N N N -0.008 7.861 -8.993 -1.694 -4.382 1.222 H3T PYP 46 PYP HOP3 HOP3 H 0 0 N N N ? ? ? -7.035 2.107 -1.690 HOP3 PYP 47 # 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 PYP P O1P DOUB N N 1 PYP P O2P SING N N 2 PYP P "O5'" SING N N 3 PYP P O3P SING N N 4 PYP O2P HOP2 SING N N 5 PYP "O5'" "C5'" SING N N 6 PYP "C5'" "C4'" SING N N 7 PYP "C5'" "H5'1" SING N N 8 PYP "C5'" "H5'2" SING N N 9 PYP "C4'" "O4'" SING N N 10 PYP "C4'" "C3'" SING N N 11 PYP "C4'" "H4'" SING N N 12 PYP "O4'" "C1'" SING N N 13 PYP "C1'" C10 SING N N 14 PYP "C1'" "C2'" SING N N 15 PYP "C1'" "H1'" SING N N 16 PYP C1 C2 DOUB Y N 17 PYP C1 C10 SING Y N 18 PYP C1 H1 SING N N 19 PYP C2 C12 SING Y N 20 PYP C2 H2 SING N N 21 PYP C3 C4 DOUB Y N 22 PYP C3 C12 SING Y N 23 PYP C3 H3 SING N N 24 PYP C4 C13 SING Y N 25 PYP C4 H4 SING N N 26 PYP C5 C6 DOUB Y N 27 PYP C5 C13 SING Y N 28 PYP C5 H5 SING N N 29 PYP C6 C7 SING Y N 30 PYP C6 H6 SING N N 31 PYP C7 C14 DOUB Y N 32 PYP C7 H7 SING N N 33 PYP C8 C9 DOUB Y N 34 PYP C8 C14 SING Y N 35 PYP C8 H8 SING N N 36 PYP C9 C11 SING Y N 37 PYP C9 H9 SING N N 38 PYP C10 C11 DOUB Y N 39 PYP C11 C15 SING Y N 40 PYP C12 C15 DOUB Y N 41 PYP C13 C16 DOUB Y N 42 PYP C14 C16 SING Y N 43 PYP C15 C16 SING Y N 44 PYP "C2'" "C3'" SING N N 45 PYP "C2'" "H2'2" SING N N 46 PYP "C2'" "H2'1" SING N N 47 PYP "C3'" "O3'" SING N N 48 PYP "C3'" "H3'" SING N N 49 PYP "O3'" H3T SING N N 50 PYP O3P HOP3 SING N N 51 # 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 PYP SMILES ACDLabs 10.04 "O=P(OCC5OC(c4c1c3c2c(cc1)cccc2ccc3cc4)CC5O)(O)O" PYP SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)c2ccc3ccc4cccc5ccc2c3c45" PYP SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)c2ccc3ccc4cccc5ccc2c3c45" PYP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O" PYP SMILES "OpenEye OEToolkits" 1.5.0 "c1cc2ccc3ccc(c4c3c2c(c1)cc4)C5CC(C(O5)COP(=O)(O)O)O" PYP InChI InChI 1.03 "InChI=1S/C21H19O6P/c22-17-10-18(27-19(17)11-26-28(23,24)25)15-8-6-14-5-4-12-2-1-3-13-7-9-16(15)21(14)20(12)13/h1-9,17-19,22H,10-11H2,(H2,23,24,25)/t17-,18+,19+/m0/s1" PYP InChIKey InChI 1.03 JJJZGYICTVDZQU-IPMKNSEASA-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 PYP "SYSTEMATIC NAME" ACDLabs 10.04 "(1R)-1,4-anhydro-2-deoxy-5-O-phosphono-1-pyren-1-yl-D-erythro-pentitol" PYP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-pyren-1-yl-oxolan-2-yl]methyl dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site PYP "Create component" 2000-10-04 EBI PYP "Modify descriptor" 2011-06-04 RCSB #