data_2LA # _chem_comp.id 2LA _chem_comp.name "2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H18 N5 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-09-07 _chem_comp.pdbx_modified_date 2012-08-24 _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 375.274 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2LA _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 2LIA _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 2LA P P P 0 1 N N N 5.425 0.049 28.927 5.225 -0.745 -0.479 P 2LA 1 2LA N1 N1 N 0 1 N N N -2.123 1.080 23.061 -5.421 0.288 -0.570 N1 2LA 2 2LA C2 C2 C 0 1 N N N -2.423 0.102 23.928 -4.700 1.377 -0.960 C2 2LA 3 2LA N2 N2 N 0 1 N N N -3.578 -0.490 23.775 -5.357 2.439 -1.530 N2 2LA 4 2LA N3 N3 N 0 1 N N N -1.624 -0.374 24.857 -3.397 1.443 -0.808 N3 2LA 5 2LA C4 C4 C 0 1 Y N N -0.415 0.211 24.818 -2.710 0.432 -0.257 C4 2LA 6 2LA C5 C5 C 0 1 Y N N 0.011 1.180 23.950 -3.399 -0.714 0.163 C5 2LA 7 2LA C6 C6 C 0 1 N N N -0.912 1.685 22.986 -4.800 -0.773 -0.006 C6 2LA 8 2LA O6 O6 O 0 1 N N N -0.749 2.570 22.155 -5.432 -1.753 0.348 O6 2LA 9 2LA C7 C7 C 0 1 Y N N 1.369 1.552 24.139 -2.392 -1.621 0.711 C7 2LA 10 2LA C8 C8 C 0 1 Y N N 1.698 0.688 25.169 -1.208 -0.999 0.596 C8 2LA 11 2LA N9 N9 N 0 1 Y N N 0.666 -0.099 25.607 -1.388 0.232 0.017 N9 2LA 12 2LA "C1'" C1* C 0 1 N N R 0.691 -1.113 26.675 -0.318 1.191 -0.267 C1* 2LA 13 2LA C10 C10 C 0 1 N N N 2.402 2.448 23.477 -2.636 -2.990 1.294 C10 2LA 14 2LA N11 N11 N 0 1 N N N 1.816 3.576 22.704 -2.780 -3.966 0.206 N11 2LA 15 2LA OP1 OP1 O 0 1 N N N 5.968 -0.708 30.076 5.000 -1.926 0.386 O1P 2LA 16 2LA "C2'" C2* C 0 1 N N N 1.531 -2.314 26.265 -0.201 2.204 0.889 C2* 2LA 17 2LA OP2 OP2 O 0 1 N N N 6.327 0.338 27.782 5.641 -1.233 -1.955 O2P 2LA 18 2LA "C3'" C3* C 0 1 N N S 2.119 -2.823 27.586 1.257 2.046 1.386 C3* 2LA 19 2LA "O3'" O3* O 0 1 N N N 1.432 -3.969 28.094 1.834 3.319 1.683 O3* 2LA 20 2LA "C4'" C4* C 0 1 N N R 1.869 -1.651 28.555 1.949 1.397 0.160 C4* 2LA 21 2LA "O4'" O4* O 0 1 N N N 1.265 -0.578 27.856 0.941 0.505 -0.362 O4* 2LA 22 2LA "C5'" C5* C 0 1 N N N 3.115 -1.154 29.259 3.190 0.614 0.594 C5* 2LA 23 2LA "O5'" O5* O 0 1 N N N 4.105 -0.690 28.374 3.872 0.124 -0.562 O5* 2LA 24 2LA H1N1 H1N1 H 0 0 N N N -2.838 1.382 22.430 -6.383 0.275 -0.694 H1N1 2LA 25 2LA H8 H8 H 0 1 N N N 2.690 0.638 25.594 -0.258 -1.405 0.911 H8 2LA 26 2LA H10 H10 H 0 1 N N N 3.040 2.872 24.266 -1.794 -3.271 1.926 H10 2LA 27 2LA H10A H10A H 0 0 N N N 2.993 1.831 22.784 -3.549 -2.973 1.890 H10A 2LA 28 2LA "H1'" H1* H 0 1 N N N -0.350 -1.419 26.854 -0.528 1.716 -1.199 H1* 2LA 29 2LA HN11 HN11 H 0 0 N N N 2.551 4.120 22.299 -1.973 -3.954 -0.400 HN11 2LA 30 2LA HN1A HN1A H 0 0 N N N 1.230 3.214 21.979 -2.944 -4.892 0.571 HN1A 2LA 31 2LA "H12'" H12* H 0 0 N N N 0.916 -3.085 25.777 -0.373 3.217 0.527 H12* 2LA 32 2LA "H22'" H22* H 0 0 N N N 2.324 -2.026 25.559 -0.904 1.957 1.685 H22* 2LA 33 2LA HN2 HN2 H 0 1 N N N -3.821 -1.270 24.352 -6.319 2.407 -1.649 HN2 2LA 34 2LA HN2A HN2A H 0 0 N N N -4.219 -0.163 23.081 -4.859 3.222 -1.813 HN2A 2LA 35 2LA "H3'" H3* H 0 1 N N N 3.170 -3.121 27.461 1.303 1.388 2.253 H3* 2LA 36 2LA "H4'" H4* H 0 1 N N N 1.203 -2.039 29.340 2.211 2.155 -0.578 H4* 2LA 37 2LA "H15'" H15* H 0 0 N N N 2.828 -0.323 29.921 3.854 1.269 1.159 H15* 2LA 38 2LA "H25'" H25* H 0 0 N N N 3.537 -1.987 29.841 2.888 -0.226 1.221 H25* 2LA 39 2LA OP3 OP3 O 0 1 N Y N 5.264 1.608 29.636 6.406 0.156 0.141 O7 2LA 40 2LA HOP2 HOP2 H 0 0 N N N 7.187 -0.027 27.956 6.449 -1.764 -1.981 H16 2LA 41 2LA "HO3'" HO3* H 0 0 N Y N 1.834 -4.244 28.910 1.378 3.803 2.385 H17 2LA 42 2LA HOP3 HOP3 H 0 0 N N N 5.553 1.576 30.540 6.608 0.949 -0.375 H18 2LA 43 # 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 2LA P OP1 DOUB N N 1 2LA P OP2 SING N N 2 2LA P "O5'" SING N N 3 2LA N1 C2 SING N N 4 2LA N1 C6 SING N N 5 2LA N1 H1N1 SING N N 6 2LA C2 N2 SING N N 7 2LA C2 N3 DOUB N N 8 2LA N2 HN2 SING N N 9 2LA N2 HN2A SING N N 10 2LA N3 C4 SING N N 11 2LA C4 C5 DOUB Y N 12 2LA C4 N9 SING Y N 13 2LA C5 C6 SING N N 14 2LA C5 C7 SING Y N 15 2LA C6 O6 DOUB N N 16 2LA C7 C8 DOUB Y N 17 2LA C7 C10 SING N N 18 2LA C8 N9 SING Y N 19 2LA C8 H8 SING N N 20 2LA N9 "C1'" SING N N 21 2LA "C1'" "C2'" SING N N 22 2LA "C1'" "O4'" SING N N 23 2LA "C1'" "H1'" SING N N 24 2LA C10 N11 SING N N 25 2LA C10 H10 SING N N 26 2LA C10 H10A SING N N 27 2LA N11 HN11 SING N N 28 2LA N11 HN1A SING N N 29 2LA "C2'" "C3'" SING N N 30 2LA "C2'" "H12'" SING N N 31 2LA "C2'" "H22'" SING N N 32 2LA "C3'" "O3'" SING N N 33 2LA "C3'" "C4'" SING N N 34 2LA "C3'" "H3'" SING N N 35 2LA "C4'" "O4'" SING N N 36 2LA "C4'" "C5'" SING N N 37 2LA "C4'" "H4'" SING N N 38 2LA "C5'" "O5'" SING N N 39 2LA "C5'" "H15'" SING N N 40 2LA "C5'" "H25'" SING N N 41 2LA P OP3 SING N N 42 2LA OP2 HOP2 SING N N 43 2LA "O3'" "HO3'" SING N N 44 2LA OP3 HOP3 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 2LA SMILES ACDLabs 12.01 "O=P(O)(O)OCC3OC(n2c1N=C(N)NC(=O)c1c(c2)CN)CC3O" 2LA InChI InChI 1.03 "InChI=1S/C12H18N5O7P/c13-2-5-3-17(10-9(5)11(19)16-12(14)15-10)8-1-6(18)7(24-8)4-23-25(20,21)22/h3,6-8,18H,1-2,4,13H2,(H2,20,21,22)(H3,14,15,16,19)/t6-,7+,8+/m0/s1" 2LA InChIKey InChI 1.03 XWOYGAPHZUWPLY-XLPZGREQSA-N 2LA SMILES_CANONICAL CACTVS 3.370 "NCc1cn([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)c3N=C(N)NC(=O)c13" 2LA SMILES CACTVS 3.370 "NCc1cn([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)c3N=C(N)NC(=O)c13" 2LA SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "c1c(c2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N)CN" 2LA SMILES "OpenEye OEToolkits" 1.7.2 "c1c(c2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N)CN" # 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 2LA "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" 2LA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(2R,3S,5R)-5-[5-(aminomethyl)-2-azanyl-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-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 2LA "Create component" 2011-09-07 RCSB 2LA "Initial release" 2012-08-24 RCSB #