data_8YN
#
_chem_comp.id 8YN
_chem_comp.name Pseudoisocytidine
_chem_comp.type "DNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H14 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id DC
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-03-27
_chem_comp.pdbx_modified_date 2019-05-07
_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 307.197
_chem_comp.one_letter_code C
_chem_comp.three_letter_code 8YN
_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 5NIP
_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
8YN P P1 P 0 1 N N N N N N 26.249 26.755 11.852 -3.932 1.021 -0.110 P 8YN 1
8YN C1 C1 C 0 1 N N N N N N 20.568 24.914 11.401 2.516 -0.359 -0.375 C1 8YN 2
8YN C2 C2 C 0 1 N N N N N N 19.967 23.661 11.714 2.484 0.606 0.646 C2 8YN 3
8YN C4 C3 C 0 1 N N N N N N 18.991 24.540 13.674 4.585 1.353 -0.078 C4 8YN 4
8YN C6 C4 C 0 1 N N N N N N 20.338 25.986 12.308 3.602 -0.410 -1.201 C6 8YN 5
8YN O1P O1 O 0 1 N N N N N N 27.687 26.416 11.788 -4.469 1.803 -1.411 O1P 8YN 6
8YN O2P O2 O 0 1 N N N N N N 25.834 28.155 12.065 -5.019 0.184 0.446 O2P 8YN 7
8YN "O5'" O3 O 0 1 N N N N N N 25.620 26.227 10.460 -2.690 0.084 -0.522 "O5'" 8YN 8
8YN "C5'" C5 C 0 1 N N N N N N 24.494 26.866 9.861 -2.058 -0.817 0.390 "C5'" 8YN 9
8YN "C4'" C6 C 0 1 N N R N N N 23.448 25.851 9.387 -0.919 -1.549 -0.322 "C4'" 8YN 10
8YN "O4'" O4 O 0 1 N N N N N N 22.776 25.296 10.517 0.121 -0.618 -0.665 "O4'" 8YN 11
8YN "C1'" C7 C 0 1 N N R N N N 21.425 25.101 10.159 1.374 -1.327 -0.552 "C1'" 8YN 12
8YN O2 O5 O 0 1 N N N N N N 20.135 22.719 10.939 1.529 0.679 1.403 O2 8YN 13
8YN N3 N1 N 0 1 N N N N N N 19.233 23.487 12.855 3.529 1.450 0.775 N3 8YN 14
8YN N4 N2 N 0 1 N N N N N N 18.179 24.330 14.668 5.641 2.213 0.059 N4 8YN 15
8YN N5 N3 N 0 1 N N N N N N 19.521 25.780 13.423 4.608 0.445 -1.033 N5 8YN 16
8YN "C2'" C8 C 0 1 N N N N N N 21.142 26.391 9.390 1.188 -2.190 0.722 "C2'" 8YN 17
8YN "C3'" C9 C 0 1 N N S N N N 22.366 26.472 8.490 -0.302 -2.600 0.621 "C3'" 8YN 18
8YN "O3'" O6 O 0 1 N N N N N N 22.215 25.665 7.331 -0.423 -3.908 0.060 "O3'" 8YN 19
8YN H6 H1 H 0 1 N N N N N N 20.791 26.951 12.136 3.644 -1.144 -1.991 H6 8YN 20
8YN H1 H2 H 0 1 N N N N N N 28.204 27.205 11.901 -5.219 2.388 -1.237 H1 8YN 21
8YN "H52'" H4 H 0 0 N N N N N N 24.837 27.454 8.997 -1.658 -0.257 1.235 "H52'" 8YN 22
8YN "H51'" H5 H 0 0 N N N N N N 24.030 27.536 10.600 -2.789 -1.542 0.749 "H51'" 8YN 23
8YN "H4'" H6 H 0 1 N N N N N N 23.959 25.057 8.823 -1.296 -2.033 -1.223 "H4'" 8YN 24
8YN "H1'" H7 H 0 1 N N N N N N 21.307 24.236 9.490 1.539 -1.958 -1.426 "H1'" 8YN 25
8YN H3 H8 H 0 1 N N N N N N 18.875 22.582 13.085 3.528 2.124 1.473 H3 8YN 26
8YN H41 H9 H 0 1 N N N N N N 17.925 25.084 15.274 5.633 2.884 0.759 H41 8YN 27
8YN H42 H10 H 0 1 N N N N N N 17.808 23.415 14.826 6.398 2.151 -0.545 H42 8YN 28
8YN "H22'" H11 H 0 0 N N N N N N 21.080 27.257 10.065 1.835 -3.066 0.696 "H22'" 8YN 29
8YN "H21'" H12 H 0 0 N N N N N N 20.214 26.316 8.803 1.370 -1.601 1.621 "H21'" 8YN 30
8YN "H3'" H13 H 0 1 N N N N N N 22.610 27.517 8.249 -0.776 -2.559 1.601 "H3'" 8YN 31
8YN H4 H14 H 0 1 N N N N N N 21.548 26.040 6.768 -0.051 -4.609 0.612 H4 8YN 32
8YN O3P O3P O 0 1 N Y N N N N 25.580 25.829 12.976 -3.456 2.088 0.998 O3P 8YN 33
8YN H2 H15 H 0 1 N Y N N N N 25.050 26.365 13.555 -2.744 2.671 0.702 H2 8YN 34
#
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
8YN "O3'" "C3'" SING N N 1
8YN "C3'" "C4'" SING N N 2
8YN "C3'" "C2'" SING N N 3
8YN "C4'" "C5'" SING N N 4
8YN "C4'" "O4'" SING N N 5
8YN "C2'" "C1'" SING N N 6
8YN "C5'" "O5'" SING N N 7
8YN "C1'" "O4'" SING N N 8
8YN "C1'" C1 SING N N 9
8YN "O5'" P SING N N 10
8YN O2 C2 DOUB N N 11
8YN C1 C2 SING N N 12
8YN C1 C6 DOUB N N 13
8YN C2 N3 SING N N 14
8YN O1P P SING N N 15
8YN P O2P DOUB N N 16
8YN C6 N5 SING N N 17
8YN N3 C4 SING N N 18
8YN N5 C4 DOUB N N 19
8YN C4 N4 SING N N 20
8YN C6 H6 SING N N 21
8YN O1P H1 SING N N 22
8YN "C5'" "H52'" SING N N 23
8YN "C5'" "H51'" SING N N 24
8YN "C4'" "H4'" SING N N 25
8YN "C1'" "H1'" SING N N 26
8YN N3 H3 SING N N 27
8YN N4 H41 SING N N 28
8YN N4 H42 SING N N 29
8YN "C2'" "H22'" SING N N 30
8YN "C2'" "H21'" SING N N 31
8YN "C3'" "H3'" SING N N 32
8YN "O3'" H4 SING N N 33
8YN P O3P SING N N 34
8YN O3P H2 SING N N 35
#
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
8YN InChI InChI 1.03 InChI=1S/C9H14N3O7P/c10-9-11-2-4(8(14)12-9)6-1-5(13)7(19-6)3-18-20(15,16)17/h2,5-7,13H,1,3H2,(H2,15,16,17)(H3,10,11,12,14)/t5-,6+,7+/m0/s1
8YN InChIKey InChI 1.03 LMPCXRMBUOVHQD-RRKCRQDMSA-N
8YN SMILES_CANONICAL CACTVS 3.385 NC1=NC=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N1
8YN SMILES CACTVS 3.385 NC1=NC=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1
8YN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1[C@@H]([C@H](O[C@H]1C2=CN=C(NC2=O)N)COP(=O)(O)O)O
8YN SMILES "OpenEye OEToolkits" 2.0.7 C1C(C(OC1C2=CN=C(NC2=O)N)COP(=O)(O)O)O
#
_pdbx_chem_comp_identifier.comp_id 8YN
_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},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-pyrimidin-5-yl)-3-oxidanyl-oxolan-2-yl]methyl 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
8YN 'Create component' 2017-03-27 EBI
8YN 'Initial release' 2017-06-28 RCSB
8YN 'Other modification' 2019-05-07 EBI
#
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
8YN P P 4.807 1.406 1
8YN C1 C 12.345 -0.748 2
8YN C2 C 12.345 -2.248 3
8YN C4 C 14.943 -2.248 4
8YN C6 C 13.644 0.002 5
8YN O1P O 3.925 2.620 6
8YN O2P O 4.196 0.036 7
8YN "O5'" O 6.298 1.563 8
8YN "C5'" C 7.180 0.350 9
8YN "C4'" C 8.672 0.506 10
8YN "O4'" O 9.676 -0.608 11
8YN "C1'" C 11.046 0.002 12
8YN O2 O 11.046 -2.998 13
8YN N3 N 13.644 -2.998 14
8YN N4 N 16.242 -2.998 15
8YN N5 N 14.943 -0.748 16
8YN "C2'" C 10.889 1.494 17
8YN "C3'" C 9.422 1.806 18
8YN "O3'" O 8.812 3.176 19
8YN O3P O 5.688 0.193 20
#
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
8YN "C3'" "O3'" SINGLE BEGINWEDGE 1
8YN "C3'" "C4'" SINGLE NONE 2
8YN "C3'" "C2'" SINGLE NONE 3
8YN "C4'" "C5'" SINGLE BEGINDASH 4
8YN "C4'" "O4'" SINGLE NONE 5
8YN "C2'" "C1'" SINGLE NONE 6
8YN "C5'" "O5'" SINGLE NONE 7
8YN "C1'" "O4'" SINGLE NONE 8
8YN "C1'" C1 SINGLE BEGINDASH 9
8YN "O5'" P SINGLE NONE 10
8YN O2 C2 DOUBLE NONE 11
8YN C1 C2 SINGLE NONE 12
8YN C1 C6 DOUBLE NONE 13
8YN C2 N3 SINGLE NONE 14
8YN O1P P SINGLE NONE 15
8YN P O2P DOUBLE NONE 16
8YN C6 N5 SINGLE NONE 17
8YN N3 C4 SINGLE NONE 18
8YN N5 C4 DOUBLE NONE 19
8YN C4 N4 SINGLE NONE 20
8YN P O3P SINGLE NONE 21
#
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
8YN MurckoScaffold S1 scaffold 'O=c1[nH]cncc1[C@H]1CCCO1' InChI=1S/C8H10N2O2/c11-8-6(4-9-5-10-8)7-2-1-3-12-7/h4-5,7H,1-3H2,(H,9,10,11)/t7-/m1/s1 GMTFOCTWVDJJNL-SSDOTTSWSA-N
8YN deoxyribose F1 fragment 'OCC1OC[CH2]C1O' InChI=1S/C5H10O3/c6-3-5-4(7)1-2-8-5/h4-7H,1-3H2 NSMOSDAEGJTOIQ-UHFFFAOYSA-N
8YN phosphate F2 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
8YN pyrimidine F3 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
8YN C1 S1 1
8YN C2 S1 1
8YN C4 S1 1
8YN C6 S1 1
8YN "C4'" S1 1
8YN "O4'" S1 1
8YN "C1'" S1 1
8YN O2 S1 1
8YN N3 S1 1
8YN N5 S1 1
8YN "C2'" S1 1
8YN "C3'" S1 1
8YN "C1'" F1 1
8YN "C2'" F1 1
8YN "C3'" F1 1
8YN "O3'" F1 1
8YN "C4'" F1 1
8YN "O4'" F1 1
8YN "C5'" F1 1
8YN "O5'" F1 1
8YN O1P F2 1
8YN P F2 1
8YN O2P F2 1
8YN "O5'" F2 1
8YN H6 F2 1
8YN C1 F3 1
8YN C2 F3 1
8YN N3 F3 1
8YN C4 F3 1
8YN N5 F3 1
8YN C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 8YN
_pdbe_chem_comp_rdkit_properties.exactmw 307.057
_pdbe_chem_comp_rdkit_properties.amw 307.199
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 132.454
_pdbe_chem_comp_rdkit_properties.tpsa 167.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.883
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.522
_pdbe_chem_comp_rdkit_properties.chi0v 10.041
_pdbe_chem_comp_rdkit_properties.chi1v 6.080
_pdbe_chem_comp_rdkit_properties.chi2v 2.113
_pdbe_chem_comp_rdkit_properties.chi3v 2.113
_pdbe_chem_comp_rdkit_properties.chi4v 1.280
_pdbe_chem_comp_rdkit_properties.chi0n 23.147
_pdbe_chem_comp_rdkit_properties.chi1n 11.185
_pdbe_chem_comp_rdkit_properties.chi2n 1.798
_pdbe_chem_comp_rdkit_properties.chi3n 1.798
_pdbe_chem_comp_rdkit_properties.chi4n 1.085
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.290
_pdbe_chem_comp_rdkit_properties.kappa1 5.164
_pdbe_chem_comp_rdkit_properties.kappa2 5.602
_pdbe_chem_comp_rdkit_properties.kappa3 3.629
_pdbe_chem_comp_rdkit_properties.Phi 1.447
#
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
8YN UniChem PDBe 8YN
8YN UniChem PubChem 138753110
#
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
8YN P -4.495 -1.161 0.432 ETKDGv3 1
8YN C1 1.983 0.727 -0.076 ETKDGv3 2
8YN C2 3.365 1.234 -0.212 ETKDGv3 3
8YN C4 4.060 -0.401 1.503 ETKDGv3 4
8YN C6 1.767 -0.285 0.783 ETKDGv3 5
8YN O1P -5.846 -1.726 -0.414 ETKDGv3 6
8YN O2P -3.806 -2.332 1.096 ETKDGv3 7
8YN "O5'" -3.429 -0.406 -0.666 ETKDGv3 8
8YN "C5'" -2.363 0.156 0.063 ETKDGv3 9
8YN "C4'" -1.360 0.789 -0.905 ETKDGv3 10
8YN "O4'" -0.320 1.400 -0.178 ETKDGv3 11
8YN "C1'" 0.865 1.274 -0.940 ETKDGv3 12
8YN O2 3.646 2.151 -1.028 ETKDGv3 13
8YN N3 4.393 0.659 0.599 ETKDGv3 14
8YN N4 5.071 -0.990 2.321 ETKDGv3 15
8YN N5 2.835 -0.833 1.577 ETKDGv3 16
8YN "C2'" 0.603 0.372 -2.147 ETKDGv3 17
8YN "C3'" -0.740 -0.234 -1.848 ETKDGv3 18
8YN "O3'" -1.512 -0.376 -3.011 ETKDGv3 19
8YN H6 0.778 -0.711 0.890 ETKDGv3 20
8YN H1 -6.207 -0.927 -0.874 ETKDGv3 21
8YN "H52'" -1.836 -0.616 0.670 ETKDGv3 22
8YN "H51'" -2.737 0.958 0.739 ETKDGv3 23
8YN "H4'" -1.882 1.579 -1.494 ETKDGv3 24
8YN "H1'" 1.141 2.289 -1.301 ETKDGv3 25
8YN H3 5.376 1.006 0.528 ETKDGv3 26
8YN H41 6.057 -0.652 2.268 ETKDGv3 27
8YN H42 4.835 -1.764 2.980 ETKDGv3 28
8YN "H22'" 1.376 -0.415 -2.287 ETKDGv3 29
8YN "H21'" 0.552 0.992 -3.070 ETKDGv3 30
8YN "H3'" -0.606 -1.216 -1.335 ETKDGv3 31
8YN H4 -1.142 -1.157 -3.499 ETKDGv3 32
8YN O3P -5.001 -0.061 1.616 ETKDGv3 33
8YN H2 -5.421 0.679 1.109 ETKDGv3 34
#