data_1DP # _chem_comp.id 1DP _chem_comp.name "N1-deaza-adenosine-5'-monophosphate" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C11 H15 N4 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-01 _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 346.233 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 1DP _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 3I2Q _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 1DP O3P O3P O 0 1 N Y N 41.119 19.805 60.235 -5.130 2.082 -1.237 O3P 1DP 1 1DP P P P 0 1 N N N 41.322 20.381 58.754 -4.753 1.026 -0.081 P 1DP 2 1DP O1P O1P O 0 1 N N N 39.971 20.409 58.136 -4.530 1.746 1.192 O1P 1DP 3 1DP O2P O2P O 0 1 N N N 42.122 21.631 58.824 -5.960 -0.024 0.101 O2P 1DP 4 1DP "O5'" "O5'" O 0 1 N N N 42.194 19.261 58.032 -3.412 0.236 -0.493 "O5'" 1DP 5 1DP "C5'" "C5'" C 0 1 N N N 43.538 19.006 58.414 -2.761 -0.697 0.372 "C5'" 1DP 6 1DP "C4'" "C4'" C 0 1 N N R 44.142 17.985 57.482 -1.523 -1.262 -0.327 "C4'" 1DP 7 1DP "O4'" "O4'" O 0 1 N N N 43.444 16.726 57.650 -0.548 -0.222 -0.511 "O4'" 1DP 8 1DP "C1'" "C1'" C 0 1 N N R 43.319 16.077 56.397 0.753 -0.835 -0.380 "C1'" 1DP 9 1DP N9 N9 N 0 1 Y N N 41.902 16.049 56.050 1.766 0.170 -0.051 N9 1DP 10 1DP C4 C4 C 0 1 Y N N 41.328 15.336 55.031 3.119 0.073 -0.292 C4 1DP 11 1DP N3 N3 N 0 1 Y N N 41.945 14.517 54.165 3.888 -0.856 -0.842 N3 1DP 12 1DP C2 C2 C 0 1 Y N N 41.069 14.009 53.307 5.192 -0.700 -0.956 C2 1DP 13 1DP C1 C1 C 0 1 Y N N 39.747 14.212 53.227 5.823 0.445 -0.507 C1 1DP 14 1DP C6 C6 C 0 1 Y N N 39.163 15.040 54.119 5.069 1.456 0.079 C6 1DP 15 1DP N6 N6 N 0 1 N N N 37.848 15.241 54.046 5.671 2.621 0.543 N6 1DP 16 1DP C5 C5 C 0 1 Y N N 39.980 15.641 55.073 3.681 1.266 0.190 C5 1DP 17 1DP N7 N7 N 0 1 Y N N 39.706 16.523 56.103 2.667 2.014 0.690 N7 1DP 18 1DP C8 C8 C 0 1 Y N N 40.876 16.731 56.653 1.543 1.375 0.545 C8 1DP 19 1DP "C2'" "C2'" C 0 1 N N R 44.114 16.898 55.385 0.566 -1.831 0.793 "C2'" 1DP 20 1DP "O2'" "O2'" O 0 1 N N N 45.446 16.438 55.348 1.511 -2.900 0.710 "O2'" 1DP 21 1DP "C3'" "C3'" C 0 1 N N S 44.024 18.286 55.995 -0.874 -2.347 0.554 "C3'" 1DP 22 1DP "O3'" "O3'" O 0 1 N Y N 45.097 19.091 55.536 -0.849 -3.600 -0.133 "O3'" 1DP 23 1DP HO3P HO3P H 0 0 N Y N 41.079 18.856 60.204 -5.930 2.595 -1.055 HO3P 1DP 24 1DP HO2P HO2P H 0 0 N N N 42.293 21.848 59.733 -6.162 -0.533 -0.696 HO2P 1DP 25 1DP "H5'" "H5'" H 0 1 N N N 44.118 19.939 58.360 -2.461 -0.192 1.290 "H5'" 1DP 26 1DP "H5'A" "H5'A" H 0 0 N N N 43.559 18.619 59.444 -3.446 -1.510 0.611 "H5'A" 1DP 27 1DP "H4'" "H4'" H 0 1 N N N 45.208 17.978 57.753 -1.802 -1.683 -1.293 "H4'" 1DP 28 1DP "H1'" "H1'" H 0 1 N N N 43.701 15.046 56.414 1.022 -1.364 -1.294 "H1'" 1DP 29 1DP H2 H2 H 0 1 N N N 41.480 13.337 52.569 5.780 -1.484 -1.410 H2 1DP 30 1DP H1 H1 H 0 1 N N N 39.160 13.723 52.464 6.893 0.553 -0.609 H1 1DP 31 1DP HN6 HN6 H 0 1 N N N 37.466 15.291 54.969 6.630 2.738 0.460 HN6 1DP 32 1DP HN6A HN6A H 0 0 N N N 37.668 16.098 53.564 5.131 3.317 0.950 HN6A 1DP 33 1DP H8 H8 H 0 1 N N N 41.020 17.380 57.504 0.576 1.744 0.853 H8 1DP 34 1DP "H2'" "H2'" H 0 1 N N N 43.750 16.848 54.348 0.642 -1.320 1.753 "H2'" 1DP 35 1DP "HO2'" "HO2'" H 0 0 N N N 45.721 16.335 54.445 1.434 -3.549 1.422 "HO2'" 1DP 36 1DP "H3'" "H3'" H 0 1 N N N 43.110 18.842 55.738 -1.407 -2.440 1.500 "H3'" 1DP 37 1DP "HO3'" "HO3'" H 0 0 N Y N 44.985 19.271 54.610 -0.399 -4.306 0.352 "HO3'" 1DP 38 # # 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 1DP P O3P SING N N 1 1DP O3P HO3P SING N N 2 1DP "O5'" P SING N N 3 1DP O1P P DOUB N N 4 1DP P O2P SING N N 5 1DP O2P HO2P SING N N 6 1DP "O5'" "C5'" SING N N 7 1DP "C4'" "C5'" SING N N 8 1DP "C5'" "H5'" SING N N 9 1DP "C5'" "H5'A" SING N N 10 1DP "C3'" "C4'" SING N N 11 1DP "C4'" "O4'" SING N N 12 1DP "C4'" "H4'" SING N N 13 1DP "C1'" "O4'" SING N N 14 1DP "C2'" "C1'" SING N N 15 1DP N9 "C1'" SING N N 16 1DP "C1'" "H1'" SING N N 17 1DP C4 N9 SING Y N 18 1DP N9 C8 SING Y N 19 1DP N3 C4 DOUB Y N 20 1DP C4 C5 SING Y N 21 1DP C2 N3 SING Y N 22 1DP C1 C2 DOUB Y N 23 1DP C2 H2 SING N N 24 1DP C1 C6 SING Y N 25 1DP C1 H1 SING N N 26 1DP N6 C6 SING N N 27 1DP C6 C5 DOUB Y N 28 1DP N6 HN6 SING N N 29 1DP N6 HN6A SING N N 30 1DP C5 N7 SING Y N 31 1DP N7 C8 DOUB Y N 32 1DP C8 H8 SING N N 33 1DP "O2'" "C2'" SING N N 34 1DP "C2'" "C3'" SING N N 35 1DP "C2'" "H2'" SING N N 36 1DP "O2'" "HO2'" SING N N 37 1DP "O3'" "C3'" SING N N 38 1DP "C3'" "H3'" SING N N 39 1DP "O3'" "HO3'" SING N N 40 # # 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 1DP SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1c(N)ccnc12)C(O)C3O" 1DP SMILES_CANONICAL CACTVS 3.341 "Nc1ccnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" 1DP SMILES CACTVS 3.341 "Nc1ccnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" 1DP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cnc2c(c1N)ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" 1DP SMILES "OpenEye OEToolkits" 1.5.0 "c1cnc2c(c1N)ncn2C3C(C(C(O3)COP(=O)(O)O)O)O" 1DP InChI InChI 1.03 "InChI=1S/C11H15N4O7P/c12-5-1-2-13-10-7(5)14-4-15(10)11-9(17)8(16)6(22-11)3-21-23(18,19)20/h1-2,4,6,8-9,11,16-17H,3H2,(H2,12,13)(H2,18,19,20)/t6-,8-,9-,11-/m1/s1" 1DP InChIKey InChI 1.03 MKNCBTMEOTYSIQ-PNHWDRBUSA-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 1DP "SYSTEMATIC NAME" ACDLabs 10.04 "3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine" 1DP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(7-aminoimidazo[5,4-b]pyridin-3-yl)-3,4-dihydroxy-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 1DP "Create component" 2009-07-01 RCSB 1DP "Modify aromatic_flag" 2011-06-04 RCSB 1DP "Modify descriptor" 2011-06-04 RCSB 1DP "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 1DP _pdbx_chem_comp_synonyms.name "3-(5-O-phosphono-beta-D-ribofuranosyl)-3H-imidazo[4,5-b]pyridin-7-amine" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##