data_YA4
#
_chem_comp.id YA4
_chem_comp.name '[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid'
_chem_comp.type 'RNA linking'
_chem_comp.pdbx_type ATOMN
_chem_comp.formula 'C5 H11 O6 P S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-02-12
_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 230.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YA4
_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 7LPJ
_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_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
YA4 "C1'" C1 C 0 1 N N N N N N -149.244 -52.772 -68.581 3.204 1.489 -0.247 "C1'" YA4 1
YA4 "C2'" C2 C 0 1 N N S N N N -149.870 -54.239 -68.635 3.719 0.218 0.465 "C2'" YA4 2
YA4 "C3'" C3 C 0 1 N N S N N N -149.796 -54.681 -67.469 2.501 -0.734 0.462 "C3'" YA4 3
YA4 "C4'" C4 C 0 1 N N R N N N -149.814 -53.348 -66.463 1.395 0.075 -0.252 "C4'" YA4 4
YA4 "C5'" C5 C 0 1 N N N N N N -148.736 -53.596 -65.491 0.035 -0.198 0.395 "C5'" YA4 5
YA4 "O2'" O1 O 0 1 N N N N N N -151.307 -54.177 -68.963 4.806 -0.357 -0.262 "O2'" YA4 6
YA4 "O3'" O2 O 0 1 N N N N N N -150.995 -55.476 -67.231 2.800 -1.926 -0.267 "O3'" YA4 7
YA4 "O4'" O3 O 0 1 N N N N N N -149.574 -52.287 -67.156 1.771 1.457 -0.068 "O4'" YA4 8
YA4 "O5'" O4 O 0 1 N N N N N N -148.447 -52.418 -64.828 -0.988 0.465 -0.350 "O5'" YA4 9
YA4 OP1 O5 O 0 1 N N N N N N -147.902 -50.923 -62.634 -2.719 0.836 1.449 OP1 YA4 10
YA4 P P1 P 0 1 N N N N N N -147.850 -52.411 -63.410 -2.547 0.395 0.047 P YA4 11
YA4 SP3 S1 S 0 1 N N N N N N -145.888 -53.215 -63.680 -3.239 -1.598 -0.157 SP3 YA4 12
YA4 "H1'" H1 H 0 1 N N N N N N -148.156 -52.803 -68.743 3.624 2.381 0.217 H1 YA4 13
YA4 "H1''" H2 H 0 0 N N N N N N -149.708 -52.119 -69.335 3.454 1.459 -1.307 H2 YA4 14
YA4 "H2'" H3 H 0 1 N N N N N N -149.327 -54.833 -69.385 4.021 0.449 1.487 H3 YA4 15
YA4 "H3'" H4 H 0 1 N N N N N N -148.888 -55.263 -67.254 2.203 -0.976 1.482 H4 YA4 16
YA4 "H4'" H5 H 0 1 N N N N N N -150.789 -53.324 -65.954 1.367 -0.175 -1.312 H5 YA4 17
YA4 "H5'" H6 H 0 1 N N N N N N -149.061 -54.357 -64.766 -0.156 -1.271 0.399 H6 YA4 18
YA4 "H5''" H7 H 0 0 N N N N N N -147.839 -53.952 -66.018 0.039 0.174 1.419 H7 YA4 19
YA4 "HO2'" H8 H 0 0 N N N N N N -151.664 -55.057 -68.991 5.576 0.223 -0.343 H8 YA4 20
YA4 "HO3'" H9 H 0 0 N Y N N N N -150.972 -55.829 -66.349 3.529 -2.441 0.104 H9 YA4 21
YA4 HSP3 H11 H 0 0 N N N N N N -145.418 -53.193 -62.468 -4.532 -1.507 0.201 H11 YA4 22
YA4 OP3 OP3 O 0 1 N Y N N N N -148.847 -53.399 -62.731 -3.392 1.359 -0.927 OP3 YA4 23
YA4 HOP3 H10 H 0 0 N Y N N N N -149.287 -52.961 -62.011 -3.326 1.128 -1.863 "HO3'" YA4 24
#
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
YA4 "O2'" "C2'" SING N N 1
YA4 "C2'" "C1'" SING N N 2
YA4 "C2'" "C3'" SING N N 3
YA4 "C1'" "O4'" SING N N 4
YA4 "C3'" "O3'" SING N N 5
YA4 "C3'" "C4'" SING N N 6
YA4 "O4'" "C4'" SING N N 7
YA4 "C4'" "C5'" SING N N 8
YA4 "C5'" "O5'" SING N N 9
YA4 "O5'" P SING N N 10
YA4 SP3 P SING N N 11
YA4 P OP1 DOUB N N 12
YA4 "C1'" "H1'" SING N N 13
YA4 "C1'" "H1''" SING N N 14
YA4 "C2'" "H2'" SING N N 15
YA4 "C3'" "H3'" SING N N 16
YA4 "C4'" "H4'" SING N N 17
YA4 "C5'" "H5'" SING N N 18
YA4 "C5'" "H5''" SING N N 19
YA4 "O2'" "HO2'" SING N N 20
YA4 "O3'" "HO3'" SING N N 21
YA4 SP3 HSP3 SING N N 22
YA4 P OP3 SING N N 23
YA4 OP3 HOP3 SING N N 24
#
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
YA4 InChI InChI 1.03 'InChI=1S/C5H11O6PS/c6-3-1-10-4(5(3)7)2-11-12(8,9)13/h3-7H,1-2H2,(H2,8,9,13)/t3-,4+,5-/m0/s1'
YA4 InChIKey InChI 1.03 HBCHIJUQXWEATM-LMVFSUKVSA-N
YA4 SMILES_CANONICAL CACTVS 3.385 'O[C@H]1CO[C@H](CO[P](O)(S)=O)[C@H]1O'
YA4 SMILES CACTVS 3.385 'O[CH]1CO[CH](CO[P](O)(S)=O)[CH]1O'
YA4 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C1[C@@H]([C@@H]([C@H](O1)COP(=O)(O)S)O)O'
YA4 SMILES 'OpenEye OEToolkits' 2.0.7 'C1C(C(C(O1)COP(=O)(O)S)O)O'
#
_pdbx_chem_comp_identifier.comp_id YA4
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
'[(2~{R},3~{S},4~{S})-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphinic acid'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YA4 'Create component' 2021-02-12 RCSB
YA4 'Initial release' 2021-08-04 RCSB
YA4 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YA4
_pdbx_chem_comp_pcm.modified_residue_id ASN
_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 "O2'"
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ND2
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 8W6P
#
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
YA4 "C1'" C 10.212 0.262 1
YA4 "C2'" C 9.748 1.689 2
YA4 "C3'" C 8.248 1.689 3
YA4 "C4'" C 7.785 0.262 4
YA4 "C5'" C 6.358 -0.201 5
YA4 "O2'" O 10.630 2.902 6
YA4 "O3'" O 7.367 2.902 7
YA4 "O4'" O 8.998 -0.619 8
YA4 "O5'" O 6.046 -1.668 9
YA4 OP1 O 4.156 -0.706 10
YA4 P P 4.620 -2.132 11
YA4 SP3 S 3.193 -2.596 12
YA4 OP3 O 5.083 -3.559 13
#
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
YA4 "C2'" "O2'" SINGLE BEGINWEDGE 1
YA4 "C2'" "C1'" SINGLE NONE 2
YA4 "C2'" "C3'" SINGLE NONE 3
YA4 "C1'" "O4'" SINGLE NONE 4
YA4 "C3'" "O3'" SINGLE BEGINWEDGE 5
YA4 "C3'" "C4'" SINGLE NONE 6
YA4 "O4'" "C4'" SINGLE NONE 7
YA4 "C4'" "C5'" SINGLE BEGINDASH 8
YA4 "C5'" "O5'" SINGLE NONE 9
YA4 "O5'" P SINGLE NONE 10
YA4 SP3 P SINGLE NONE 11
YA4 P OP1 DOUBLE NONE 12
YA4 P OP3 SINGLE BEGINDASH 13
#
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
YA4 MurckoScaffold S1 scaffold C1CCOC1 InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2 WYURNTSHIVDZCO-UHFFFAOYSA-N
YA4 ribose F1 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
YA4 "C1'" S1 1
YA4 "C2'" S1 1
YA4 "C3'" S1 1
YA4 "C4'" S1 1
YA4 "O4'" S1 1
YA4 "C2'" F1 1
YA4 "C3'" F1 1
YA4 "C4'" F1 1
YA4 "O4'" F1 1
YA4 "C1'" F1 1
YA4 "C5'" F1 1
YA4 "O5'" F1 1
YA4 "O3'" F1 1
YA4 "O2'" F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YA4
_pdbe_chem_comp_rdkit_properties.exactmw 230.001
_pdbe_chem_comp_rdkit_properties.amw 230.178
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 95.565
_pdbe_chem_comp_rdkit_properties.tpsa 96.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.846
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.517
_pdbe_chem_comp_rdkit_properties.chi0v 7.516
_pdbe_chem_comp_rdkit_properties.chi1v 5.307
_pdbe_chem_comp_rdkit_properties.chi2v 1.447
_pdbe_chem_comp_rdkit_properties.chi3v 1.447
_pdbe_chem_comp_rdkit_properties.chi4v 0.764
_pdbe_chem_comp_rdkit_properties.chi0n 16.805
_pdbe_chem_comp_rdkit_properties.chi1n 7.884
_pdbe_chem_comp_rdkit_properties.chi2n 0.908
_pdbe_chem_comp_rdkit_properties.chi3n 0.908
_pdbe_chem_comp_rdkit_properties.chi4n 0.458
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.380
_pdbe_chem_comp_rdkit_properties.kappa1 3.450
_pdbe_chem_comp_rdkit_properties.kappa2 4.269
_pdbe_chem_comp_rdkit_properties.kappa3 3.551
_pdbe_chem_comp_rdkit_properties.Phi 1.133
#
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
YA4 UniChem PDBe YA4
YA4 UniChem PubChem 77003900
#
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
YA4 "C1'" -1.569 1.791 -0.405 ETKDGv3 1
YA4 "C2'" -2.408 0.521 -0.424 ETKDGv3 2
YA4 "C3'" -1.479 -0.497 0.192 ETKDGv3 3
YA4 "C4'" -0.594 0.365 1.091 ETKDGv3 4
YA4 "C5'" 0.838 -0.171 1.191 ETKDGv3 5
YA4 "O2'" -3.598 0.679 0.315 ETKDGv3 6
YA4 "O3'" -2.168 -1.466 0.940 ETKDGv3 7
YA4 "O4'" -0.583 1.689 0.600 ETKDGv3 8
YA4 "O5'" 1.474 -0.072 -0.063 ETKDGv3 9
YA4 OP1 3.858 0.185 1.040 ETKDGv3 10
YA4 P 3.060 -0.678 0.088 ETKDGv3 11
YA4 SP3 3.982 -0.638 -1.813 ETKDGv3 12
YA4 "H1'" -2.200 2.687 -0.222 ETKDGv3 13
YA4 "H1''" -1.062 1.919 -1.386 ETKDGv3 14
YA4 "H2'" -2.669 0.236 -1.467 ETKDGv3 15
YA4 "H3'" -0.876 -0.982 -0.612 ETKDGv3 16
YA4 "H4'" -1.026 0.387 2.118 ETKDGv3 17
YA4 "H5'" 1.378 0.439 1.952 ETKDGv3 18
YA4 "H5''" 0.794 -1.229 1.536 ETKDGv3 19
YA4 "HO2'" -3.357 0.976 1.232 ETKDGv3 20
YA4 "HO3'" -2.605 -2.068 0.283 ETKDGv3 21
YA4 HSP3 3.805 0.753 -1.927 ETKDGv3 22
YA4 OP3 3.028 -2.274 0.653 ETKDGv3 23
YA4 HOP3 3.977 -2.555 0.671 ETKDGv3 24
#