data_A1AEK
#
_chem_comp.id A1AEK
_chem_comp.name "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H21 N4 O8 P2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2024-02-12
_chem_comp.pdbx_modified_date 2024-09-27
_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 455.340
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1AEK
_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 8VZE
_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.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
A1AEK C2 C1 C 0 1 Y N N N N N 6.250 44.335 17.005 3.184 -2.031 -0.560 C2 A1AEK 1
A1AEK "C2'" C2 C 0 1 Y N N N N N 4.302 46.542 21.934 4.834 3.085 -0.731 "C2'" A1AEK 2
A1AEK C27 C3 C 0 1 N N N N N N 5.879 45.625 15.876 4.454 -2.300 -1.326 C27 A1AEK 3
A1AEK C4 C4 C 0 1 Y N N N N N 6.648 42.998 18.784 1.913 -1.169 1.051 C4 A1AEK 4
A1AEK "C4'" C5 C 0 1 Y N N N N N 4.879 46.311 19.683 5.618 1.459 0.696 "C4'" A1AEK 5
A1AEK C5 C6 C 0 1 Y N N N N N 6.119 41.997 17.828 0.933 -1.814 0.410 C5 A1AEK 6
A1AEK "C5'" C7 C 0 1 Y N N N N N 6.119 45.811 20.052 4.482 0.693 0.425 "C5'" A1AEK 7
A1AEK C6 C8 C 0 1 N N N N N N 5.883 40.520 17.910 -0.522 -1.832 0.803 C6 A1AEK 8
A1AEK "C6'" C9 C 0 1 Y N N N N N 6.398 45.695 21.403 3.550 1.194 -0.462 "C6'" A1AEK 9
A1AEK C7 C10 C 0 1 N N N N N N 6.467 39.836 16.686 -1.249 -0.671 0.121 C7 A1AEK 10
A1AEK "C7'" C11 C 0 1 N N N N N N 7.173 45.392 19.042 4.285 -0.652 1.075 "C7'" A1AEK 11
A1AEK CM2 C12 C 0 1 N N N N N N 3.305 46.932 22.951 5.025 4.429 -1.385 CM2 A1AEK 12
A1AEK CM4 C13 C 0 1 N N N N N N 7.086 42.616 20.164 1.674 -0.350 2.293 CM4 A1AEK 13
A1AEK "N1'" N1 N 0 1 Y N N N N N 5.497 46.061 22.309 3.754 2.383 -1.012 "N1'" A1AEK 14
A1AEK N3 N2 N 1 1 Y N N N N N 6.696 44.252 18.271 3.104 -1.303 0.502 N3 A1AEK 15
A1AEK "N3'" N3 N 0 1 Y N N N N N 3.998 46.659 20.636 5.754 2.641 0.101 "N3'" A1AEK 16
A1AEK "N4'" N4 N 0 1 N N N N N N 4.517 46.474 18.401 6.582 1.001 1.579 "N4'" A1AEK 17
A1AEK O1A O1 O 0 1 N N N N N N 4.295 37.877 17.396 -3.677 0.415 -1.520 O1A A1AEK 18
A1AEK O1B O2 O 0 1 N N N N N N 5.480 35.703 13.304 -6.709 1.806 -0.373 O1B A1AEK 19
A1AEK O28 O3 O 0 1 N N N N N N 6.426 46.901 16.153 5.085 -3.472 -0.806 O28 A1AEK 20
A1AEK O2A O4 O 0 1 N N N N N N 6.006 36.106 17.350 -3.305 1.853 0.521 O2A A1AEK 21
A1AEK O2B O5 O 0 1 N N N N N N 7.438 36.045 14.807 -7.060 -0.526 -1.273 O2B A1AEK 22
A1AEK O3A O6 O 0 1 N N N N N N 5.281 37.336 15.182 -5.167 -0.003 0.475 O3A A1AEK 23
A1AEK O3B O7 O 0 1 N N N N N N 6.783 37.765 13.224 -7.691 0.096 1.202 O3B A1AEK 24
A1AEK O7 O8 O 0 1 N N N N N N 6.716 38.478 16.991 -2.628 -0.687 0.494 O7 A1AEK 25
A1AEK PA P1 P 0 1 N N N N N N 5.560 37.400 16.762 -3.694 0.395 -0.040 PA A1AEK 26
A1AEK PB P2 P 0 1 N N N N N N 6.281 36.680 14.109 -6.658 0.375 -0.001 PB A1AEK 27
A1AEK S1 S1 S 0 1 Y N N N N N 5.719 42.816 16.374 1.642 -2.639 -0.976 S1 A1AEK 28
A1AEK H272 H1 H 0 0 N N N N N N 6.246 45.315 14.886 4.217 -2.452 -2.379 H272 A1AEK 29
A1AEK H271 H2 H 0 0 N N N N N N 4.785 45.733 15.844 5.127 -1.449 -1.225 H271 A1AEK 30
A1AEK H61 H3 H 0 1 N N N N N N 6.366 40.123 18.815 -0.971 -2.774 0.492 H61 A1AEK 31
A1AEK H62 H4 H 0 1 N N N N N N 4.801 40.325 17.956 -0.607 -1.728 1.885 H62 A1AEK 32
A1AEK "H6'" H5 H 0 1 N N N N N N 7.353 45.305 21.723 2.660 0.629 -0.696 "H6'" A1AEK 33
A1AEK H72 H6 H 0 1 N N N N N N 5.753 39.901 15.852 -0.799 0.272 0.433 H72 A1AEK 34
A1AEK H71 H7 H 0 1 N N N N N N 7.409 40.329 16.403 -1.164 -0.774 -0.961 H71 A1AEK 35
A1AEK "H7'1" H8 H 0 0 N N N N N N 7.380 46.231 18.362 5.163 -1.273 0.898 "H7'1" A1AEK 36
A1AEK "H7'2" H9 H 0 0 N N N N N N 8.096 45.113 19.572 4.143 -0.520 2.147 "H7'2" A1AEK 37
A1AEK HM22 H10 H 0 0 N N N N N N 3.718 46.758 23.956 5.561 4.302 -2.325 HM22 A1AEK 38
A1AEK HM21 H11 H 0 0 N N N N N N 3.060 47.998 22.835 4.051 4.879 -1.580 HM21 A1AEK 39
A1AEK H1 H12 H 0 1 N N N N N N 2.393 46.330 22.820 5.599 5.077 -0.723 H1 A1AEK 40
A1AEK HM43 H13 H 0 0 N N N N N N 6.234 42.698 20.855 1.717 -0.997 3.169 HM43 A1AEK 41
A1AEK HM41 H14 H 0 0 N N N N N N 7.454 41.580 20.158 2.440 0.421 2.372 HM41 A1AEK 42
A1AEK HM42 H15 H 0 0 N N N N N N 7.891 43.289 20.493 0.691 0.118 2.236 HM42 A1AEK 43
A1AEK H2 H16 H 0 1 N N N N N N 3.592 46.852 18.361 6.509 0.111 1.958 H2 A1AEK 44
A1AEK "HN4'" H17 H 0 0 N N N N N N 5.153 47.102 17.952 7.330 1.570 1.819 "HN4'" A1AEK 45
A1AEK HO28 H18 H 0 0 N N N N N N 6.159 47.514 15.478 5.910 -3.706 -1.254 HO28 A1AEK 46
A1AEK H3 H19 H 0 1 N N N N N N 5.391 35.834 18.021 -3.296 1.914 1.486 H3 A1AEK 47
A1AEK H4 H20 H 0 1 N N N N N N 7.457 35.116 14.609 -7.047 -1.477 -1.102 H4 A1AEK 48
A1AEK H5 H21 H 0 1 N N N N N N 6.490 37.610 12.334 -8.611 0.301 0.986 H5 A1AEK 49
#
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
A1AEK "N1'" "C2'" DOUB Y N 1
A1AEK "C6'" "N1'" SING Y N 2
A1AEK CM2 "C2'" SING N N 3
A1AEK "C2'" "N3'" SING Y N 4
A1AEK "N3'" "C4'" DOUB Y N 5
A1AEK "N4'" "C4'" SING N N 6
A1AEK "C4'" "C5'" SING Y N 7
A1AEK "C5'" "C6'" DOUB Y N 8
A1AEK "C5'" "C7'" SING N N 9
A1AEK "C7'" N3 SING N N 10
A1AEK C2 N3 DOUB Y N 11
A1AEK N3 C4 SING Y N 12
A1AEK S1 C2 SING Y N 13
A1AEK C5 S1 SING Y N 14
A1AEK C4 C5 DOUB Y N 15
A1AEK C5 C6 SING N N 16
A1AEK CM4 C4 SING N N 17
A1AEK C6 C7 SING N N 18
A1AEK C7 O7 SING N N 19
A1AEK O7 PA SING N N 20
A1AEK O1A PA DOUB N N 21
A1AEK PA O2A SING N N 22
A1AEK O3A PA SING N N 23
A1AEK PB O3A SING N N 24
A1AEK O1B PB DOUB N N 25
A1AEK O2B PB SING N N 26
A1AEK O3B PB SING N N 27
A1AEK C27 C2 SING N N 28
A1AEK O28 C27 SING N N 29
A1AEK C27 H272 SING N N 30
A1AEK C27 H271 SING N N 31
A1AEK C6 H61 SING N N 32
A1AEK C6 H62 SING N N 33
A1AEK "C6'" "H6'" SING N N 34
A1AEK C7 H72 SING N N 35
A1AEK C7 H71 SING N N 36
A1AEK "C7'" "H7'1" SING N N 37
A1AEK "C7'" "H7'2" SING N N 38
A1AEK CM2 HM22 SING N N 39
A1AEK CM2 HM21 SING N N 40
A1AEK CM2 H1 SING N N 41
A1AEK CM4 HM43 SING N N 42
A1AEK CM4 HM41 SING N N 43
A1AEK CM4 HM42 SING N N 44
A1AEK "N4'" H2 SING N N 45
A1AEK "N4'" "HN4'" SING N N 46
A1AEK O28 HO28 SING N N 47
A1AEK O2A H3 SING N N 48
A1AEK O2B H4 SING N N 49
A1AEK O3B H5 SING N N 50
#
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
A1AEK SMILES ACDLabs 12.01 "OCc1sc(CCOP(=O)(O)OP(=O)(O)O)c(C)[n+]1Cc1cnc(C)nc1N"
A1AEK InChI InChI 1.06 "InChI=1S/C13H20N4O8P2S/c1-8-11(3-4-24-27(22,23)25-26(19,20)21)28-12(7-18)17(8)6-10-5-15-9(2)16-13(10)14/h5,18H,3-4,6-7H2,1-2H3,(H4-,14,15,16,19,20,21,22,23)/p+1"
A1AEK InChIKey InChI 1.06 DKVWQSZJFWOHFA-UHFFFAOYSA-O
A1AEK SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2CO)c(N)n1"
A1AEK SMILES CACTVS 3.385 "Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2CO)c(N)n1"
A1AEK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)CO)CCOP(=O)(O)OP(=O)(O)O"
A1AEK SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(sc([n+]1Cc2cnc(nc2N)C)CO)CCOP(=O)(O)OP(=O)(O)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
A1AEK "SYSTEMATIC NAME" ACDLabs 12.01 "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(hydroxymethyl)-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium"
A1AEK "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-(hydroxymethyl)-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl 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
A1AEK "Create component" 2024-02-12 RCSB
A1AEK "Initial release" 2024-10-02 RCSB
#