data_8RJ
#
_chem_comp.id 8RJ
_chem_comp.name "(R)-1'-(2',3'-DIHYDROXYPROPYL)-THYMINE"
_chem_comp.type "RNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C8 H13 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-03-03
_chem_comp.pdbx_modified_date 2022-06-13
_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 280.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8RJ
_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 5V1K
_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_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
8RJ P P1 P 0 1 N N N N N N 25.943 30.276 15.279 4.321 0.010 0.174 P 8RJ 1
8RJ OP2 O1 O 0 1 N N N N N N 27.239 30.339 14.558 4.796 -1.220 -0.748 O1P 8RJ 2
8RJ O1 O2 O 0 1 N N N N N N 24.671 30.434 14.543 4.652 1.287 -0.498 O2P 8RJ 3
8RJ "O5'" O3 O 0 1 N N N N N N 26.031 31.249 16.551 2.730 -0.076 0.408 O3G 8RJ 4
8RJ O4 O4 O 0 1 N N N N N N 26.044 35.009 23.858 -5.630 0.234 0.909 O4 8RJ 5
8RJ C4 C1 C 0 1 N N N N N N 25.892 34.274 22.858 -4.509 0.219 0.433 C4 8RJ 6
8RJ N3 N1 N 0 1 N N N N N N 27.023 34.071 22.082 -3.781 1.352 0.368 N3 8RJ 7
8RJ C2 C2 C 0 1 N N N N N N 27.036 33.294 20.934 -2.542 1.334 -0.157 C2 8RJ 8
8RJ O2 O5 O 0 1 N N N N N N 28.114 33.203 20.341 -1.898 2.364 -0.209 O2 8RJ 9
8RJ C5 C3 C 0 1 N N N N N N 24.709 33.662 22.482 -3.955 -0.991 -0.051 C5 8RJ 10
8RJ C5M C4 C 0 1 N N N N N N 23.510 33.804 23.192 -4.745 -2.273 0.015 C5M 8RJ 11
8RJ C6 C5 C 0 1 N N N N N N 24.735 32.877 21.327 -2.710 -0.981 -0.573 C6 8RJ 12
8RJ N1 N2 N 0 1 N N N N N N 25.894 32.697 20.558 -2.007 0.192 -0.626 N1 8RJ 13
8RJ C1G C6 C 0 1 N N N N N N 25.806 31.848 19.368 -0.656 0.203 -1.192 C1G 8RJ 14
8RJ C2G C7 C 0 1 N N R N N N 25.045 32.618 18.289 0.364 -0.071 -0.085 C2G 8RJ 15
8RJ O2G O6 O 0 1 N N N N N N 25.910 33.738 17.904 0.176 -1.395 0.419 O2G 8RJ 16
8RJ C3G C8 C 0 1 N N N N N N 24.827 31.721 17.105 1.779 0.064 -0.650 C3G 8RJ 17
8RJ OP3 O7 O 0 1 N Y N N N N 25.907 28.950 16.178 5.076 -0.060 1.594 O1 8RJ 18
8RJ HOP2 H1 H 0 0 N Y N N N N 27.080 30.486 13.633 4.610 -2.091 -0.370 H1 8RJ 19
8RJ H2 H2 H 0 1 N N N N N N 27.876 34.509 22.366 -4.153 2.184 0.702 H2 8RJ 20
8RJ H3 H3 H 0 1 N N N N N N 23.675 34.451 24.066 -5.718 -2.077 0.465 H3 8RJ 21
8RJ H4 H4 H 0 1 N N N N N N 22.749 34.257 22.539 -4.883 -2.667 -0.992 H4 8RJ 22
8RJ H5 H5 H 0 1 N N N N N N 23.164 32.815 23.528 -4.205 -3.001 0.620 H5 8RJ 23
8RJ H6 H6 H 0 1 N N N N N N 23.825 32.388 21.013 -2.271 -1.894 -0.947 H6 8RJ 24
8RJ H7 H7 H 0 1 N N N N N N 25.269 30.919 19.612 -0.576 -0.568 -1.958 H7 8RJ 25
8RJ H8 H8 H 0 1 N N N N N N 26.817 31.604 19.009 -0.456 1.179 -1.637 H8 8RJ 26
8RJ H9 H9 H 0 1 N N N N N N 24.084 32.977 18.685 0.225 0.648 0.723 H9 8RJ 27
8RJ H10 H10 H 0 1 N N N N N N 26.047 34.305 18.654 0.285 -2.088 -0.247 H10 8RJ 28
8RJ H11 H11 H 0 1 N N N N N N 24.282 32.284 16.333 1.894 1.044 -1.113 H11 8RJ 29
8RJ H12 H12 H 0 1 N N N N N N 24.224 30.858 17.424 1.948 -0.712 -1.396 H12 8RJ 30
8RJ HOP3 H13 H 0 0 N Y N N N N 25.070 28.514 16.067 6.040 -0.013 1.530 H13 8RJ 31
#
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
8RJ O1 P DOUB N N 1
8RJ OP2 P SING N N 2
8RJ P "O5'" SING N N 3
8RJ "O5'" C3G SING N N 4
8RJ C3G C2G SING N N 5
8RJ O2G C2G SING N N 6
8RJ C2G C1G SING N N 7
8RJ C1G N1 SING N N 8
8RJ O2 C2 DOUB N N 9
8RJ N1 C2 SING N N 10
8RJ N1 C6 SING N N 11
8RJ C2 N3 SING N N 12
8RJ C6 C5 DOUB N N 13
8RJ N3 C4 SING N N 14
8RJ C5 C4 SING N N 15
8RJ C5 C5M SING N N 16
8RJ C4 O4 DOUB N N 17
8RJ P OP3 SING N N 18
8RJ OP2 HOP2 SING N N 19
8RJ N3 H2 SING N N 20
8RJ C5M H3 SING N N 21
8RJ C5M H4 SING N N 22
8RJ C5M H5 SING N N 23
8RJ C6 H6 SING N N 24
8RJ C1G H7 SING N N 25
8RJ C1G H8 SING N N 26
8RJ C2G H9 SING N N 27
8RJ O2G H10 SING N N 28
8RJ C3G H11 SING N N 29
8RJ C3G H12 SING N N 30
8RJ OP3 HOP3 SING N N 31
#
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
8RJ SMILES ACDLabs 12.01 P(OCC(CN1C(NC(=O)C(C)=C1)=O)O)(O)(O)=O
8RJ InChI InChI 1.03 InChI=1S/C8H13N2O7P/c1-5-2-10(8(13)9-7(5)12)3-6(11)4-17-18(14,15)16/h2,6,11H,3-4H2,1H3,(H,9,12,13)(H2,14,15,16)/t6-/m1/s1
8RJ InChIKey InChI 1.03 WWYWEFRSGDVKHI-ZCFIWIBFSA-N
8RJ SMILES_CANONICAL CACTVS 3.385 CC1=CN(C[C@@H](O)CO[P](O)(O)=O)C(=O)NC1=O
8RJ SMILES CACTVS 3.385 CC1=CN(C[CH](O)CO[P](O)(O)=O)C(=O)NC1=O
8RJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC1=CN(C(=O)NC1=O)C[C@H](COP(=O)(O)O)O
8RJ SMILES "OpenEye OEToolkits" 2.0.6 CC1=CN(C(=O)NC1=O)CC(COP(=O)(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
8RJ "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-hydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)propyl dihydrogen phosphate"
8RJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-propyl] dihydrogen 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
8RJ 'Create component' 2017-03-03 RCSB
8RJ 'Initial release' 2017-06-21 RCSB
8RJ 'Modify parent residue' 2022-06-13 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
8RJ P P 4.965 -4.268 1
8RJ OP2 O 3.465 -4.268 2
8RJ O1 O 4.965 -5.768 3
8RJ "O5'" O 4.965 -2.768 4
8RJ O4 O 7.563 6.232 5
8RJ C4 C 7.563 4.732 6
8RJ N3 N 8.862 3.982 7
8RJ C2 C 8.862 2.482 8
8RJ O2 O 10.161 1.732 9
8RJ C5 C 6.264 3.982 10
8RJ C5M C 4.965 4.732 11
8RJ C6 C 6.264 2.482 12
8RJ N1 N 7.563 1.732 13
8RJ C1G C 7.563 0.233 14
8RJ C2G C 6.264 -0.517 15
8RJ O2G O 4.965 0.233 16
8RJ C3G C 6.264 -2.018 17
8RJ OP3 O 6.465 -4.268 18
#
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
8RJ O1 P DOUBLE NONE 1
8RJ OP2 P SINGLE NONE 2
8RJ P "O5'" SINGLE NONE 3
8RJ "O5'" C3G SINGLE NONE 4
8RJ C3G C2G SINGLE NONE 5
8RJ C2G O2G SINGLE BEGINDASH 6
8RJ C2G C1G SINGLE NONE 7
8RJ C1G N1 SINGLE NONE 8
8RJ O2 C2 DOUBLE NONE 9
8RJ N1 C2 SINGLE NONE 10
8RJ N1 C6 SINGLE NONE 11
8RJ C2 N3 SINGLE NONE 12
8RJ C6 C5 DOUBLE NONE 13
8RJ N3 C4 SINGLE NONE 14
8RJ C5 C4 SINGLE NONE 15
8RJ C5 C5M SINGLE NONE 16
8RJ C4 O4 DOUBLE NONE 17
8RJ P OP3 SINGLE NONE 18
#
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
8RJ MurckoScaffold S1 scaffold 'O=c1cc[nH]c(=O)[nH]1' InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8) ISAKRJDGNUQOIC-UHFFFAOYSA-N
8RJ phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
8RJ pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
8RJ O4 S1 1
8RJ C4 S1 1
8RJ N3 S1 1
8RJ C2 S1 1
8RJ O2 S1 1
8RJ C5 S1 1
8RJ C6 S1 1
8RJ N1 S1 1
8RJ OP2 F1 1
8RJ P F1 1
8RJ O1 F1 1
8RJ "O5'" F1 1
8RJ OP3 F1 1
8RJ C5 F2 1
8RJ C6 F2 1
8RJ N1 F2 1
8RJ C2 F2 1
8RJ N3 F2 1
8RJ C4 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 8RJ
_pdbe_chem_comp_rdkit_properties.exactmw 280.046
_pdbe_chem_comp_rdkit_properties.amw 280.173
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 119.492
_pdbe_chem_comp_rdkit_properties.tpsa 141.850
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.060
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.013
_pdbe_chem_comp_rdkit_properties.chi0v 9.094
_pdbe_chem_comp_rdkit_properties.chi1v 5.375
_pdbe_chem_comp_rdkit_properties.chi2v 1.604
_pdbe_chem_comp_rdkit_properties.chi3v 1.604
_pdbe_chem_comp_rdkit_properties.chi4v 0.892
_pdbe_chem_comp_rdkit_properties.chi0n 21.199
_pdbe_chem_comp_rdkit_properties.chi1n 10.087
_pdbe_chem_comp_rdkit_properties.chi2n 1.289
_pdbe_chem_comp_rdkit_properties.chi3n 1.289
_pdbe_chem_comp_rdkit_properties.chi4n 0.698
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.250
_pdbe_chem_comp_rdkit_properties.kappa1 4.695
_pdbe_chem_comp_rdkit_properties.kappa2 5.594
_pdbe_chem_comp_rdkit_properties.kappa3 4.552
_pdbe_chem_comp_rdkit_properties.Phi 1.459
#
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
8RJ UniChem PDBe 8RJ
8RJ UniChem PubChem 137348747
#
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
8RJ P 4.573 0.898 0.355 ETKDGv3 1
8RJ OP2 5.445 0.227 -0.931 ETKDGv3 2
8RJ O1 4.445 2.392 0.153 ETKDGv3 3
8RJ "O5'" 3.025 0.190 0.457 ETKDGv3 4
8RJ O4 -4.958 -1.736 0.657 ETKDGv3 5
8RJ C4 -3.806 -1.232 0.570 ETKDGv3 6
8RJ N3 -2.745 -1.750 1.373 ETKDGv3 7
8RJ C2 -1.448 -1.160 1.289 ETKDGv3 8
8RJ O2 -0.505 -1.622 1.985 ETKDGv3 9
8RJ C5 -3.545 -0.109 -0.357 ETKDGv3 10
8RJ C5M -4.663 0.454 -1.192 ETKDGv3 11
8RJ C6 -2.324 0.450 -0.400 ETKDGv3 12
8RJ N1 -1.235 -0.040 0.409 ETKDGv3 13
8RJ C1G 0.095 0.567 0.275 ETKDGv3 14
8RJ C2G 0.965 -0.236 -0.709 ETKDGv3 15
8RJ O2G 0.393 -0.200 -1.992 ETKDGv3 16
8RJ C3G 2.382 0.342 -0.788 ETKDGv3 17
8RJ OP3 5.403 0.605 1.800 ETKDGv3 18
8RJ HOP2 5.503 -0.739 -0.718 ETKDGv3 19
8RJ H2 -2.917 -2.553 2.019 ETKDGv3 20
8RJ H3 -5.264 1.157 -0.579 ETKDGv3 21
8RJ H4 -5.320 -0.363 -1.557 ETKDGv3 22
8RJ H5 -4.272 0.994 -2.082 ETKDGv3 23
8RJ H6 -2.147 1.288 -1.064 ETKDGv3 24
8RJ H7 0.003 1.619 -0.077 ETKDGv3 25
8RJ H8 0.584 0.609 1.273 ETKDGv3 26
8RJ H9 1.047 -1.291 -0.355 ETKDGv3 27
8RJ H10 -0.279 -0.930 -2.031 ETKDGv3 28
8RJ H11 2.936 -0.216 -1.576 ETKDGv3 29
8RJ H12 2.314 1.416 -1.080 ETKDGv3 30
8RJ HOP3 6.312 0.968 1.648 ETKDGv3 31
#