data_42E
#
_chem_comp.id 42E
_chem_comp.name "[(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H12 N3 O6 P S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 3TC-MP
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-01-29
_chem_comp.pdbx_modified_date 2020-06-17
_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 309.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 42E
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4S07
_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
42E PA PA P 0 1 N N N N N N 9.008 -21.479 13.463 3.118 -0.976 -0.094 PA 42E 1
42E O1A O1A O 0 1 N N N N N N 10.331 -21.863 12.835 3.671 -1.284 1.244 O1A 42E 2
42E O2A O2A O 0 1 N N N N N N 7.776 -22.293 13.123 2.497 -2.314 -0.739 O2A 42E 3
42E "O5'" "O5'" O 0 1 N N N N N N 9.226 -21.451 15.076 1.964 0.138 0.046 "O5'" 42E 4
42E "C5'" "C5'" C 0 1 N N N N N N 10.468 -20.989 15.586 2.174 1.401 0.679 "C5'" 42E 5
42E "C4'" "C4'" C 0 1 N N R N N N 10.397 -19.869 16.621 0.879 2.214 0.639 "C4'" 42E 6
42E "O4'" "O4'" O 0 1 N N N N N N 9.373 -20.123 17.614 -0.180 1.521 1.325 "O4'" 42E 7
42E "S3'" "S3'" S 0 1 N N N N N N 10.140 -18.295 15.809 0.234 2.331 -1.082 "S3'" 42E 8
42E "C2'" "C2'" C 0 1 N N N N N N 9.473 -17.693 17.340 -1.520 2.470 -0.533 "C2'" 42E 9
42E "C1'" "C1'" C 0 1 N N S N N N 8.821 -18.868 18.056 -1.479 1.634 0.769 "C1'" 42E 10
42E N1 N1 N 0 1 N N N N N N 7.404 -18.810 17.694 -1.985 0.290 0.480 N1 42E 11
42E C2 C2 C 0 1 N N N N N N 6.621 -17.837 18.205 -3.197 0.138 -0.085 C2 42E 12
42E O2 O2 O 0 1 N N N N N N 7.155 -16.925 19.041 -3.863 1.125 -0.350 O2 42E 13
42E N3 N3 N 0 1 N N N N N N 5.305 -17.719 17.886 -3.681 -1.072 -0.358 N3 42E 14
42E C4 C4 C 0 1 N N N N N N 4.751 -18.640 17.070 -2.978 -2.162 -0.080 C4 42E 15
42E N4 N4 N 0 1 N N N N N N 3.468 -18.549 16.764 -3.488 -3.407 -0.367 N4 42E 16
42E C5 C5 C 0 1 N N N N N N 5.467 -19.669 16.505 -1.704 -2.037 0.513 C5 42E 17
42E C6 C6 C 0 1 N N N N N N 6.890 -19.830 16.764 -1.224 -0.799 0.779 C6 42E 18
42E H2 H2 H 0 1 N N N N N N 8.011 -22.987 12.518 3.137 -3.030 -0.853 H2 42E 19
42E H3 H3 H 0 1 N N N N N N 10.979 -21.845 16.052 2.472 1.242 1.716 H3 42E 20
42E H4 H4 H 0 1 N N N N N N 11.065 -20.624 14.737 2.961 1.944 0.155 H4 42E 21
42E H5 H5 H 0 1 N N N N N N 11.376 -19.791 17.116 1.033 3.205 1.066 H5 42E 22
42E H6 H6 H 0 1 N N N N N N 10.279 -17.276 17.962 -1.787 3.507 -0.327 H6 42E 23
42E H7 H7 H 0 1 N N N N N N 8.723 -16.913 17.141 -2.198 2.029 -1.263 H7 42E 24
42E H8 H8 H 0 1 N N N N N N 8.944 -18.750 19.143 -2.135 2.100 1.504 H8 42E 25
42E H9 H9 H 0 1 N N N N N N 2.917 -17.802 17.136 -4.364 -3.489 -0.775 H9 42E 26
42E H10 H10 H 0 1 N N N N N N 3.049 -19.227 16.160 -2.971 -4.201 -0.162 H10 42E 27
42E H11 H11 H 0 1 N N N N N N 4.964 -20.371 15.857 -1.118 -2.914 0.742 H11 42E 28
42E H12 H12 H 0 1 N N N N N N 7.498 -20.607 16.325 -0.251 -0.678 1.232 H12 42E 29
42E OP3 OP3 O 0 1 N Y N N N N ? ? ? 4.292 -0.417 -1.044 OP3 42E 30
42E H1 H1 H 0 1 N Y N N N N ? ? ? 4.001 -0.194 -1.938 H1 42E 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
42E O1A PA DOUB N N 1
42E O2A PA SING N N 2
42E PA "O5'" SING N N 3
42E "O5'" "C5'" SING N N 4
42E "C5'" "C4'" SING N N 5
42E "S3'" "C4'" SING N N 6
42E "S3'" "C2'" SING N N 7
42E C5 C6 DOUB N N 8
42E C5 C4 SING N N 9
42E "C4'" "O4'" SING N N 10
42E C6 N1 SING N N 11
42E N4 C4 SING N N 12
42E C4 N3 DOUB N N 13
42E "C2'" "C1'" SING N N 14
42E "O4'" "C1'" SING N N 15
42E N1 "C1'" SING N N 16
42E N1 C2 SING N N 17
42E N3 C2 SING N N 18
42E C2 O2 DOUB N N 19
42E O2A H2 SING N N 20
42E "C5'" H3 SING N N 21
42E "C5'" H4 SING N N 22
42E "C4'" H5 SING N N 23
42E "C2'" H6 SING N N 24
42E "C2'" H7 SING N N 25
42E "C1'" H8 SING N N 26
42E N4 H9 SING N N 27
42E N4 H10 SING N N 28
42E C5 H11 SING N N 29
42E C6 H12 SING N N 30
42E PA OP3 SING N N 31
42E OP3 H1 SING N N 32
#
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
42E SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CS2
42E InChI InChI 1.03 InChI=1S/C8H12N3O6PS/c9-5-1-2-11(8(12)10-5)6-4-19-7(17-6)3-16-18(13,14)15/h1-2,6-7H,3-4H2,(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1
42E InChIKey InChI 1.03 WUMZLKDCOINBEA-NKWVEPMBSA-N
42E SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(O)=O)O2
42E SMILES CACTVS 3.385 NC1=NC(=O)N(C=C1)[CH]2CS[CH](CO[P](O)(O)=O)O2
42E SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1[C@H](O[C@H](S1)COP(=O)(O)O)N2C=CC(=NC2=O)N
42E SMILES "OpenEye OEToolkits" 1.7.6 C1C(OC(S1)COP(=O)(O)O)N2C=CC(=NC2=O)N
#
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
42E "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate"
42E "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-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
42E 'Create component' 2015-01-29 RCSB
42E 'Initial release' 2017-01-11 RCSB
42E 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 42E
_pdbx_chem_comp_synonyms.name 3TC-MP
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 42E
_pdbe_chem_comp_synonyms.name 3TC-MP
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
42E PA P 6.202 -5.254 1
42E O1A O 7.084 -6.467 2
42E O2A O 4.989 -6.136 3
42E "O5'" O 5.321 -4.040 4
42E "C5'" C 5.931 -2.670 5
42E "C4'" C 5.049 -1.456 6
42E "O4'" O 5.513 -0.030 7
42E "S3'" S 3.549 -1.456 8
42E "C2'" C 3.086 -0.030 9
42E "C1'" C 4.299 0.852 10
42E N1 N 4.299 2.352 11
42E C2 C 5.598 3.102 12
42E O2 O 6.897 2.352 13
42E N3 N 5.598 4.602 14
42E C4 C 4.299 5.352 15
42E N4 N 4.299 6.852 16
42E C5 C 3.000 4.602 17
42E C6 C 3.000 3.102 18
42E OP3 O 7.416 -4.372 19
#
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
42E O1A PA DOUBLE NONE 1
42E O2A PA SINGLE NONE 2
42E PA "O5'" SINGLE NONE 3
42E "O5'" "C5'" SINGLE NONE 4
42E "C4'" "C5'" SINGLE BEGINWEDGE 5
42E "S3'" "C4'" SINGLE NONE 6
42E "S3'" "C2'" SINGLE NONE 7
42E C5 C6 DOUBLE NONE 8
42E C5 C4 SINGLE NONE 9
42E "C4'" "O4'" SINGLE NONE 10
42E C6 N1 SINGLE NONE 11
42E N4 C4 SINGLE NONE 12
42E C4 N3 DOUBLE NONE 13
42E "C2'" "C1'" SINGLE NONE 14
42E "O4'" "C1'" SINGLE NONE 15
42E "C1'" N1 SINGLE BEGINWEDGE 16
42E N1 C2 SINGLE NONE 17
42E N3 C2 SINGLE NONE 18
42E C2 O2 DOUBLE NONE 19
42E PA OP3 SINGLE NONE 20
#
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
42E MurckoScaffold S1 scaffold 'O=c1ncccn1[C@@H]1CSCO1' InChI=1S/C7H8N2O2S/c10-7-8-2-1-3-9(7)6-4-12-5-11-6/h1-3,6H,4-5H2/t6-/m0/s1 RSKYNOBRSYJMLD-LURJTMIESA-N
42E 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
42E 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
42E "C4'" S1 1
42E "O4'" S1 1
42E "S3'" S1 1
42E "C2'" S1 1
42E "C1'" S1 1
42E N1 S1 1
42E C2 S1 1
42E O2 S1 1
42E N3 S1 1
42E C4 S1 1
42E C5 S1 1
42E C6 S1 1
42E O2A F1 1
42E PA F1 1
42E O1A F1 1
42E "O5'" F1 1
42E H2 F1 1
42E C5 F2 1
42E C6 F2 1
42E N1 F2 1
42E C2 F2 1
42E N3 F2 1
42E C4 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 42E
_pdbe_chem_comp_rdkit_properties.exactmw 309.018
_pdbe_chem_comp_rdkit_properties.amw 309.240
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.673
_pdbe_chem_comp_rdkit_properties.tpsa 136.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.042
_pdbe_chem_comp_rdkit_properties.CrippenMR 66.558
_pdbe_chem_comp_rdkit_properties.chi0v 10.358
_pdbe_chem_comp_rdkit_properties.chi1v 6.574
_pdbe_chem_comp_rdkit_properties.chi2v 2.480
_pdbe_chem_comp_rdkit_properties.chi3v 2.480
_pdbe_chem_comp_rdkit_properties.chi4v 1.679
_pdbe_chem_comp_rdkit_properties.chi0n 20.647
_pdbe_chem_comp_rdkit_properties.chi1n 10.008
_pdbe_chem_comp_rdkit_properties.chi2n 1.537
_pdbe_chem_comp_rdkit_properties.chi3n 1.537
_pdbe_chem_comp_rdkit_properties.chi4n 0.906
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 5.472
_pdbe_chem_comp_rdkit_properties.kappa2 5.614
_pdbe_chem_comp_rdkit_properties.kappa3 4.031
_pdbe_chem_comp_rdkit_properties.Phi 1.617
#
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
42E UniChem PDBe 42E
42E UniChem ZINC ZINC000003590790
42E UniChem SureChEMBL SCHEMBL12595493
42E UniChem 'PubChem TPHARMA' 15346343
42E UniChem Nikkaji J1.241.492G
42E UniChem PubChem 503017
#
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
42E PA -4.274 0.729 -0.680 ETKDGv3 1
42E O1A -5.442 0.214 0.133 ETKDGv3 2
42E O2A -4.357 2.417 -0.803 ETKDGv3 3
42E "O5'" -2.805 0.253 0.043 ETKDGv3 4
42E "C5'" -2.686 0.901 1.289 ETKDGv3 5
42E "C4'" -1.419 0.424 1.993 ETKDGv3 6
42E "O4'" -0.298 0.701 1.185 ETKDGv3 7
42E "S3'" -1.537 -1.361 2.362 ETKDGv3 8
42E "C2'" 0.086 -1.605 1.632 ETKDGv3 9
42E "C1'" 0.705 -0.225 1.518 ETKDGv3 10
42E N1 1.765 -0.217 0.499 ETKDGv3 11
42E C2 1.477 -0.202 -0.914 ETKDGv3 12
42E O2 0.291 -0.161 -1.337 ETKDGv3 13
42E N3 2.559 -0.240 -1.850 ETKDGv3 14
42E C4 3.795 -0.313 -1.453 ETKDGv3 15
42E N4 4.845 -0.350 -2.418 ETKDGv3 16
42E C5 4.118 -0.366 -0.010 ETKDGv3 17
42E C6 3.143 -0.324 0.902 ETKDGv3 18
42E H2 -4.744 2.722 0.056 ETKDGv3 19
42E H3 -3.557 0.677 1.946 ETKDGv3 20
42E H4 -2.606 2.002 1.148 ETKDGv3 21
42E H5 -1.318 0.974 2.955 ETKDGv3 22
42E H6 0.705 -2.266 2.276 ETKDGv3 23
42E H7 -0.044 -2.073 0.633 ETKDGv3 24
42E H8 1.134 0.064 2.506 ETKDGv3 25
42E H9 5.843 -0.411 -2.118 ETKDGv3 26
42E H10 4.627 -0.316 -3.439 ETKDGv3 27
42E H11 5.150 -0.442 0.310 ETKDGv3 28
42E H12 3.402 -0.372 1.953 ETKDGv3 29
42E OP3 -4.354 0.068 -2.236 ETKDGv3 30
42E H1 -4.205 -0.902 -2.106 ETKDGv3 31
#