data_A1CAM
# 
_chem_comp.id                                    A1CAM 
_chem_comp.name                                  "1-{5-O-[(R)-hydroxy(3-phenylpropoxy)phosphoryl]-2-O-methyl-beta-L-arabinofuranosyl}pyrimidine-2,4(1H,3H)-dione" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C19 H25 N2 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-04-23 
_chem_comp.pdbx_modified_date                    2026-04-24 
_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                        456.384 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1CAM 
_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        9OBE 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1CAM C2     C1  C 0 1 N N N N N N -23.655 28.178 22.843 -4.267 -1.538 0.869  C2    A1CAM 1  
A1CAM C4     C2  C 0 1 N N N N N N -22.651 25.958 22.275 -5.178 -3.670 0.572  C4    A1CAM 2  
A1CAM C5     C3  C 0 1 N N N N N N -22.180 25.892 23.654 -5.064 -3.510 -0.830 C5    A1CAM 3  
A1CAM C6     C4  C 0 1 N N N N N N -22.438 26.900 24.536 -4.553 -2.361 -1.322 C6    A1CAM 4  
A1CAM "C1'"  C5  C 0 1 N N R N N N -23.480 29.233 25.180 -3.599 -0.128 -0.994 "C1'" A1CAM 5  
A1CAM "C2'"  C6  C 0 1 N N R N N N -24.260 28.824 26.500 -4.484 1.073  -0.593 "C2'" A1CAM 6  
A1CAM "C3'"  C7  C 0 1 N N R N N N -23.793 29.904 27.448 -3.474 2.210  -0.320 "C3'" A1CAM 7  
A1CAM "C4'"  C8  C 0 1 N N R N N N -22.321 30.072 27.035 -2.098 1.561  -0.588 "C4'" A1CAM 8  
A1CAM "C5'"  C9  C 0 1 N N N N N N -21.397 29.074 27.769 -1.060 2.084  0.407  "C5'" A1CAM 9  
A1CAM "CB'"  C10 C 0 1 N N N N N N -21.812 27.925 31.159 4.091  1.053  0.925  "CB'" A1CAM 10 
A1CAM "CC'"  C11 C 0 1 N N N N N N -22.386 26.645 31.885 5.022  0.136  0.128  "CC'" A1CAM 11 
A1CAM "CD'"  C12 C 0 1 N N N N N N -23.415 25.785 31.090 6.412  0.140  0.768  "CD'" A1CAM 12 
A1CAM "CE'"  C13 C 0 1 Y N N N N N -23.027 25.357 29.660 7.328  -0.763 -0.017 "CE'" A1CAM 13 
A1CAM "CF'"  C14 C 0 1 Y N N N N N -21.729 24.914 29.328 7.428  -2.102 0.313  "CF'" A1CAM 14 
A1CAM "CG'"  C15 C 0 1 Y N N N N N -21.383 24.525 28.026 8.269  -2.930 -0.407 "CG'" A1CAM 15 
A1CAM "CH'"  C16 C 0 1 Y N N N N N -22.336 24.563 27.006 9.010  -2.419 -1.456 "CH'" A1CAM 16 
A1CAM "CI'"  C17 C 0 1 Y N N N N N -23.632 24.995 27.303 8.910  -1.080 -1.786 "CI'" A1CAM 17 
A1CAM "CJ'"  C18 C 0 1 Y N N N N N -23.967 25.383 28.611 8.065  -0.254 -1.070 "CJ'" A1CAM 18 
A1CAM CM2    C19 C 0 1 N N N N N N -26.375 28.312 27.406 -6.601 1.996  -1.237 CM2   A1CAM 19 
A1CAM N1     N1  N 0 1 N N N N N N -23.168 28.070 24.202 -4.154 -1.374 -0.461 N1    A1CAM 20 
A1CAM N3     N2  N 0 1 N N N N N N -23.384 27.122 21.917 -4.774 -2.673 1.386  N3    A1CAM 21 
A1CAM O2     O1  O 0 1 N N N N N N -24.290 29.172 22.512 -3.903 -0.651 1.615  O2    A1CAM 22 
A1CAM "O2'"  O2  O 0 1 N N N N N N -25.662 29.027 26.414 -5.361 1.429  -1.664 "O2'" A1CAM 23 
A1CAM "O3'"  O3  O 0 1 N N N N N N -24.523 31.072 27.195 -3.698 3.303  -1.212 "O3'" A1CAM 24 
A1CAM O4     O4  O 0 1 N N N N N N -22.461 25.102 21.426 -5.636 -4.697 1.038  O4    A1CAM 25 
A1CAM "O4'"  O5  O 0 1 N N N N N N -22.275 29.739 25.627 -2.313 0.146  -0.397 "O4'" A1CAM 26 
A1CAM "O5'"  O6  O 0 1 N N N N N N -20.509 29.748 28.579 0.228  1.563  0.070  "O5'" A1CAM 27 
A1CAM OP1    O7  O 0 1 N N N N N N -19.458 29.934 30.966 1.348  1.567  2.331  OP1   A1CAM 28 
A1CAM OP2    O8  O 0 1 N N N N N N -18.436 28.352 29.173 1.887  3.477  0.772  OP2   A1CAM 29 
A1CAM OP3    O9  O 0 1 N N N N N N -20.626 27.670 30.470 2.793  1.049  0.328  OP3   A1CAM 30 
A1CAM P      P1  P 0 1 N N N N N N -19.629 28.944 29.860 1.559  1.907  0.907  P     A1CAM 31 
A1CAM "H3'"  H1  H 0 1 N N N N N N -21.617 25.030 23.982 -5.382 -4.297 -1.498 H24   A1CAM 32 
A1CAM "HO3'" H2  H 0 1 N N N N N N -22.066 26.802 25.545 -4.458 -2.222 -2.388 H23   A1CAM 33 
A1CAM "H1'"  H3  H 0 1 N N N N N N -24.066 29.999 24.650 -3.508 -0.187 -2.079 H22   A1CAM 34 
A1CAM "H2'"  H4  H 0 1 N N N N N N -23.974 27.817 26.837 -5.056 0.842  0.306  H4    A1CAM 35 
A1CAM H4     H5  H 0 1 N N N N N N -23.868 29.572 28.494 -3.544 2.542  0.716  H5    A1CAM 36 
A1CAM "H4'"  H6  H 0 1 N N N N N N -21.988 31.104 27.219 -1.777 1.761  -1.611 H7    A1CAM 37 
A1CAM "H5''" H7  H 0 1 N N N N N N -20.837 28.486 27.027 -1.033 3.173  0.365  H9    A1CAM 38 
A1CAM "H5'"  H8  H 0 1 N N N N N N -22.009 28.399 28.385 -1.329 1.765  1.414  H8    A1CAM 39 
A1CAM H11    H9  H 0 1 N N N N N N -21.620 28.701 31.915 4.020  0.695  1.952  H11   A1CAM 40 
A1CAM H12    H10 H 0 1 N N N N N N -22.563 28.289 30.443 4.490  2.068  0.921  H12   A1CAM 41 
A1CAM H14    H11 H 0 1 N N N N N N -21.534 25.996 32.137 4.623  -0.878 0.132  H14   A1CAM 42 
A1CAM H13    H12 H 0 1 N N N N N N -22.878 26.980 32.810 5.093  0.495  -0.899 H13   A1CAM 43 
A1CAM H16    H13 H 0 1 N N N N N N -23.598 24.869 31.671 6.811  1.155  0.764  H16   A1CAM 44 
A1CAM H15    H14 H 0 1 N N N N N N -24.346 26.366 31.019 6.340  -0.218 1.794  H15   A1CAM 45 
A1CAM H17    H15 H 0 1 N N N N N N -20.977 24.873 30.102 6.849  -2.500 1.133  H17   A1CAM 46 
A1CAM H18    H16 H 0 1 N N N N N N -20.377 24.195 27.812 8.347  -3.976 -0.149 H18   A1CAM 47 
A1CAM H19    H17 H 0 1 N N N N N N -22.076 24.263 26.002 9.667  -3.066 -2.018 H19   A1CAM 48 
A1CAM H20    H18 H 0 1 N N N N N N -24.379 25.031 26.524 9.490  -0.682 -2.605 H20   A1CAM 49 
A1CAM H21    H19 H 0 1 N N N N N N -24.975 25.711 28.818 7.983  0.791  -1.331 H21   A1CAM 50 
A1CAM H5     H20 H 0 1 N N N N N N -27.452 28.504 27.294 -6.407 2.903  -0.664 H3    A1CAM 51 
A1CAM H2     H21 H 0 1 N N N N N N -26.181 27.235 27.292 -7.209 2.239  -2.108 H2    A1CAM 52 
A1CAM H1     H22 H 0 1 N N N N N N -26.046 28.641 28.403 -7.132 1.278  -0.611 H1    A1CAM 53 
A1CAM H3     H23 H 0 1 N N N N N N -23.724 27.206 20.980 -4.848 -2.775 2.347  H25   A1CAM 54 
A1CAM H7     H24 H 0 1 N N N N N N -24.237 31.759 27.786 -3.091 4.045  -1.084 H6    A1CAM 55 
A1CAM HOP2   H25 H 0 1 N N N N N N -17.642 28.707 29.555 2.037  3.771  -0.136 H10   A1CAM 56 
# 
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 
A1CAM "O2'" CM2    SING N N 1  
A1CAM "C2'" "O2'"  SING N N 2  
A1CAM "C3'" "C2'"  SING N N 3  
A1CAM "O3'" "C3'"  SING N N 4  
A1CAM "C4'" "C3'"  SING N N 5  
A1CAM "O5'" "C5'"  SING N N 6  
A1CAM P     "O5'"  SING N N 7  
A1CAM OP2   P      SING N N 8  
A1CAM "CB'" OP3    SING N N 9  
A1CAM "CC'" "CB'"  SING N N 10 
A1CAM "CD'" "CC'"  SING N N 11 
A1CAM "CE'" "CD'"  SING N N 12 
A1CAM "CF'" "CE'"  DOUB Y N 13 
A1CAM "CG'" "CF'"  SING Y N 14 
A1CAM "CH'" "CG'"  DOUB Y N 15 
A1CAM "CI'" "CH'"  SING Y N 16 
A1CAM "CJ'" "CI'"  DOUB Y N 17 
A1CAM OP3   P      SING N N 18 
A1CAM OP1   P      DOUB N N 19 
A1CAM "C5'" "C4'"  SING N N 20 
A1CAM "O4'" "C4'"  SING N N 21 
A1CAM "C1'" "O4'"  SING N N 22 
A1CAM N1    "C1'"  SING N N 23 
A1CAM C6    N1     SING N N 24 
A1CAM C5    C6     DOUB N N 25 
A1CAM C4    C5     SING N N 26 
A1CAM C2    N3     SING N N 27 
A1CAM O2    C2     DOUB N N 28 
A1CAM N3    C4     SING N N 29 
A1CAM O4    C4     DOUB N N 30 
A1CAM "C2'" "C1'"  SING N N 31 
A1CAM "CE'" "CJ'"  SING Y N 32 
A1CAM N1    C2     SING N N 33 
A1CAM C5    "H3'"  SING N N 34 
A1CAM C6    "HO3'" SING N N 35 
A1CAM "C1'" "H1'"  SING N N 36 
A1CAM "C2'" "H2'"  SING N N 37 
A1CAM "C3'" H4     SING N N 38 
A1CAM "C4'" "H4'"  SING N N 39 
A1CAM "C5'" "H5''" SING N N 40 
A1CAM "C5'" "H5'"  SING N N 41 
A1CAM "CB'" H11    SING N N 42 
A1CAM "CB'" H12    SING N N 43 
A1CAM "CC'" H14    SING N N 44 
A1CAM "CC'" H13    SING N N 45 
A1CAM "CD'" H16    SING N N 46 
A1CAM "CD'" H15    SING N N 47 
A1CAM "CF'" H17    SING N N 48 
A1CAM "CG'" H18    SING N N 49 
A1CAM "CH'" H19    SING N N 50 
A1CAM "CI'" H20    SING N N 51 
A1CAM "CJ'" H21    SING N N 52 
A1CAM CM2   H5     SING N N 53 
A1CAM CM2   H2     SING N N 54 
A1CAM CM2   H1     SING N N 55 
A1CAM N3    H3     SING N N 56 
A1CAM "O3'" H7     SING N N 57 
A1CAM OP2   HOP2   SING N N 58 
# 
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 
A1CAM SMILES           ACDLabs              14.52   "O=P(O)(OCCCc1ccccc1)OCC1OC(N2C=CC(=O)NC2=O)C(OC)C1O"                                                                                                                                                        
A1CAM InChI            InChI                1.06    "InChI=1S/C19H25N2O9P/c1-27-17-16(23)14(30-18(17)21-10-9-15(22)20-19(21)24)12-29-31(25,26)28-11-5-8-13-6-3-2-4-7-13/h2-4,6-7,9-10,14,16-18,23H,5,8,11-12H2,1H3,(H,25,26)(H,20,22,24)/t14?,16?,17-,18+/m1/s1" 
A1CAM InChIKey         InChI                1.06    CUENRHBNYZMWDV-SYNTWQANSA-N                                                                                                                                                                                  
A1CAM SMILES_CANONICAL CACTVS               3.385   "CO[C@@H]1[C@H](O)[C@@H](CO[P](O)(=O)OCCCc2ccccc2)O[C@H]1N3C=CC(=O)NC3=O"                                                                                                                                    
A1CAM SMILES           CACTVS               3.385   "CO[CH]1[CH](O)[CH](CO[P](O)(=O)OCCCc2ccccc2)O[CH]1N3C=CC(=O)NC3=O"                                                                                                                                          
A1CAM SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)OCCCc3ccccc3)O"                                                                                                                                      
A1CAM SMILES           "OpenEye OEToolkits" 3.1.0.0 "COC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)OCCCc3ccccc3)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 
A1CAM "SYSTEMATIC NAME" ACDLabs              14.52   "1-{5-O-[(R)-hydroxy(3-phenylpropoxy)phosphoryl]-2-O-methyl-beta-L-arabinofuranosyl}pyrimidine-2,4(1H,3H)-dione"                                
A1CAM "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl 3-phenylpropyl hydrogen 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 
A1CAM "Create component" 2025-04-23 RCSB 
A1CAM "Initial release"  2026-04-29 RCSB 
# 
