data_A1BBB
# 
_chem_comp.id                                    A1BBB 
_chem_comp.name                                  
;5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H15 N2 O10 P" 
_chem_comp.mon_nstd_parent_comp_id               U 
_chem_comp.pdbx_synonyms                         
;5-(hydroxymethyl)uridine 5'-monophosphate
;
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-09-29 
_chem_comp.pdbx_modified_date                    2025-01-31 
_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                        354.207 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1BBB 
_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        9DA1 
_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 
A1BBB N1     N1  N 0 1 N N N N N N -27.128 -14.893 -8.136  -1.942 -0.084 0.032  N1     A1BBB 1  
A1BBB C2     C1  C 0 1 N N N N N N -28.112 -14.160 -7.419  -1.723 0.832  -0.929 C2     A1BBB 2  
A1BBB O2     O1  O 0 1 N N N N N N -28.519 -13.133 -7.868  -0.660 0.840  -1.519 O2     A1BBB 3  
A1BBB N3     N2  N 0 1 N N N N N N -28.518 -14.634 -6.180  -2.664 1.740  -1.247 N3     A1BBB 4  
A1BBB C4     C2  C 0 1 N N N N N N -28.056 -15.819 -5.656  -3.849 1.745  -0.602 C4     A1BBB 5  
A1BBB O4     O2  O 0 1 N N N N N N -28.435 -16.225 -4.586  -4.701 2.566  -0.890 O4     A1BBB 6  
A1BBB C5     C3  C 0 1 N N N N N N -27.092 -16.636 -6.459  -4.092 0.787  0.411  C5     A1BBB 7  
A1BBB C6     C4  C 0 1 N N N N N N -26.658 -16.179 -7.632  -3.130 -0.112 0.709  C6     A1BBB 8  
A1BBB "C1'"  C5  C 0 1 N N R N N N -26.638 -14.321 -9.343  -0.900 -1.063 0.351  "C1'"  A1BBB 9  
A1BBB "C2'"  C6  C 0 1 N N R N N N -25.876 -13.044 -9.028  -0.642 -1.999 -0.857 "C2'"  A1BBB 10 
A1BBB "C3'"  C7  C 0 1 N N S N N N -24.421 -13.248 -9.199  0.809  -2.471 -0.598 "C3'"  A1BBB 11 
A1BBB "C4'"  C8  C 0 1 N N R N N N -24.260 -14.644 -9.746  1.391  -1.402 0.347  "C4'"  A1BBB 12 
A1BBB "C5'"  C9  C 0 1 N N N N N N -23.510 -15.529 -8.777  2.625  -0.760 -0.290 "C5'"  A1BBB 13 
A1BBB C5A    C10 C 0 1 N N N N N N -26.637 -17.955 -5.891  -5.406 0.771  1.147  C5A    A1BBB 14 
A1BBB OP3    O3  O 0 1 N N N N N N -23.753 -18.117 -7.146  4.227  2.040  -0.882 OP3    A1BBB 15 
A1BBB "O2'"  O4  O 0 1 N N N N N N -26.317 -11.980 -9.894  -1.548 -3.105 -0.848 "O2'"  A1BBB 16 
A1BBB "O3'"  O5  O 0 1 N N N N N N -23.741 -12.308 -10.054 0.813  -3.754 0.031  "O3'"  A1BBB 17 
A1BBB "O4'"  O6  O 0 1 N N N N N N -25.614 -15.182 -9.942  0.371  -0.408 0.547  "O4'"  A1BBB 18 
A1BBB "O5'"  O7  O 0 1 N N N N N N -23.399 -16.852 -9.294  3.224  0.145  0.640  "O5'"  A1BBB 19 
A1BBB O5B    O8  O 0 1 N N N N N N -26.158 -18.809 -6.918  -5.400 -0.283 2.112  O5B    A1BBB 20 
A1BBB OP1    O9  O 0 1 N N N N N N -22.844 -19.225 -9.300  5.630  0.083  -0.123 OP1    A1BBB 21 
A1BBB OP2    O10 O 0 1 N N N N N N -21.440 -17.649 -7.982  5.013  1.806  1.616  OP2    A1BBB 22 
A1BBB P      P1  P 0 1 N N N N N N -22.808 -18.044 -8.398  4.548  0.998  0.303  P      A1BBB 23 
A1BBB H3     H1  H 0 1 N N N N N N -29.171 -14.094 -5.648  -2.490 2.394  -1.943 H3     A1BBB 24 
A1BBB H6     H2  H 0 1 N N N N N N -25.957 -16.761 -8.211  -3.298 -0.851 1.479  H6     A1BBB 25 
A1BBB "H1'"  H3  H 0 1 N N N N N N -27.450 -14.116 -10.056 -1.176 -1.642 1.232  "H1'"  A1BBB 26 
A1BBB "H2'"  H4  H 0 1 N N N N N N -26.076 -12.770 -7.982  -0.711 -1.450 -1.796 "H2'"  A1BBB 27 
A1BBB "H3'"  H5  H 0 1 N N N N N N -23.952 -13.221 -8.204  1.372  -2.502 -1.531 "H3'"  A1BBB 28 
A1BBB "H4'"  H6  H 0 1 N N N N N N -23.723 -14.607 -10.705 1.660  -1.857 1.300  "H4'"  A1BBB 29 
A1BBB "H5''" H7  H 0 0 N N N N N N -22.503 -15.117 -8.616  3.342  -1.537 -0.555 "H5''" A1BBB 30 
A1BBB "H5'"  H8  H 0 1 N N N N N N -24.051 -15.558 -7.820  2.330  -0.217 -1.187 "H5'"  A1BBB 31 
A1BBB H10    H9  H 0 1 N N N N N N -27.484 -18.441 -5.384  -5.551 1.726  1.653  H10    A1BBB 32 
A1BBB H11    H10 H 0 1 N N N N N N -25.830 -17.776 -5.166  -6.218 0.610  0.438  H11    A1BBB 33 
A1BBB HOP3   H11 H 0 0 N N N N N N -24.226 -18.941 -7.153  3.526  2.671  -0.672 HOP3   A1BBB 34 
A1BBB "HO2'" H12 H 0 0 N N N N N N -25.836 -11.186 -9.691  -1.426 -3.719 -1.585 "HO2'" A1BBB 35 
A1BBB "HO3'" H13 H 0 0 N N N N N N -23.845 -11.430 -9.706  0.406  -4.453 -0.499 "HO3'" A1BBB 36 
A1BBB H12    H14 H 0 1 N N N N N N -25.877 -19.634 -6.539  -6.217 -0.352 2.625  H12    A1BBB 37 
A1BBB HOP2   H15 H 0 0 N N N N N N -20.806 -18.237 -8.376  5.807  2.343  1.486  HOP2   A1BBB 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 
A1BBB "O3'" "C3'"  SING N N 1  
A1BBB "O4'" "C4'"  SING N N 2  
A1BBB "O4'" "C1'"  SING N N 3  
A1BBB "O2'" "C2'"  SING N N 4  
A1BBB "C4'" "C3'"  SING N N 5  
A1BBB "C4'" "C5'"  SING N N 6  
A1BBB "C1'" "C2'"  SING N N 7  
A1BBB "C1'" N1     SING N N 8  
A1BBB OP1   P      DOUB N N 9  
A1BBB "O5'" "C5'"  SING N N 10 
A1BBB "O5'" P      SING N N 11 
A1BBB "C3'" "C2'"  SING N N 12 
A1BBB P     OP2    SING N N 13 
A1BBB P     OP3    SING N N 14 
A1BBB N1    C6     SING N N 15 
A1BBB N1    C2     SING N N 16 
A1BBB O2    C2     DOUB N N 17 
A1BBB C6    C5     DOUB N N 18 
A1BBB C2    N3     SING N N 19 
A1BBB O5B   C5A    SING N N 20 
A1BBB C5    C5A    SING N N 21 
A1BBB C5    C4     SING N N 22 
A1BBB N3    C4     SING N N 23 
A1BBB C4    O4     DOUB N N 24 
A1BBB N3    H3     SING N N 25 
A1BBB C6    H6     SING N N 26 
A1BBB "C1'" "H1'"  SING N N 27 
A1BBB "C2'" "H2'"  SING N N 28 
A1BBB "C3'" "H3'"  SING N N 29 
A1BBB "C4'" "H4'"  SING N N 30 
A1BBB "C5'" "H5''" SING N N 31 
A1BBB "C5'" "H5'"  SING N N 32 
A1BBB C5A   H10    SING N N 33 
A1BBB C5A   H11    SING N N 34 
A1BBB OP3   HOP3   SING N N 35 
A1BBB "O2'" "HO2'" SING N N 36 
A1BBB "O3'" "HO3'" SING N N 37 
A1BBB O5B   H12    SING N N 38 
A1BBB OP2   HOP2   SING N N 39 
# 
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 
A1BBB SMILES           ACDLabs              14.52 "O=P(O)(O)OCC1OC(N2C=C(CO)C(=O)NC2=O)C(O)C1O"                                                                                                               
A1BBB InChI            InChI                1.06  "InChI=1S/C10H15N2O10P/c13-2-4-1-12(10(17)11-8(4)16)9-7(15)6(14)5(22-9)3-21-23(18,19)20/h1,5-7,9,13-15H,2-3H2,(H,11,16,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1" 
A1BBB InChIKey         InChI                1.06  WQCABYUOJVUOEC-JXOAFFINSA-N                                                                                                                                 
A1BBB SMILES_CANONICAL CACTVS               3.385 "OCC1=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=O)NC1=O"                                                                                           
A1BBB SMILES           CACTVS               3.385 "OCC1=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C(=O)NC1=O"                                                                                                 
A1BBB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)CO"                                                                                         
A1BBB SMILES           "OpenEye OEToolkits" 2.0.7 "C1=C(C(=O)NC(=O)N1C2C(C(C(O2)COP(=O)(O)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 
A1BBB "SYSTEMATIC NAME" ACDLabs              14.52 
;5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)
;
A1BBB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},4~{R},5~{R})-5-[5-(hydroxymethyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1BBB 
_pdbx_chem_comp_synonyms.name         
;5-(hydroxymethyl)uridine 5'-monophosphate
;
_pdbx_chem_comp_synonyms.provenance   PDB 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1BBB "Create component" 2024-09-29 RCSB 
A1BBB "Initial release"  2025-02-05 RCSB 
# 
