data_Y3U
#
_chem_comp.id Y3U
_chem_comp.name
"[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C19 H24 N4 O10 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-08-10
_chem_comp.pdbx_modified_date 2019-04-12
_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 500.480
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Y3U
_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 6HB7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_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
Y3U C3U C1 C 0 1 N N N N N N -57.889 8.992 -51.317 5.254 -4.095 1.589 C3U Y3U 1
Y3U N3 N1 N 0 1 N N N N N N -58.006 8.289 -50.026 4.331 -3.331 0.746 N3 Y3U 2
Y3U C4 C2 C 0 1 N N N N N N -59.078 8.618 -49.183 3.387 -3.974 0.029 C4 Y3U 3
Y3U O4 O1 O 0 1 N N N N N N -59.876 9.480 -49.532 3.299 -5.188 0.079 O4 Y3U 4
Y3U C5 C3 C 0 1 N N N N N N -59.149 7.880 -47.941 2.500 -3.226 -0.781 C5 Y3U 5
Y3U C6 C4 C 0 1 N N N N N N -58.223 6.946 -47.647 2.620 -1.881 -0.818 C6 Y3U 6
Y3U N1 N2 N 0 1 N N N N N N -57.180 6.684 -48.517 3.591 -1.266 -0.076 N1 Y3U 7
Y3U "C1'" C5 C 0 1 N N R N N N -56.113 5.703 -48.186 3.720 0.192 -0.116 "C1'" Y3U 8
Y3U "O4'" O2 O 0 1 N N N N N N -56.657 4.402 -48.071 2.456 0.818 0.192 "O4'" Y3U 9
Y3U "C4'" C6 C 0 1 N N R N N N -55.680 3.588 -47.373 2.552 2.155 -0.345 "C4'" Y3U 10
Y3U "C5'" C7 C 0 1 N N N N N N -56.365 2.748 -46.321 1.157 2.748 -0.551 "C5'" Y3U 11
Y3U "O5'" O3 O 0 1 N N N N N N -56.921 3.677 -45.323 0.528 2.937 0.718 "O5'" Y3U 12
Y3U SBI S1 S 0 1 N N N N N N -56.741 3.350 -43.776 -0.873 3.526 0.633 SBI Y3U 13
Y3U OAD O4 O 0 1 N N N N N N -57.220 4.476 -43.053 -1.262 3.831 1.966 OAD Y3U 14
Y3U OAE O5 O 0 1 N N N N N N -57.316 2.065 -43.593 -0.840 4.493 -0.407 OAE Y3U 15
Y3U NAT N3 N 0 1 N N N N N N -55.170 3.150 -43.626 -1.882 2.318 0.117 NAT Y3U 16
Y3U C C8 C 0 1 N N N N N N -54.422 3.157 -42.483 -2.089 1.235 0.892 C Y3U 17
Y3U O O6 O 0 1 N N N N N N -54.928 3.370 -41.383 -1.536 1.145 1.968 O Y3U 18
Y3U CA C9 C 0 1 N N S N N N -52.977 2.798 -42.688 -3.006 0.136 0.422 CA Y3U 19
Y3U N N4 N 0 1 N N N N N N -52.181 3.139 -41.508 -2.711 -1.098 1.162 N Y3U 20
Y3U CB C10 C 0 1 N N N N N N -53.099 1.267 -42.839 -4.460 0.544 0.671 CB Y3U 21
Y3U CG C11 C 0 1 Y N N N N N -51.767 0.566 -42.871 -5.381 -0.498 0.091 CG Y3U 22
Y3U CD1 C12 C 0 1 Y N N N N N -50.840 0.845 -43.875 -5.810 -0.387 -1.219 CD1 Y3U 23
Y3U CE1 C13 C 0 1 Y N N N N N -49.617 0.190 -43.919 -6.654 -1.342 -1.753 CE1 Y3U 24
Y3U CZ C14 C 0 1 Y N N N N N -49.298 -0.744 -42.940 -7.070 -2.412 -0.974 CZ Y3U 25
Y3U OH O7 O 0 1 N N N N N N -48.087 -1.368 -42.974 -7.900 -3.352 -1.498 OH Y3U 26
Y3U CE2 C15 C 0 1 Y N N N N N -50.214 -1.031 -41.932 -6.638 -2.520 0.339 CE2 Y3U 27
Y3U CD2 C16 C 0 1 Y N N N N N -51.430 -0.365 -41.895 -5.790 -1.566 0.867 CD2 Y3U 28
Y3U "C3'" C17 C 0 1 N N S N N N -54.632 4.568 -46.816 3.269 1.985 -1.703 "C3'" Y3U 29
Y3U "O3'" O8 O 0 1 N N N N N N -53.468 4.593 -47.640 4.161 3.076 -1.939 "O3'" Y3U 30
Y3U "C2'" C18 C 0 1 N N R N N N -55.366 5.910 -46.884 4.056 0.663 -1.548 "C2'" Y3U 31
Y3U "O2'" O9 O 0 1 N N N N N N -54.473 7.003 -46.973 5.459 0.897 -1.683 "O2'" Y3U 32
Y3U C2 C19 C 0 1 N N N N N N -57.038 7.333 -49.733 4.425 -1.989 0.694 C2 Y3U 33
Y3U O2 O10 O 0 1 N N N N N N -56.135 7.090 -50.521 5.278 -1.422 1.349 O2 Y3U 34
Y3U H1 H1 H 0 1 N N N N N N -58.713 9.714 -51.418 4.827 -4.208 2.585 H1 Y3U 35
Y3U H2 H2 H 0 1 N N N N N N -56.928 9.525 -51.358 5.418 -5.078 1.149 H2 Y3U 36
Y3U H3 H3 H 0 1 N N N N N N -57.939 8.262 -52.138 6.205 -3.565 1.658 H3 Y3U 37
Y3U H4 H4 H 0 1 N N N N N N -59.950 8.079 -47.244 1.738 -3.723 -1.362 H4 Y3U 38
Y3U H5 H5 H 0 1 N N N N N N -58.296 6.395 -46.721 1.952 -1.294 -1.431 H5 Y3U 39
Y3U H6 H6 H 0 1 N N N N N N -55.375 5.713 -49.001 4.488 0.524 0.584 H6 Y3U 40
Y3U H7 H7 H 0 1 N N N N N N -55.181 2.918 -48.089 3.141 2.789 0.318 H7 Y3U 41
Y3U H8 H8 H 0 1 N N N N N N -57.172 2.156 -46.777 1.241 3.708 -1.061 H8 Y3U 42
Y3U H9 H9 H 0 1 N N N N N N -55.639 2.073 -45.845 0.558 2.067 -1.155 H9 Y3U 43
Y3U H10 H10 H 0 1 N N N N N N -54.666 3.000 -44.477 -2.324 2.390 -0.743 H10 Y3U 44
Y3U H11 H11 H 0 1 N N N N N N -52.574 3.253 -43.605 -2.854 -0.033 -0.643 H11 Y3U 45
Y3U H12 H12 H 0 1 N N N N N N -52.113 4.133 -41.427 -1.777 -1.424 0.964 H12 Y3U 46
Y3U H13 H13 H 0 1 N N N N N N -52.621 2.767 -40.690 -2.845 -0.966 2.153 H13 Y3U 47
Y3U H15 H15 H 0 1 N N N N N N -53.631 1.050 -43.777 -4.635 0.628 1.743 H15 Y3U 48
Y3U H16 H16 H 0 1 N N N N N N -53.679 0.877 -41.990 -4.654 1.506 0.195 H16 Y3U 49
Y3U H17 H17 H 0 1 N N N N N N -51.077 1.581 -44.629 -5.486 0.446 -1.825 H17 Y3U 50
Y3U H18 H18 H 0 1 N N N N N N -48.915 0.405 -44.711 -6.990 -1.255 -2.776 H18 Y3U 51
Y3U H19 H19 H 0 1 N N N N N N -48.021 -1.972 -42.244 -7.441 -4.092 -1.918 H19 Y3U 52
Y3U H20 H20 H 0 1 N N N N N N -49.978 -1.770 -41.181 -6.961 -3.352 0.947 H20 Y3U 53
Y3U H21 H21 H 0 1 N N N N N N -52.126 -0.573 -41.096 -5.450 -1.653 1.888 H21 Y3U 54
Y3U H22 H22 H 0 1 N N N N N N -54.391 4.316 -45.773 2.543 1.904 -2.511 H22 Y3U 55
Y3U H23 H23 H 0 1 N N N N N N -52.836 5.203 -47.278 4.638 3.020 -2.778 H23 Y3U 56
Y3U H24 H24 H 0 1 N N N N N N -56.068 6.010 -46.043 3.718 -0.070 -2.281 H24 Y3U 57
Y3U H25 H25 H 0 1 N N N N N N -54.019 7.110 -46.145 5.725 1.196 -2.564 H25 Y3U 58
#
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
Y3U C3U N3 SING N N 1
Y3U O2 C2 DOUB N N 2
Y3U N3 C2 SING N N 3
Y3U N3 C4 SING N N 4
Y3U C2 N1 SING N N 5
Y3U O4 C4 DOUB N N 6
Y3U C4 C5 SING N N 7
Y3U N1 "C1'" SING N N 8
Y3U N1 C6 SING N N 9
Y3U "C1'" "O4'" SING N N 10
Y3U "C1'" "C2'" SING N N 11
Y3U "O4'" "C4'" SING N N 12
Y3U C5 C6 DOUB N N 13
Y3U "O3'" "C3'" SING N N 14
Y3U "C4'" "C3'" SING N N 15
Y3U "C4'" "C5'" SING N N 16
Y3U "O2'" "C2'" SING N N 17
Y3U "C2'" "C3'" SING N N 18
Y3U "C5'" "O5'" SING N N 19
Y3U "O5'" SBI SING N N 20
Y3U CE1 CD1 DOUB Y N 21
Y3U CE1 CZ SING Y N 22
Y3U CD1 CG SING Y N 23
Y3U SBI NAT SING N N 24
Y3U SBI OAE DOUB N N 25
Y3U SBI OAD DOUB N N 26
Y3U NAT C SING N N 27
Y3U OH CZ SING N N 28
Y3U CZ CE2 DOUB Y N 29
Y3U CG CB SING N N 30
Y3U CG CD2 DOUB Y N 31
Y3U CB CA SING N N 32
Y3U CA C SING N N 33
Y3U CA N SING N N 34
Y3U C O DOUB N N 35
Y3U CE2 CD2 SING Y N 36
Y3U C3U H1 SING N N 37
Y3U C3U H2 SING N N 38
Y3U C3U H3 SING N N 39
Y3U C5 H4 SING N N 40
Y3U C6 H5 SING N N 41
Y3U "C1'" H6 SING N N 42
Y3U "C4'" H7 SING N N 43
Y3U "C5'" H8 SING N N 44
Y3U "C5'" H9 SING N N 45
Y3U NAT H10 SING N N 46
Y3U CA H11 SING N N 47
Y3U N H12 SING N N 48
Y3U N H13 SING N N 49
Y3U CB H15 SING N N 50
Y3U CB H16 SING N N 51
Y3U CD1 H17 SING N N 52
Y3U CE1 H18 SING N N 53
Y3U OH H19 SING N N 54
Y3U CE2 H20 SING N N 55
Y3U CD2 H21 SING N N 56
Y3U "C3'" H22 SING N N 57
Y3U "O3'" H23 SING N N 58
Y3U "C2'" H24 SING N N 59
Y3U "O2'" H25 SING N N 60
#
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
Y3U InChI InChI 1.03 InChI=1S/C19H24N4O10S/c1-22-14(25)6-7-23(19(22)29)18-16(27)15(26)13(33-18)9-32-34(30,31)21-17(28)12(20)8-10-2-4-11(24)5-3-10/h2-7,12-13,15-16,18,24,26-27H,8-9,20H2,1H3,(H,21,28)/t12-,13+,15+,16+,18+/m0/s1
Y3U InChIKey InChI 1.03 JZICRHJSYJTEMP-IQNGCQKYSA-N
Y3U SMILES_CANONICAL CACTVS 3.385 CN1C(=O)C=CN([C@@H]2O[C@H](CO[S](=O)(=O)NC(=O)[C@@H](N)Cc3ccc(O)cc3)[C@@H](O)[C@H]2O)C1=O
Y3U SMILES CACTVS 3.385 CN1C(=O)C=CN([CH]2O[CH](CO[S](=O)(=O)NC(=O)[CH](N)Cc3ccc(O)cc3)[CH](O)[CH]2O)C1=O
Y3U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COS(=O)(=O)NC(=O)[C@H](Cc3ccc(cc3)O)N)O)O
Y3U SMILES "OpenEye OEToolkits" 2.0.6 CN1C(=O)C=CN(C1=O)C2C(C(C(O2)COS(=O)(=O)NC(=O)C(Cc3ccc(cc3)O)N)O)O
#
_pdbx_chem_comp_identifier.comp_id Y3U
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier
"[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-(4-hydroxyphenyl)propanoyl]sulfamate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Y3U 'Create component' 2018-08-10 EBI
Y3U 'Initial release' 2019-04-17 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
Y3U C3U C 8.929 7.273 1
Y3U N3 N 7.630 6.523 2
Y3U C4 C 6.331 7.273 3
Y3U O4 O 6.331 8.773 4
Y3U C5 C 5.032 6.523 5
Y3U C6 C 5.032 5.023 6
Y3U N1 N 6.331 4.273 7
Y3U "C1'" C 6.331 2.773 8
Y3U "O4'" O 7.545 1.891 9
Y3U "C4'" C 7.081 0.465 10
Y3U "C5'" C 7.963 -0.749 11
Y3U "O5'" O 9.455 -0.592 12
Y3U SBI S 10.336 -1.806 13
Y3U OAD O 9.123 -2.687 14
Y3U OAE O 11.550 -0.924 15
Y3U NAT N 11.218 -3.019 16
Y3U C C 12.710 -2.862 17
Y3U O O 13.320 -1.492 18
Y3U CA C 13.591 -4.076 19
Y3U N N 12.981 -5.446 20
Y3U CB C 15.083 -3.919 21
Y3U CG C 15.965 -5.132 22
Y3U CD1 C 17.457 -4.976 23
Y3U CE1 C 18.338 -6.189 24
Y3U CZ C 17.728 -7.559 25
Y3U OH O 18.610 -8.773 26
Y3U CE2 C 16.237 -7.716 27
Y3U CD2 C 15.355 -6.503 28
Y3U "C3'" C 5.581 0.465 29
Y3U "O3'" O 4.699 -0.749 30
Y3U "C2'" C 5.118 1.891 31
Y3U "O2'" O 3.691 2.355 32
Y3U C2 C 7.630 5.023 33
Y3U O2 O 8.929 4.273 34
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
Y3U C3U N3 SINGLE NONE 1
Y3U O2 C2 DOUBLE NONE 2
Y3U N3 C2 SINGLE NONE 3
Y3U N3 C4 SINGLE NONE 4
Y3U C2 N1 SINGLE NONE 5
Y3U O4 C4 DOUBLE NONE 6
Y3U C4 C5 SINGLE NONE 7
Y3U "C1'" N1 SINGLE BEGINDASH 8
Y3U N1 C6 SINGLE NONE 9
Y3U "C1'" "O4'" SINGLE NONE 10
Y3U "C1'" "C2'" SINGLE NONE 11
Y3U "O4'" "C4'" SINGLE NONE 12
Y3U C5 C6 DOUBLE NONE 13
Y3U "C3'" "O3'" SINGLE BEGINWEDGE 14
Y3U "C4'" "C3'" SINGLE NONE 15
Y3U "C4'" "C5'" SINGLE BEGINDASH 16
Y3U "C2'" "O2'" SINGLE BEGINWEDGE 17
Y3U "C2'" "C3'" SINGLE NONE 18
Y3U "C5'" "O5'" SINGLE NONE 19
Y3U "O5'" SBI SINGLE NONE 20
Y3U CE1 CD1 DOUBLE NONE 21
Y3U CE1 CZ SINGLE NONE 22
Y3U CD1 CG SINGLE NONE 23
Y3U SBI NAT SINGLE NONE 24
Y3U SBI OAE DOUBLE NONE 25
Y3U SBI OAD DOUBLE NONE 26
Y3U NAT C SINGLE NONE 27
Y3U OH CZ SINGLE NONE 28
Y3U CZ CE2 DOUBLE NONE 29
Y3U CG CB SINGLE NONE 30
Y3U CG CD2 DOUBLE NONE 31
Y3U CB CA SINGLE NONE 32
Y3U CA C SINGLE NONE 33
Y3U CA N SINGLE BEGINDASH 34
Y3U C O DOUBLE NONE 35
Y3U CE2 CD2 SINGLE NONE 36
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
Y3U MurckoScaffold S1 scaffold 'O=C(CCc1ccccc1)NS(=O)(=O)OC[C@@H]1CC[C@H](n2ccc(=O)[nH]c2=O)O1' InChI=1S/C18H21N3O7S/c22-15-10-11-21(18(24)19-15)17-9-7-14(28-17)12-27-29(25,26)20-16(23)8-6-13-4-2-1-3-5-13/h1-5,10-11,14,17H,6-9,12H2,(H,20,23)(H,19,22,24)/t14-,17+/m0/s1 FOPZRQJQUVPWNN-WMLDXEAASA-N
Y3U amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
Y3U peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
Y3U phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
Y3U pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
Y3U ribose F5 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
Y3U N3 S1 1
Y3U C4 S1 1
Y3U O4 S1 1
Y3U C5 S1 1
Y3U C6 S1 1
Y3U N1 S1 1
Y3U "C1'" S1 1
Y3U "O4'" S1 1
Y3U "C4'" S1 1
Y3U "C5'" S1 1
Y3U "O5'" S1 1
Y3U SBI S1 1
Y3U OAD S1 1
Y3U OAE S1 1
Y3U NAT S1 1
Y3U C S1 1
Y3U O S1 1
Y3U CA S1 1
Y3U CB S1 1
Y3U CG S1 1
Y3U CD1 S1 1
Y3U CE1 S1 1
Y3U CZ S1 1
Y3U CE2 S1 1
Y3U CD2 S1 1
Y3U "C3'" S1 1
Y3U "C2'" S1 1
Y3U C2 S1 1
Y3U O2 S1 1
Y3U NAT F1 1
Y3U C F1 1
Y3U O F1 1
Y3U CA F1 1
Y3U O F2 1
Y3U C F2 1
Y3U CA F2 1
Y3U N F2 1
Y3U CG F3 1
Y3U CD1 F3 1
Y3U CE1 F3 1
Y3U CZ F3 1
Y3U CE2 F3 1
Y3U CD2 F3 1
Y3U C5 F4 1
Y3U C4 F4 1
Y3U N3 F4 1
Y3U C2 F4 1
Y3U N1 F4 1
Y3U C6 F4 1
Y3U "C2'" F5 1
Y3U "C3'" F5 1
Y3U "C4'" F5 1
Y3U "O4'" F5 1
Y3U "C1'" F5 1
Y3U "C5'" F5 1
Y3U "O5'" F5 1
Y3U "O3'" F5 1
Y3U "O2'" F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Y3U
_pdbe_chem_comp_rdkit_properties.exactmw 500.121
_pdbe_chem_comp_rdkit_properties.amw 500.486
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 14
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 13
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 13
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 34
_pdbe_chem_comp_rdkit_properties.NumAtoms 58
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 15
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.421
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 226.734
_pdbe_chem_comp_rdkit_properties.tpsa 212.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.898
_pdbe_chem_comp_rdkit_properties.CrippenMR 114.007
_pdbe_chem_comp_rdkit_properties.chi0v 16.596
_pdbe_chem_comp_rdkit_properties.chi1v 9.424
_pdbe_chem_comp_rdkit_properties.chi2v 4.035
_pdbe_chem_comp_rdkit_properties.chi3v 4.035
_pdbe_chem_comp_rdkit_properties.chi4v 2.433
_pdbe_chem_comp_rdkit_properties.chi0n 39.780
_pdbe_chem_comp_rdkit_properties.chi1n 19.625
_pdbe_chem_comp_rdkit_properties.chi2n 3.351
_pdbe_chem_comp_rdkit_properties.chi3n 3.351
_pdbe_chem_comp_rdkit_properties.chi4n 1.925
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.080
_pdbe_chem_comp_rdkit_properties.kappa1 8.543
_pdbe_chem_comp_rdkit_properties.kappa2 10.042
_pdbe_chem_comp_rdkit_properties.kappa3 5.694
_pdbe_chem_comp_rdkit_properties.Phi 2.523
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
Y3U UniChem ChEMBL CHEMBL4518549
Y3U UniChem PDBe Y3U
Y3U UniChem PubChem 137796767
Y3U UniChem BindingDb 50524353
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
Y3U C3U -9.375 -0.768 -0.744 ETKDGv3 1
Y3U N3 -7.980 -0.357 -0.928 ETKDGv3 2
Y3U C4 -7.528 0.161 -2.191 ETKDGv3 3
Y3U O4 -8.314 0.239 -3.173 ETKDGv3 4
Y3U C5 -6.138 0.603 -2.347 ETKDGv3 5
Y3U C6 -5.297 0.581 -1.312 ETKDGv3 6
Y3U N1 -5.720 0.147 -0.003 ETKDGv3 7
Y3U "C1'" -4.745 0.103 1.100 ETKDGv3 8
Y3U "O4'" -3.901 1.233 1.060 ETKDGv3 9
Y3U "C4'" -2.595 0.811 1.398 ETKDGv3 10
Y3U "C5'" -1.640 1.180 0.257 ETKDGv3 11
Y3U "O5'" -0.313 0.918 0.651 ETKDGv3 12
Y3U SBI 0.715 1.268 -0.650 ETKDGv3 13
Y3U OAD 0.564 2.708 -1.056 ETKDGv3 14
Y3U OAE 0.397 0.368 -1.812 ETKDGv3 15
Y3U NAT 2.348 0.990 -0.147 ETKDGv3 16
Y3U C 3.455 1.191 -1.034 ETKDGv3 17
Y3U O 3.255 1.578 -2.217 ETKDGv3 18
Y3U CA 4.862 0.914 -0.573 ETKDGv3 19
Y3U N 5.115 1.607 0.693 ETKDGv3 20
Y3U CB 5.063 -0.605 -0.415 ETKDGv3 21
Y3U CG 6.506 -0.959 -0.157 ETKDGv3 22
Y3U CD1 6.969 -1.223 1.228 ETKDGv3 23
Y3U CE1 8.255 -1.512 1.466 ETKDGv3 24
Y3U CZ 9.223 -1.569 0.350 ETKDGv3 25
Y3U OH 10.557 -1.874 0.617 ETKDGv3 26
Y3U CE2 8.809 -1.326 -0.903 ETKDGv3 27
Y3U CD2 7.392 -1.003 -1.168 ETKDGv3 28
Y3U "C3'" -2.603 -0.701 1.670 ETKDGv3 29
Y3U "O3'" -2.652 -0.942 3.054 ETKDGv3 30
Y3U "C2'" -3.882 -1.147 1.012 ETKDGv3 31
Y3U "O2'" -4.464 -2.232 1.687 ETKDGv3 32
Y3U C2 -7.067 -0.335 0.185 ETKDGv3 33
Y3U O2 -7.447 -0.735 1.320 ETKDGv3 34
Y3U H1 -9.794 -1.176 -1.688 ETKDGv3 35
Y3U H2 -9.980 0.105 -0.422 ETKDGv3 36
Y3U H3 -9.451 -1.569 0.022 ETKDGv3 37
Y3U H4 -5.790 0.948 -3.312 ETKDGv3 38
Y3U H5 -4.276 0.905 -1.471 ETKDGv3 39
Y3U H6 -5.271 0.124 2.082 ETKDGv3 40
Y3U H7 -2.273 1.365 2.308 ETKDGv3 41
Y3U H8 -1.913 0.589 -0.646 ETKDGv3 42
Y3U H9 -1.766 2.264 0.036 ETKDGv3 43
Y3U H10 2.515 0.662 0.830 ETKDGv3 44
Y3U H11 5.570 1.296 -1.346 ETKDGv3 45
Y3U H12 6.135 1.537 0.912 ETKDGv3 46
Y3U H13 4.928 2.627 0.554 ETKDGv3 47
Y3U H15 4.428 -0.985 0.416 ETKDGv3 48
Y3U H16 4.726 -1.124 -1.340 ETKDGv3 49
Y3U H17 6.270 -1.179 2.053 ETKDGv3 50
Y3U H18 8.588 -1.703 2.478 ETKDGv3 51
Y3U H19 11.251 -1.923 -0.120 ETKDGv3 52
Y3U H20 9.508 -1.363 -1.729 ETKDGv3 53
Y3U H21 7.079 -0.801 -2.185 ETKDGv3 54
Y3U H22 -1.733 -1.236 1.220 ETKDGv3 55
Y3U H23 -1.728 -0.817 3.395 ETKDGv3 56
Y3U H24 -3.670 -1.411 -0.051 ETKDGv3 57
Y3U H25 -5.175 -2.584 1.090 ETKDGv3 58
#