data_YBM # _chem_comp.id YBM _chem_comp.name "[(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H18 N5 O5 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-02-04 _chem_comp.pdbx_modified_date 2022-12-02 _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 331.265 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YBM _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 7TUX _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 YBM O1 O1 O 0 1 N N N -23.918 -21.605 -14.691 5.377 -1.041 0.340 O1 YBM 1 YBM P P1 P 0 1 N N N -24.489 -20.385 -13.963 3.951 -1.419 -0.305 P YBM 2 YBM O2 O2 O 0 1 N N N -25.605 -19.737 -14.771 3.983 -1.157 -1.761 O2 YBM 3 YBM O3 O3 O 0 1 N N N -25.032 -20.731 -12.618 3.643 -2.978 -0.047 O3 YBM 4 YBM CA C1 C 0 1 N N N -23.102 -19.273 -13.636 2.647 -0.406 0.466 CA YBM 5 YBM CB C2 C 0 1 N N N -22.434 -18.733 -14.897 2.871 1.066 0.116 CB YBM 6 YBM CG C3 C 0 1 N N S -21.401 -17.692 -14.471 1.776 1.917 0.764 CG YBM 7 YBM CD C4 C 0 1 N N N -20.253 -18.400 -13.778 2.069 3.398 0.519 CD YBM 8 YBM OD O4 O 0 1 N N N -19.124 -17.546 -13.801 2.215 3.629 -0.884 OD YBM 9 YBM N N1 N 0 1 N N N -20.847 -16.866 -15.589 0.475 1.571 0.176 N YBM 10 YBM C10 C5 C 0 1 N N N -21.859 -16.213 -16.425 -0.621 1.877 1.105 C10 YBM 11 YBM C9 C6 C 0 1 Y N N -22.920 -15.354 -15.755 -1.936 1.510 0.468 C9 YBM 12 YBM C8 C7 C 0 1 Y N N -24.156 -15.765 -15.254 -2.797 2.353 -0.132 C8 YBM 13 YBM N7 N2 N 0 1 Y N N -24.852 -14.694 -14.793 -3.880 1.662 -0.590 N7 YBM 14 YBM C5 C8 C 0 1 Y N N -24.128 -13.578 -15.022 -3.740 0.324 -0.290 C5 YBM 15 YBM C4 C9 C 0 1 Y N N -22.939 -13.971 -15.625 -2.514 0.173 0.380 C4 YBM 16 YBM N3 N3 N 0 1 Y N N -21.982 -13.085 -15.997 -2.135 -1.044 0.780 N3 YBM 17 YBM C6 C10 C 0 1 Y N N -24.347 -12.224 -14.805 -4.518 -0.815 -0.512 C6 YBM 18 YBM O6 O5 O 0 1 N N N -25.483 -11.774 -14.231 -5.706 -0.725 -1.158 O6 YBM 19 YBM N1 N4 N 0 1 Y N N -23.389 -11.359 -15.170 -4.073 -1.987 -0.077 N1 YBM 20 YBM C2 C11 C 0 1 Y N N -22.234 -11.780 -15.756 -2.903 -2.093 0.543 C2 YBM 21 YBM N2 N5 N 0 1 N N N -21.350 -10.842 -16.110 -2.482 -3.343 0.970 N2 YBM 22 YBM H1 H1 H 0 1 N N N -24.374 -21.725 -15.516 5.429 -1.188 1.294 H1 YBM 23 YBM H2 H2 H 0 1 N N N -25.945 -20.472 -12.568 4.297 -3.578 -0.431 H2 YBM 24 YBM H3 H3 H 0 1 N N N -22.348 -19.821 -13.052 1.673 -0.724 0.095 H3 YBM 25 YBM H4 H4 H 0 1 N N N -23.472 -18.421 -13.048 2.682 -0.532 1.549 H4 YBM 26 YBM H5 H5 H 0 1 N N N -23.187 -18.267 -15.549 3.845 1.384 0.488 H5 YBM 27 YBM H6 H6 H 0 1 N N N -21.938 -19.553 -15.438 2.836 1.192 -0.966 H6 YBM 28 YBM H7 H7 H 0 1 N N N -21.877 -17.018 -13.744 1.753 1.724 1.837 H7 YBM 29 YBM H8 H8 H 0 1 N N N -20.529 -18.624 -12.737 1.245 4.000 0.902 H8 YBM 30 YBM H9 H9 H 0 1 N N N -20.021 -19.337 -14.306 2.991 3.676 1.031 H9 YBM 31 YBM H10 H10 H 0 1 N N N -18.394 -17.974 -13.370 2.403 4.550 -1.113 H10 YBM 32 YBM H11 H11 H 0 1 N N N -20.296 -17.462 -16.174 0.451 0.603 -0.105 H11 YBM 33 YBM H13 H13 H 0 1 N N N -22.386 -17.007 -16.975 -0.489 1.304 2.023 H13 YBM 34 YBM H14 H14 H 0 1 N N N -21.323 -15.568 -17.137 -0.614 2.942 1.337 H14 YBM 35 YBM H15 H15 H 0 1 N N N -24.508 -16.786 -15.236 -2.653 3.418 -0.235 H15 YBM 36 YBM H16 H16 H 0 1 N N N -25.751 -14.727 -14.357 -4.635 2.053 -1.057 H16 YBM 37 YBM H18 H18 H 0 1 N N N -20.558 -11.275 -16.541 -1.635 -3.437 1.434 H18 YBM 38 YBM H19 H19 H 0 1 N N N -21.776 -10.209 -16.757 -3.034 -4.123 0.805 H19 YBM 39 YBM H12 H12 H 0 1 N N N -25.448 -10.828 -14.157 -5.640 -0.829 -2.118 H12 YBM 40 # 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 YBM C10 C9 SING N N 1 YBM C10 N SING N N 2 YBM N2 C2 SING N N 3 YBM N3 C2 DOUB Y N 4 YBM N3 C4 SING Y N 5 YBM C2 N1 SING Y N 6 YBM C9 C4 SING Y N 7 YBM C9 C8 DOUB Y N 8 YBM C4 C5 DOUB Y N 9 YBM N CG SING N N 10 YBM C8 N7 SING Y N 11 YBM N1 C6 DOUB Y N 12 YBM C5 C6 SING Y N 13 YBM C5 N7 SING Y N 14 YBM CB CG SING N N 15 YBM CB CA SING N N 16 YBM C6 O6 SING N N 17 YBM O2 P DOUB N N 18 YBM O1 P SING N N 19 YBM CG CD SING N N 20 YBM P CA SING N N 21 YBM P O3 SING N N 22 YBM OD CD SING N N 23 YBM O1 H1 SING N N 24 YBM O3 H2 SING N N 25 YBM CA H3 SING N N 26 YBM CA H4 SING N N 27 YBM CB H5 SING N N 28 YBM CB H6 SING N N 29 YBM CG H7 SING N N 30 YBM CD H8 SING N N 31 YBM CD H9 SING N N 32 YBM OD H10 SING N N 33 YBM N H11 SING N N 34 YBM C10 H13 SING N N 35 YBM C10 H14 SING N N 36 YBM C8 H15 SING N N 37 YBM N7 H16 SING N N 38 YBM N2 H18 SING N N 39 YBM N2 H19 SING N N 40 YBM O6 H12 SING N N 41 # 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 YBM SMILES ACDLabs 12.01 "O=P(O)(O)CCC(CO)NCc1c[NH]c2c(O)nc(N)nc21" YBM InChI InChI 1.03 "InChI=1S/C11H18N5O5P/c12-11-15-8-6(4-14-9(8)10(18)16-11)3-13-7(5-17)1-2-22(19,20)21/h4,7,13-14,17H,1-3,5H2,(H2,19,20,21)(H3,12,15,16,18)/t7-/m0/s1" YBM InChIKey InChI 1.03 WDBHHLGLZFXXDD-ZETCQYMHSA-N YBM SMILES_CANONICAL CACTVS 3.385 "Nc1nc(O)c2[nH]cc(CN[C@H](CO)CC[P](O)(O)=O)c2n1" YBM SMILES CACTVS 3.385 "Nc1nc(O)c2[nH]cc(CN[CH](CO)CC[P](O)(O)=O)c2n1" YBM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)c(nc(n2)N)O)CN[C@@H](CCP(=O)(O)O)CO" YBM SMILES "OpenEye OEToolkits" 2.0.7 "c1c(c2c([nH]1)c(nc(n2)N)O)CNC(CCP(=O)(O)O)CO" # 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 YBM "SYSTEMATIC NAME" ACDLabs 12.01 "[(3S)-3-{[(2-amino-4-hydroxy-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]amino}-4-hydroxybutyl]phosphonic acid" YBM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(3~{S})-3-[(2-azanyl-4-oxidanyl-5~{H}-pyrrolo[3,2-d]pyrimidin-7-yl)methylamino]-4-oxidanyl-butyl]phosphonic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YBM "Create component" 2022-02-04 RCSB YBM "Initial release" 2022-12-07 RCSB #