data_56B # _chem_comp.id 56B _chem_comp.name "2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H24 N5 O10 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-08-03 _chem_comp.pdbx_modified_date 2020-06-27 _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 489.374 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 56B _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 5D0B _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 56B N9 N1 N 0 1 Y N N -24.162 -16.737 -35.563 0.257 1.569 0.022 N9 56B 1 56B "C2'" C1 C 0 1 N N R -26.225 -17.695 -34.440 2.345 2.464 0.996 "C2'" 56B 2 56B "O2'" O1 O 0 1 N N N -26.070 -19.093 -34.559 2.504 3.854 0.709 "O2'" 56B 3 56B P P1 P 0 1 N N N -28.699 -12.960 -32.525 5.159 -2.961 -0.403 P 56B 4 56B "C1'" C2 C 0 1 N N R -25.610 -16.953 -35.625 1.696 1.735 -0.201 "C1'" 56B 5 56B N10 N2 N 0 1 N N N -19.577 -16.001 -34.489 -3.316 -1.045 0.010 N10 56B 6 56B O11 O2 O 0 1 N N N -17.623 -14.033 -32.154 -3.763 -4.296 -0.240 O11 56B 7 56B C8 C3 C 0 1 Y N N -23.449 -16.247 -34.488 -0.332 0.448 0.552 C8 56B 8 56B N3 N3 N 0 1 N N N -23.629 -17.437 -37.818 -0.643 3.743 -0.780 N3 56B 9 56B O12 O3 O 0 1 N N N -15.652 -13.561 -34.024 -6.277 -4.477 0.461 O12 56B 10 56B C7 C4 C 0 1 Y N N -22.108 -16.143 -34.803 -1.661 0.627 0.620 C7 56B 11 56B N2 N4 N 0 1 N N N -22.771 -17.991 -39.888 -1.633 5.707 -1.498 N2 56B 12 56B O6 O4 O 0 1 N N N -19.729 -16.489 -36.859 -4.198 2.293 0.197 O6 56B 13 56B C9 C5 C 0 1 N N N -20.928 -15.650 -33.976 -2.676 -0.359 1.140 C9 56B 14 56B N1 N5 N 0 1 N N N -21.305 -17.223 -38.288 -2.970 3.969 -0.634 N1 56B 15 56B "O4'" O5 O 0 1 N N N -26.252 -15.692 -35.666 2.349 0.448 -0.249 "O4'" 56B 16 56B C10 C6 C 0 1 N N S -18.495 -15.842 -33.505 -4.313 -2.016 0.480 C10 56B 17 56B "O5'" O6 O 0 1 N N N -28.522 -14.418 -33.140 4.489 -1.505 -0.556 "O5'" 56B 18 56B C11 C7 C 0 1 N N R -17.961 -14.407 -33.489 -4.519 -3.130 -0.573 C11 56B 19 56B OP2 O7 O 0 1 N N N -27.953 -11.995 -33.363 5.147 -3.710 -1.828 OP2 56B 20 56B C12 C8 C 0 1 N N S -16.706 -14.449 -34.403 -6.036 -3.397 -0.444 C12 56B 21 56B C13 C9 C 0 1 N N N -16.240 -15.884 -34.346 -6.607 -2.111 0.108 C13 56B 22 56B OP1 O8 O 0 1 N N N -28.442 -13.023 -31.070 6.556 -2.815 0.065 OP1 56B 23 56B C14 C10 C 0 1 N N N -17.242 -16.673 -33.851 -5.667 -1.358 0.612 C14 56B 24 56B "O3'" O9 O 0 1 N N N -28.263 -17.870 -35.657 4.778 2.727 0.963 "O3'" 56B 25 56B C5 C11 C 0 1 Y N N -22.003 -16.608 -36.170 -1.934 1.962 0.092 C5 56B 26 56B C4 C12 C 0 1 Y N N -23.297 -16.964 -36.598 -0.691 2.507 -0.262 C4 56B 27 56B C2 C13 C 0 1 N N N -22.584 -17.548 -38.644 -1.736 4.448 -0.961 C2 56B 28 56B C6 C14 C 0 1 N N N -20.917 -16.740 -37.054 -3.101 2.732 -0.104 C6 56B 29 56B "C4'" C15 C 0 1 N N R -27.462 -15.742 -34.868 3.741 0.717 0.028 "C4'" 56B 30 56B "C5'" C16 C 0 1 N N N -27.276 -14.841 -33.674 4.444 -0.554 0.509 "C5'" 56B 31 56B "C3'" C17 C 0 1 N N S -27.664 -17.215 -34.535 3.723 1.782 1.152 "C3'" 56B 32 56B H1 H1 H 0 1 N N N -25.776 -17.326 -33.506 1.747 2.326 1.897 H1 56B 33 56B H2 H2 H 0 1 N N N -26.463 -19.521 -33.807 2.934 4.355 1.416 H2 56B 34 56B H3 H3 H 0 1 N N N -25.846 -17.516 -36.540 1.875 2.287 -1.124 H3 56B 35 56B H4 H4 H 0 1 N N N -19.593 -16.956 -34.785 -3.730 -0.382 -0.628 H4 56B 36 56B H6 H6 H 0 1 N N N -18.409 -14.016 -31.621 -3.860 -5.021 -0.872 H6 56B 37 56B H7 H7 H 0 1 N N N -23.879 -15.982 -33.534 0.194 -0.441 0.866 H7 56B 38 56B H8 H8 H 0 1 N N N -15.963 -12.664 -34.066 -7.214 -4.656 0.618 H8 56B 39 56B H9 H9 H 0 1 N N N -23.689 -18.238 -40.198 -2.431 6.241 -1.638 H9 56B 40 56B H10 H10 H 0 1 N N N -21.993 -18.076 -40.511 -0.763 6.063 -1.736 H10 56B 41 56B H11 H11 H 0 1 N N N -20.992 -14.553 -33.920 -3.432 0.170 1.720 H11 56B 42 56B H12 H12 H 0 1 N N N -21.025 -16.075 -32.966 -2.178 -1.092 1.775 H12 56B 43 56B H13 H13 H 0 1 N N N -20.592 -17.345 -38.978 -3.756 4.519 -0.779 H13 56B 44 56B H14 H14 H 0 1 N N N -18.848 -16.115 -32.500 -4.004 -2.446 1.433 H14 56B 45 56B H15 H15 H 0 1 N N N -18.709 -13.725 -33.920 -4.267 -2.775 -1.572 H15 56B 46 56B H16 H16 H 0 1 N N N -27.355 -11.497 -32.818 5.536 -4.595 -1.811 H16 56B 47 56B H17 H17 H 0 1 N N N -17.026 -14.225 -35.431 -6.469 -3.616 -1.420 H17 56B 48 56B H18 H18 H 0 1 N N N -15.265 -16.234 -34.650 -7.654 -1.849 0.088 H18 56B 49 56B H21 H21 H 0 1 N N N -17.166 -17.742 -33.719 -5.835 -0.392 1.064 H21 56B 50 56B H23 H23 H 0 1 N N N -28.392 -18.789 -35.456 4.813 3.417 1.639 H23 56B 51 56B H24 H24 H 0 1 N N N -28.319 -15.387 -35.460 4.235 1.112 -0.859 H24 56B 52 56B H25 H25 H 0 1 N N N -26.722 -15.388 -32.897 3.895 -0.976 1.351 H25 56B 53 56B H26 H26 H 0 1 N N N -26.700 -13.956 -33.981 5.459 -0.311 0.823 H26 56B 54 56B H27 H27 H 0 1 N N N -28.214 -17.357 -33.593 3.808 1.307 2.129 H27 56B 55 56B OP3 O10 O 0 1 N Y N ? ? ? 4.324 -3.828 0.666 O1 56B 56 56B HOP3 H5 H 0 0 N Y N ? ? ? 3.398 -3.964 0.424 H5 56B 57 # # 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 56B N2 C2 SING N N 1 56B C2 N1 SING N N 2 56B C2 N3 DOUB N N 3 56B N1 C6 SING N N 4 56B N3 C4 SING N N 5 56B C6 O6 DOUB N N 6 56B C6 C5 SING N N 7 56B C4 C5 DOUB Y N 8 56B C4 N9 SING Y N 9 56B C5 C7 SING Y N 10 56B "O4'" "C1'" SING N N 11 56B "O4'" "C4'" SING N N 12 56B "O3'" "C3'" SING N N 13 56B "C1'" N9 SING N N 14 56B "C1'" "C2'" SING N N 15 56B N9 C8 SING Y N 16 56B "C4'" "C3'" SING N N 17 56B "C4'" "C5'" SING N N 18 56B C7 C8 DOUB Y N 19 56B C7 C9 SING N N 20 56B "O2'" "C2'" SING N N 21 56B "C3'" "C2'" SING N N 22 56B N10 C9 SING N N 23 56B N10 C10 SING N N 24 56B C12 C13 SING N N 25 56B C12 O12 SING N N 26 56B C12 C11 SING N N 27 56B C13 C14 DOUB N N 28 56B C14 C10 SING N N 29 56B "C5'" "O5'" SING N N 30 56B C10 C11 SING N N 31 56B C11 O11 SING N N 32 56B OP2 P SING N N 33 56B "O5'" P SING N N 34 56B P OP1 DOUB N N 35 56B "C2'" H1 SING N N 36 56B "O2'" H2 SING N N 37 56B "C1'" H3 SING N N 38 56B N10 H4 SING N N 39 56B O11 H6 SING N N 40 56B C8 H7 SING N N 41 56B O12 H8 SING N N 42 56B N2 H9 SING N N 43 56B N2 H10 SING N N 44 56B C9 H11 SING N N 45 56B C9 H12 SING N N 46 56B N1 H13 SING N N 47 56B C10 H14 SING N N 48 56B C11 H15 SING N N 49 56B OP2 H16 SING N N 50 56B C12 H17 SING N N 51 56B C13 H18 SING N N 52 56B C14 H21 SING N N 53 56B "O3'" H23 SING N N 54 56B "C4'" H24 SING N N 55 56B "C5'" H25 SING N N 56 56B "C5'" H26 SING N N 57 56B "C3'" H27 SING N N 58 56B P OP3 SING N N 59 56B OP3 HOP3 SING N N 60 # # 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 56B SMILES ACDLabs 12.01 "n2(cc(CNC1C(O)C(O)C=C1)c3c2N=C(N)NC3=O)C4C(O)C(O)C(O4)COP(=O)(O)O" 56B InChI InChI 1.03 "InChI=1S/C17H24N5O10P/c18-17-20-14-10(15(27)21-17)6(3-19-7-1-2-8(23)11(7)24)4-22(14)16-13(26)12(25)9(32-16)5-31-33(28,29)30/h1-2,4,7-9,11-13,16,19,23-26H,3,5H2,(H2,28,29,30)(H3,18,20,21,27)/t7-,8-,9+,11+,12+,13+,16+/m0/s1" 56B InChIKey InChI 1.03 BSABGNSIPKXNDL-AEZJAUAXSA-N 56B SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(cc(CN[C@H]3C=C[C@H](O)[C@@H]3O)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O" 56B SMILES CACTVS 3.385 "NC1=Nc2n(cc(CN[CH]3C=C[CH](O)[CH]3O)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O" 56B SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "c1c(c2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CN[C@H]4C=C[C@@H]([C@@H]4O)O" 56B SMILES "OpenEye OEToolkits" 1.9.2 "c1c(c2c(n1C3C(C(C(O3)COP(=O)(O)O)O)O)N=C(NC2=O)N)CNC4C=CC(C4O)O" # # 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 56B "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one" 56B "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "[(2R,3S,4R,5R)-5-[2-azanyl-5-[[[(1S,4S,5R)-4,5-bis(oxidanyl)cyclopent-2-en-1-yl]amino]methyl]-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(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 56B "Create component" 2015-08-03 RCSB 56B "Initial release" 2016-09-28 RCSB 56B "Other modification" 2020-06-27 RCSB ##