data_NP3 # _chem_comp.id NP3 _chem_comp.name "1-[2-DEOXY-RIBOFURANOSYL]-1H-[3-NITRO-PYRROL]-5'-PHOSPHATE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-12-20 _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 308.182 _chem_comp.one_letter_code N _chem_comp.three_letter_code NP3 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "Corina V3.40" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1DK6 _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 NP3 P P P 0 1 N N N -1.567 -8.712 11.284 4.322 -1.093 -0.031 P NP3 1 NP3 O1P O1P O 0 1 N N N -2.224 -9.789 10.510 4.047 -1.788 1.247 O1P NP3 2 NP3 O2P O2P O 0 1 N N N -0.226 -8.225 10.882 5.569 -0.093 0.160 O2P NP3 3 NP3 O3P O3P O 0 1 N Y N -1.527 -9.160 12.844 4.673 -2.178 -1.168 O3P NP3 4 NP3 "O5'" O5* O 0 1 N N N -2.575 -7.437 11.351 3.022 -0.252 -0.474 "O5'" NP3 5 NP3 "C5'" C5* C 0 1 N N N -3.863 -7.588 11.983 2.397 0.717 0.369 "C5'" NP3 6 NP3 "C4'" C4* C 0 1 N N R -4.528 -6.288 12.468 1.196 1.326 -0.356 "C4'" NP3 7 NP3 "O4'" O4* O 0 1 N N N -3.617 -5.643 13.367 0.166 0.334 -0.555 "O4'" NP3 8 NP3 "C1'" C1* C 0 1 N N R -3.220 -4.424 12.746 -1.068 1.044 -0.752 "C1'" NP3 9 NP3 N1 N1 N 0 1 Y N N -1.799 -4.211 12.866 -2.180 0.283 -0.177 N1 NP3 10 NP3 C5 C5 C 0 1 Y N N -1.194 -3.301 13.677 -2.139 -0.424 0.989 C5 NP3 11 NP3 C2 C2 C 0 1 Y N N -0.816 -4.830 12.195 -3.427 0.168 -0.715 C2 NP3 12 NP3 C3 C3 C 0 1 Y N N 0.397 -4.386 12.501 -4.168 -0.609 0.101 C3 NP3 13 NP3 C4 C4 C 0 1 Y N N 0.128 -3.409 13.456 -3.349 -0.985 1.184 C4 NP3 14 NP3 N3 N3 N 1 1 N N N 1.542 -4.749 11.975 -5.583 -0.993 -0.102 N3 NP3 15 NP3 ON1 ON1 O -1 1 N N N 1.966 -4.114 10.970 -6.187 -0.598 -1.084 ON1 NP3 16 NP3 ON2 ON2 O 0 1 N N N 2.198 -5.707 12.458 -6.144 -1.704 0.712 ON2 NP3 17 NP3 "C2'" C2* C 0 1 N N N -3.605 -4.566 11.280 -0.936 2.401 -0.035 "C2'" NP3 18 NP3 "C3'" C3* C 0 1 N N S -4.912 -5.273 11.379 0.505 2.392 0.531 "C3'" NP3 19 NP3 "O3'" O3* O 0 1 N N N -5.966 -4.392 11.819 1.125 3.670 0.370 "O3'" NP3 20 NP3 HOP2 2HOP H 0 0 N N N -0.196 -8.121 9.938 5.805 0.398 -0.639 HOP2 NP3 21 NP3 HOP3 3HOP H 0 0 N N N -1.519 -10.108 12.902 5.446 -2.722 -0.967 HOP3 NP3 22 NP3 "H5'1" 1H5* H 0 0 N N N -4.539 -8.049 11.247 2.062 0.237 1.288 "H5'1" NP3 23 NP3 "H5'2" 2H5* H 0 0 N N N -3.688 -8.193 12.885 3.112 1.504 0.611 "H5'2" NP3 24 NP3 "H4'" H4* H 0 1 N N N -5.478 -6.596 12.928 1.502 1.757 -1.309 "H4'" NP3 25 NP3 "H1'" H1* H 0 1 N N N -3.708 -3.562 13.224 -1.239 1.201 -1.817 "H1'" NP3 26 NP3 H5 H5 H 0 1 N N N -1.681 -2.624 14.364 -1.284 -0.518 1.642 H5 NP3 27 NP3 H2 H2 H 0 1 N N N -0.994 -5.615 11.475 -3.764 0.621 -1.635 H2 NP3 28 NP3 H4 H4 H 0 1 N N N 0.881 -2.816 13.953 -3.638 -1.607 2.018 H4 NP3 29 NP3 "H2'1" 1H2* H 0 0 N N N -3.698 -3.591 10.779 -1.063 3.221 -0.742 "H2'1" NP3 30 NP3 "H2'2" 2H2* H 0 0 N N N -2.857 -5.099 10.674 -1.663 2.478 0.774 "H2'2" NP3 31 NP3 "H3'" H3* H 0 1 N N N -5.305 -5.694 10.442 0.510 2.089 1.578 "H3'" NP3 32 NP3 H3T H3T H 0 1 N Y N -5.853 -4.198 12.742 0.727 4.370 0.905 H3T NP3 33 # 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 NP3 P O1P DOUB N N 1 NP3 P O2P SING N N 2 NP3 P O3P SING N N 3 NP3 P "O5'" SING N N 4 NP3 O2P HOP2 SING N N 5 NP3 O3P HOP3 SING N N 6 NP3 "O5'" "C5'" SING N N 7 NP3 "C5'" "C4'" SING N N 8 NP3 "C5'" "H5'1" SING N N 9 NP3 "C5'" "H5'2" SING N N 10 NP3 "C4'" "O4'" SING N N 11 NP3 "C4'" "C3'" SING N N 12 NP3 "C4'" "H4'" SING N N 13 NP3 "O4'" "C1'" SING N N 14 NP3 "C1'" N1 SING N N 15 NP3 "C1'" "C2'" SING N N 16 NP3 "C1'" "H1'" SING N N 17 NP3 N1 C5 SING Y N 18 NP3 N1 C2 SING Y N 19 NP3 C5 C4 DOUB Y N 20 NP3 C5 H5 SING N N 21 NP3 C2 C3 DOUB Y N 22 NP3 C2 H2 SING N N 23 NP3 C3 C4 SING Y N 24 NP3 C3 N3 SING N N 25 NP3 C4 H4 SING N N 26 NP3 N3 ON1 SING N N 27 NP3 N3 ON2 DOUB N N 28 NP3 "C2'" "C3'" SING N N 29 NP3 "C2'" "H2'1" SING N N 30 NP3 "C2'" "H2'2" SING N N 31 NP3 "C3'" "O3'" SING N N 32 NP3 "C3'" "H3'" SING N N 33 NP3 "O3'" H3T SING N N 34 # 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 NP3 SMILES ACDLabs 10.04 "[O-][N+](=O)c1ccn(c1)C2OC(C(O)C2)COP(=O)(O)O" NP3 SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccc(c2)[N+]([O-])=O" NP3 SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccc(c2)[N+]([O-])=O" NP3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cn(cc1[N+](=O)[O-])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" NP3 SMILES "OpenEye OEToolkits" 1.5.0 "c1cn(cc1[N+](=O)[O-])C2CC(C(O2)COP(=O)(O)O)O" NP3 InChI InChI 1.03 "InChI=1S/C9H13N2O8P/c12-7-3-9(10-2-1-6(4-10)11(13)14)19-8(7)5-18-20(15,16)17/h1-2,4,7-9,12H,3,5H2,(H2,15,16,17)/t7-,8+,9+/m0/s1" NP3 InChIKey InChI 1.03 RZUPPTSNKSBSQO-DJLDLDEBSA-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 NP3 "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-nitro-1H-pyrrole" NP3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(3-nitropyrrol-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 NP3 "Create component" 1999-12-20 RCSB NP3 "Modify descriptor" 2011-06-04 RCSB #