data_A1A3L
#
_chem_comp.id A1A3L
_chem_comp.name "4-amino-1-{(3xi)-3-C-amino-2-deoxy-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-beta-D-threo-pentofuranosyl}pyrimidin-2(1H)-one"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H16 N4 O10 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-08-27
_chem_comp.pdbx_modified_date 2024-11-01
_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 402.192
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1A3L
_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 9DB2
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
A1A3L C2 C1 C 0 1 N N N N N N 109.372 111.684 136.640 3.413 -1.024 -0.617 C2 A1A3L 1
A1A3L N3 N1 N 0 1 N N N N N N 109.303 111.107 135.242 4.089 -2.112 -0.981 N3 A1A3L 2
A1A3L C4 C2 C 0 1 N N N N N N 107.986 110.717 134.665 5.055 -2.598 -0.212 C4 A1A3L 3
A1A3L C5 C3 C 0 1 N N N N N N 106.750 110.893 135.458 5.368 -1.956 1.003 C5 A1A3L 4
A1A3L C6 C4 C 0 1 N N N N N N 106.856 111.488 136.890 4.671 -0.851 1.360 C6 A1A3L 5
A1A3L "C1'" C5 C 0 1 N N R N N N 108.286 112.412 138.759 2.934 0.812 0.905 "C1'" A1A3L 6
A1A3L "C2'" C6 C 0 1 N N N N N N 108.071 113.931 138.960 3.202 1.960 -0.100 "C2'" A1A3L 7
A1A3L "C3'" C7 C 0 1 N N R N N N 107.309 114.130 140.277 1.926 2.825 0.047 "C3'" A1A3L 8
A1A3L "C4'" C8 C 0 1 N N R N N N 106.566 112.754 140.338 0.886 1.862 0.652 "C4'" A1A3L 9
A1A3L "C5'" C9 C 0 1 N N N N N N 105.230 112.868 139.642 -0.330 1.762 -0.271 "C5'" A1A3L 10
A1A3L N01 N2 N 0 1 N N N N N N 107.987 114.283 141.566 2.171 3.954 0.954 N01 A1A3L 11
A1A3L N1 N3 N 0 1 N N N N N N 108.173 111.860 137.446 3.691 -0.386 0.534 N1 A1A3L 12
A1A3L N4 N4 N 0 1 N N N N N N 107.924 110.186 133.380 5.746 -3.723 -0.599 N4 A1A3L 13
A1A3L O01 O1 O 0 1 N N N N N N 106.404 115.222 140.116 1.489 3.294 -1.230 O01 A1A3L 14
A1A3L O1A O2 O 0 1 N N N N N N 103.755 111.195 137.868 -2.533 0.044 -1.673 O1A A1A3L 15
A1A3L O1B O3 O 0 1 N N N N N N 102.888 108.058 137.757 -5.522 -1.757 1.709 O1B A1A3L 16
A1A3L O2 O4 O 0 1 N N N N N N 110.400 111.989 137.088 2.530 -0.596 -1.342 O2 A1A3L 17
A1A3L O2A O5 O 0 1 N N N N N N 102.118 110.995 139.399 -3.593 2.010 -0.498 O2A A1A3L 18
A1A3L O2B O6 O 0 1 N N N N N N 105.195 107.969 137.742 -5.795 -0.733 -0.581 O2B A1A3L 19
A1A3L O3A O7 O 0 1 N N N N N N 104.105 109.370 139.652 -3.582 -0.387 0.581 O3A A1A3L 20
A1A3L O3B O8 O 0 1 N N N N N N 104.004 106.797 139.329 -4.268 -2.734 -0.386 O3B A1A3L 21
A1A3L "O4'" O9 O 0 1 N N N N N N 107.353 111.766 139.690 1.515 0.576 0.777 "O4'" A1A3L 22
A1A3L "O5'" O10 O 0 1 N N N N N N 104.282 111.983 140.255 -1.337 0.961 0.351 "O5'" A1A3L 23
A1A3L PA P1 P 0 1 N N N N N N 103.560 110.879 139.276 -2.756 0.644 -0.339 PA A1A3L 24
A1A3L PB P2 P 0 1 N N N N N N 104.051 108.079 138.639 -4.813 -1.388 0.311 PB A1A3L 25
A1A3L H1 H1 H 0 1 N N N N N N 105.790 110.613 135.049 6.151 -2.340 1.640 H1 A1A3L 26
A1A3L H2 H2 H 0 1 N N N N N N 105.963 111.630 137.481 4.892 -0.342 2.286 H2 A1A3L 27
A1A3L H3 H3 H 0 1 N N N N N N 109.302 112.197 139.121 3.181 1.125 1.920 H3 A1A3L 28
A1A3L H4 H4 H 0 1 N N N N N N 109.044 114.443 139.010 4.089 2.526 0.183 H4 A1A3L 29
A1A3L H5 H5 H 0 1 N N N N N N 107.485 114.339 138.124 3.295 1.575 -1.116 H5 A1A3L 30
A1A3L H6 H6 H 0 1 N N N N N N 106.405 112.489 141.393 0.576 2.220 1.634 H6 A1A3L 31
A1A3L H7 H7 H 0 1 N N N N N N 105.347 112.599 138.582 -0.726 2.760 -0.461 H7 A1A3L 32
A1A3L H8 H8 H 0 1 N N N N N N 104.866 113.903 139.720 -0.033 1.304 -1.215 H8 A1A3L 33
A1A3L H9 H9 H 0 1 N N N N N N 107.306 114.400 142.289 2.896 4.556 0.594 H9 A1A3L 34
A1A3L H10 H10 H 0 1 N N N N N N 108.535 113.468 141.753 1.322 4.471 1.125 H10 A1A3L 35
A1A3L H12 H12 H 0 1 N N N N N N 108.762 110.067 132.847 5.529 -4.163 -1.435 H12 A1A3L 36
A1A3L H13 H13 H 0 1 N N N N N N 107.042 109.923 132.990 6.452 -4.076 -0.034 H13 A1A3L 37
A1A3L H14 H14 H 0 1 N N N N N N 105.924 115.358 140.924 2.132 3.857 -1.683 H14 A1A3L 38
A1A3L H15 H15 H 0 1 N N N N N N 103.176 107.980 136.855 -6.274 -2.359 1.622 H15 A1A3L 39
A1A3L H16 H16 H 0 1 N N N N N N 101.746 111.233 138.558 -3.777 2.459 0.338 H16 A1A3L 40
A1A3L H17 H17 H 0 1 N N N N N N 104.712 106.244 139.020 -3.619 -3.216 0.145 H17 A1A3L 41
#
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
A1A3L N4 C4 SING N N 1
A1A3L C4 N3 DOUB N N 2
A1A3L C4 C5 SING N N 3
A1A3L N3 C2 SING N N 4
A1A3L C5 C6 DOUB N N 5
A1A3L C2 O2 DOUB N N 6
A1A3L C2 N1 SING N N 7
A1A3L C6 N1 SING N N 8
A1A3L N1 "C1'" SING N N 9
A1A3L O2B PB DOUB N N 10
A1A3L O1B PB SING N N 11
A1A3L O1A PA DOUB N N 12
A1A3L PB O3B SING N N 13
A1A3L PB O3A SING N N 14
A1A3L "C1'" "C2'" SING N N 15
A1A3L "C1'" "O4'" SING N N 16
A1A3L "C2'" "C3'" SING N N 17
A1A3L PA O2A SING N N 18
A1A3L PA O3A SING N N 19
A1A3L PA "O5'" SING N N 20
A1A3L "C5'" "O5'" SING N N 21
A1A3L "C5'" "C4'" SING N N 22
A1A3L "O4'" "C4'" SING N N 23
A1A3L O01 "C3'" SING N N 24
A1A3L "C3'" "C4'" SING N N 25
A1A3L "C3'" N01 SING N N 26
A1A3L C5 H1 SING N N 27
A1A3L C6 H2 SING N N 28
A1A3L "C1'" H3 SING N N 29
A1A3L "C2'" H4 SING N N 30
A1A3L "C2'" H5 SING N N 31
A1A3L "C4'" H6 SING N N 32
A1A3L "C5'" H7 SING N N 33
A1A3L "C5'" H8 SING N N 34
A1A3L N01 H9 SING N N 35
A1A3L N01 H10 SING N N 36
A1A3L N4 H12 SING N N 37
A1A3L N4 H13 SING N N 38
A1A3L O01 H14 SING N N 39
A1A3L O1B H15 SING N N 40
A1A3L O2A H16 SING N N 41
A1A3L O3B H17 SING N N 42
#
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
A1A3L SMILES ACDLabs 14.52 "O=P(O)(O)OP(=O)(O)OCC1OC(CC1(N)O)N1C=CC(N)=NC1=O"
A1A3L InChI InChI 1.06 "InChI=1S/C9H16N4O10P2/c10-6-1-2-13(8(14)12-6)7-3-9(11,15)5(22-7)4-21-25(19,20)23-24(16,17)18/h1-2,5,7,15H,3-4,11H2,(H,19,20)(H2,10,12,14)(H2,16,17,18)/t5-,7-,9-/m1/s1"
A1A3L InChIKey InChI 1.06 XAPJNFNJUSYHIU-SLBFFKMLSA-N
A1A3L SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@@](N)(O)[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O2"
A1A3L SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[C](N)(O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2"
A1A3L SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H](O[C@@H]([C@]1(N)O)COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N"
A1A3L SMILES "OpenEye OEToolkits" 2.0.7 "C1C(OC(C1(N)O)COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N"
#
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
A1A3L "SYSTEMATIC NAME" ACDLabs 14.52 "4-amino-1-{(3xi)-3-C-amino-2-deoxy-5-O-[(S)-hydroxy(phosphonooxy)phosphoryl]-beta-D-threo-pentofuranosyl}pyrimidin-2(1H)-one"
A1A3L "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},5~{R})-3-azanyl-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl phosphono 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
A1A3L "Create component" 2024-08-27 RCSB
A1A3L "Modify PCM" 2024-09-27 PDBE
A1A3L "Initial release" 2024-11-06 RCSB
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id A1A3L
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom N01
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#