data_6YG
#
_chem_comp.id 6YG
_chem_comp.name "(6P)-2-{(3S)-1-[(2-methoxypyrimidin-5-yl)methyl]piperidin-3-yl}-6-(thiophen-2-yl)pyrimidin-4-ol"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H21 N5 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-07-26
_chem_comp.pdbx_modified_date 2023-02-13
_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 383.467
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6YG
_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 5KX9
_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
6YG N01 N1 N 0 1 Y N N 27.737 35.515 19.632 2.158 2.098 -0.140 N01 6YG 1
6YG C02 C1 C 0 1 Y N N 28.017 36.728 20.040 1.893 0.861 0.231 C02 6YG 2
6YG N03 N2 N 0 1 Y N N 27.765 37.205 21.285 2.820 -0.072 0.261 N03 6YG 3
6YG C04 C2 C 0 1 Y N N 27.223 36.360 22.212 4.080 0.205 -0.089 C04 6YG 4
6YG C05 C3 C 0 1 Y N N 26.925 35.069 21.882 4.399 1.505 -0.489 C05 6YG 5
6YG C06 C4 C 0 1 Y N N 27.171 34.615 20.534 3.386 2.456 -0.504 C06 6YG 6
6YG O07 O1 O 0 1 N N N 26.879 33.477 20.146 3.645 3.731 -0.885 O07 6YG 7
6YG C08 C5 C 0 1 N N S 28.509 37.836 19.083 0.485 0.505 0.635 C08 6YG 8
6YG C09 C6 C 0 1 N N N 27.955 39.105 19.751 -0.464 0.764 -0.538 C09 6YG 9
6YG N10 N3 N 0 1 N N N 28.089 40.277 18.884 -1.839 0.437 -0.139 N10 6YG 10
6YG C11 C7 C 0 1 N N N 27.295 40.065 17.663 -2.284 1.285 0.975 C11 6YG 11
6YG C12 C8 C 0 1 N N N 27.825 38.884 16.874 -1.389 1.041 2.193 C12 6YG 12
6YG C13 C9 C 0 1 N N N 27.828 37.619 17.721 0.062 1.367 1.827 C13 6YG 13
6YG C14 C10 C 0 1 Y N N 27.049 36.996 23.511 5.116 -0.845 -0.054 C14 6YG 14
6YG S15 S1 S 0 1 Y N N 27.458 38.652 23.767 4.830 -2.543 0.307 S15 6YG 15
6YG C16 C11 C 0 1 Y N N 27.022 38.574 25.384 6.540 -2.905 0.109 C16 6YG 16
6YG C17 C12 C 0 1 Y N N 26.541 37.369 25.715 7.205 -1.787 -0.202 C17 6YG 17
6YG C18 C13 C 0 1 Y N N 26.556 36.445 24.652 6.429 -0.653 -0.298 C18 6YG 18
6YG C19 C14 C 0 1 N N N 27.666 41.515 19.562 -2.757 0.542 -1.280 C19 6YG 19
6YG C20 C15 C 0 1 Y N N 27.941 41.575 21.048 -4.098 -0.031 -0.900 C20 6YG 20
6YG C21 C16 C 0 1 Y N N 26.914 41.775 21.959 -4.376 -1.375 -1.096 C21 6YG 21
6YG N22 N4 N 0 1 Y N N 27.094 42.190 23.226 -5.563 -1.845 -0.751 N22 6YG 22
6YG C23 C17 C 0 1 Y N N 28.356 42.439 23.542 -6.479 -1.050 -0.224 C23 6YG 23
6YG N24 N5 N 0 1 Y N N 29.431 42.336 22.777 -6.247 0.238 -0.023 N24 6YG 24
6YG C25 C18 C 0 1 Y N N 29.188 41.924 21.524 -5.079 0.772 -0.340 C25 6YG 25
6YG O26 O2 O 0 1 N N N 28.530 42.860 24.800 -7.684 -1.565 0.118 O26 6YG 26
6YG C27 C19 C 0 1 N N N 29.867 43.159 25.218 -8.639 -0.664 0.683 C27 6YG 27
6YG H1 H1 H 0 1 N N N 26.511 34.397 22.619 5.407 1.764 -0.779 H1 6YG 28
6YG H3 H3 H 0 1 N N N 29.606 37.855 19.001 0.441 -0.548 0.912 H3 6YG 29
6YG H4 H4 H 0 1 N N N 28.508 39.287 20.684 -0.409 1.815 -0.824 H4 6YG 30
6YG H5 H5 H 0 1 N N N 26.890 38.951 19.980 -0.174 0.142 -1.384 H5 6YG 31
6YG H7 H7 H 0 1 N N N 27.347 40.969 17.038 -2.220 2.333 0.682 H7 6YG 32
6YG H8 H8 H 0 1 N N N 26.249 39.872 17.942 -3.316 1.041 1.227 H8 6YG 33
6YG H9 H9 H 0 1 N N N 27.187 38.725 15.992 -1.710 1.682 3.014 H9 6YG 34
6YG H10 H10 H 0 1 N N N 28.853 39.101 16.548 -1.463 -0.003 2.495 H10 6YG 35
6YG H11 H11 H 0 1 N N N 26.788 37.303 17.891 0.708 1.153 2.679 H11 6YG 36
6YG H12 H12 H 0 1 N N N 28.367 36.829 17.177 0.143 2.421 1.562 H12 6YG 37
6YG H13 H13 H 0 1 N N N 27.118 39.398 26.076 6.985 -3.882 0.222 H13 6YG 38
6YG H14 H14 H 0 1 N N N 26.176 37.129 26.703 8.272 -1.775 -0.370 H14 6YG 39
6YG H15 H15 H 0 1 N N N 26.217 35.423 24.733 6.839 0.315 -0.548 H15 6YG 40
6YG H16 H16 H 0 1 N N N 28.191 42.357 19.087 -2.875 1.590 -1.556 H16 6YG 41
6YG H17 H17 H 0 1 N N N 26.582 41.628 19.414 -2.351 -0.013 -2.125 H17 6YG 42
6YG H18 H18 H 0 1 N N N 25.903 41.585 21.629 -3.632 -2.030 -1.526 H18 6YG 43
6YG H19 H19 H 0 1 N N N 30.024 41.861 20.843 -4.894 1.822 -0.169 H19 6YG 44
6YG H20 H20 H 0 1 N N N 29.858 43.491 26.267 -8.852 0.133 -0.030 H20 6YG 45
6YG H21 H21 H 0 1 N N N 30.491 42.258 25.124 -9.558 -1.204 0.910 H21 6YG 46
6YG H22 H22 H 0 1 N N N 30.279 43.958 24.584 -8.234 -0.233 1.598 H22 6YG 47
6YG H2 H2 H 0 1 N N N 27.103 33.388 19.227 3.907 4.313 -0.158 H2 6YG 48
#
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
6YG C12 C11 SING N N 1
6YG C12 C13 SING N N 2
6YG C11 N10 SING N N 3
6YG C13 C08 SING N N 4
6YG N10 C19 SING N N 5
6YG N10 C09 SING N N 6
6YG C08 C09 SING N N 7
6YG C08 C02 SING N N 8
6YG C19 C20 SING N N 9
6YG N01 C02 DOUB Y N 10
6YG N01 C06 SING Y N 11
6YG C02 N03 SING Y N 12
6YG O07 C06 SING N N 13
6YG C06 C05 DOUB Y N 14
6YG C20 C25 DOUB Y N 15
6YG C20 C21 SING Y N 16
6YG N03 C04 DOUB Y N 17
6YG C25 N24 SING Y N 18
6YG C05 C04 SING Y N 19
6YG C21 N22 DOUB Y N 20
6YG C04 C14 SING N N 21
6YG N24 C23 DOUB Y N 22
6YG N22 C23 SING Y N 23
6YG C14 S15 SING Y N 24
6YG C14 C18 DOUB Y N 25
6YG C23 O26 SING N N 26
6YG S15 C16 SING Y N 27
6YG C18 C17 SING Y N 28
6YG O26 C27 SING N N 29
6YG C16 C17 DOUB Y N 30
6YG C05 H1 SING N N 31
6YG C08 H3 SING N N 32
6YG C09 H4 SING N N 33
6YG C09 H5 SING N N 34
6YG C11 H7 SING N N 35
6YG C11 H8 SING N N 36
6YG C12 H9 SING N N 37
6YG C12 H10 SING N N 38
6YG C13 H11 SING N N 39
6YG C13 H12 SING N N 40
6YG C16 H13 SING N N 41
6YG C17 H14 SING N N 42
6YG C18 H15 SING N N 43
6YG C19 H16 SING N N 44
6YG C19 H17 SING N N 45
6YG C21 H18 SING N N 46
6YG C25 H19 SING N N 47
6YG C27 H20 SING N N 48
6YG C27 H21 SING N N 49
6YG C27 H22 SING N N 50
6YG O07 H2 SING N N 51
#
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
6YG SMILES ACDLabs 12.01 "COc1ncc(cn1)CN1CCCC(C1)c1nc(O)cc(n1)c1cccs1"
6YG InChI InChI 1.06 "InChI=1S/C19H21N5O2S/c1-26-19-20-9-13(10-21-19)11-24-6-2-4-14(12-24)18-22-15(8-17(25)23-18)16-5-3-7-27-16/h3,5,7-10,14H,2,4,6,11-12H2,1H3,(H,22,23,25)/t14-/m0/s1"
6YG InChIKey InChI 1.06 NVEPPHORIAFPBH-AWEZNQCLSA-N
6YG SMILES_CANONICAL CACTVS 3.385 "COc1ncc(CN2CCC[C@@H](C2)c3nc(O)cc(n3)c4sccc4)cn1"
6YG SMILES CACTVS 3.385 "COc1ncc(CN2CCC[CH](C2)c3nc(O)cc(n3)c4sccc4)cn1"
6YG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ncc(cn1)CN2CCC[C@@H](C2)c3nc(cc(n3)O)c4cccs4"
6YG SMILES "OpenEye OEToolkits" 2.0.7 "COc1ncc(cn1)CN2CCCC(C2)c3nc(cc(n3)O)c4cccs4"
#
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
6YG "SYSTEMATIC NAME" ACDLabs 12.01 "(6P)-2-{(3S)-1-[(2-methoxypyrimidin-5-yl)methyl]piperidin-3-yl}-6-(thiophen-2-yl)pyrimidin-4-ol"
6YG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(3~{S})-1-[(2-methoxypyrimidin-5-yl)methyl]piperidin-3-yl]-6-thiophen-2-yl-pyrimidin-4-ol"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6YG "Create component" 2016-07-26 RCSB
6YG "Initial release" 2016-08-23 RCSB
6YG "Other modification" 2023-02-13 RCSB
#