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 
# 
