data_TA3
#
_chem_comp.id TA3
_chem_comp.name
(4S,5R)-3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYL-1,3-DIAZABICYCLO[2.2.0]HEXAN-2-ONE
_chem_comp.type "DNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C10 H17 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id DT
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-10-16
_chem_comp.pdbx_modified_date 2011-06-04
_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 308.225
_chem_comp.one_letter_code T
_chem_comp.three_letter_code TA3
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag Y
_chem_comp.pdbx_model_coordinates_db_code 1QKG
_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
TA3 OP3 O3P O 0 1 N Y N N N N -1.639 0.205 24.732 ? ? ? OP3 TA3 1
TA3 P P P 0 1 N N N N N N -2.059 -0.970 25.752 ? ? ? P TA3 2
TA3 OP1 O1P O 0 1 N N N N N N -1.880 -0.497 27.144 ? ? ? OP1 TA3 3
TA3 OP2 O2P O 0 1 N N N N N N -1.359 -2.210 25.347 ? ? ? OP2 TA3 4
TA3 "O5'" O5* O 0 1 N N N N N N -3.630 -1.148 25.461 ? ? ? "O5'" TA3 5
TA3 "C5'" C5* C 0 1 N N N N N N -4.753 -0.280 25.749 ? ? ? "C5'" TA3 6
TA3 "C4'" C4* C 0 1 N N R N N N -6.099 -0.804 25.200 ? ? ? "C4'" TA3 7
TA3 "O4'" O4* O 0 1 N N N N N N -6.039 -0.968 23.758 ? ? ? "O4'" TA3 8
TA3 "C3'" C3* C 0 1 N N S N N N -6.507 -2.150 25.745 ? ? ? "C3'" TA3 9
TA3 "O3'" O3* O 0 1 N N N N N N -7.939 -2.248 25.875 ? ? ? "O3'" TA3 10
TA3 "C2'" C2* C 0 1 N N N N N N -5.985 -3.099 24.711 ? ? ? "C2'" TA3 11
TA3 "C1'" C1* C 0 1 N N R N N N -6.330 -2.329 23.446 ? ? ? "C1'" TA3 12
TA3 N1 N1 N 0 1 N N N N N N -5.518 -2.822 22.279 ? ? ? N1 TA3 13
TA3 C2 C2 C 0 1 N N N N N N -5.610 -2.132 21.045 ? ? ? C2 TA3 14
TA3 O2 O2 O 0 1 N N N N N N -6.386 -2.307 20.098 ? ? ? O2 TA3 15
TA3 N3 N3 N 0 1 N N N N N N -4.384 -1.344 21.382 ? ? ? N3 TA3 16
TA3 C4 C4 C 0 1 N N N N N N -3.016 -1.578 20.819 ? ? ? C4 TA3 17
TA3 C5 C5 C 0 1 N N R N N N -3.079 -2.907 21.155 ? ? ? C5 TA3 18
TA3 C5M C5M C 0 1 N N N N N N -2.194 -4.058 21.011 ? ? ? C5M TA3 19
TA3 C6 C6 C 0 1 N N S N N N -4.019 -2.526 22.329 ? ? ? C6 TA3 20
TA3 HO1P HO1P H 0 0 N N N N N N -1.842 -1.244 27.730 ? ? ? HO1P TA3 21
TA3 HO2P HO2P H 0 0 N N N N N N -1.209 -2.198 24.409 ? ? ? HO2P TA3 22
TA3 "H5'" 1H5* H 0 1 N N N N N N -4.555 0.699 25.289 ? ? ? "H5'" TA3 23
TA3 "H5''" 2H5* H 0 0 N N N N N N -4.848 -0.226 26.844 ? ? ? "H5''" TA3 24
TA3 "H4'" H4* H 0 1 N N N N N N -6.830 -0.045 25.515 ? ? ? "H4'" TA3 25
TA3 "H3'" H3* H 0 1 N N N N N N -6.114 -2.350 26.753 ? ? ? "H3'" TA3 26
TA3 "HO3'" HO3* H 0 0 N Y N N N N -8.173 -2.270 26.795 ? ? ? "HO3'" TA3 27
TA3 "H2'" 1H2* H 0 1 N N N N N N -6.471 -4.085 24.755 ? ? ? "H2'" TA3 28
TA3 "H2''" 2H2* H 0 0 N N N N N N -4.920 -3.354 24.817 ? ? ? "H2''" TA3 29
TA3 "H1'" H1* H 0 1 N N N N N N -7.381 -2.459 23.148 ? ? ? "H1'" TA3 30
TA3 H41 1H4 H 0 1 N N N N N N -2.198 -1.001 21.275 ? ? ? H41 TA3 31
TA3 H42 2H4 H 0 1 N N N N N N -2.799 -1.290 19.780 ? ? ? H42 TA3 32
TA3 H5 H5 H 0 1 N N N N N N -3.165 -3.693 20.391 ? ? ? H5 TA3 33
TA3 H71 1H5M H 0 1 N N N N N N -1.971 -4.219 19.946 ? ? ? H71 TA3 34
TA3 H72 2H5M H 0 1 N N N N N N -1.258 -3.871 21.557 ? ? ? H72 TA3 35
TA3 H73 3H5M H 0 1 N N N N N N -2.686 -4.952 21.422 ? ? ? H73 TA3 36
TA3 H6 H6 H 0 1 N N N N N N -3.589 -2.752 23.316 ? ? ? H6 TA3 37
#
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
TA3 OP3 P DOUB N N 1
TA3 P OP2 SING N N 2
TA3 P "O5'" SING N N 3
TA3 P OP1 SING N N 4
TA3 OP1 HO1P SING N N 5
TA3 OP2 HO2P SING N N 6
TA3 "O5'" "C5'" SING N N 7
TA3 "C5'" "C4'" SING N N 8
TA3 "C5'" "H5'" SING N N 9
TA3 "C5'" "H5''" SING N N 10
TA3 "C4'" "O4'" SING N N 11
TA3 "C4'" "C3'" SING N N 12
TA3 "C4'" "H4'" SING N N 13
TA3 "O4'" "C1'" SING N N 14
TA3 "C3'" "C2'" SING N N 15
TA3 "C3'" "O3'" SING N N 16
TA3 "C3'" "H3'" SING N N 17
TA3 "O3'" "HO3'" SING N N 18
TA3 "C2'" "C1'" SING N N 19
TA3 "C2'" "H2'" SING N N 20
TA3 "C2'" "H2''" SING N N 21
TA3 "C1'" N1 SING N N 22
TA3 "C1'" "H1'" SING N N 23
TA3 N1 C2 SING N N 24
TA3 N1 C6 SING N N 25
TA3 C2 O2 DOUB N N 26
TA3 C2 N3 SING N N 27
TA3 N3 C4 SING N N 28
TA3 N3 C6 SING N N 29
TA3 C4 C5 SING N N 30
TA3 C4 H41 SING N N 31
TA3 C4 H42 SING N N 32
TA3 C5 C5M SING N N 33
TA3 C5 C6 SING N N 34
TA3 C5 H5 SING N N 35
TA3 C5M H71 SING N N 36
TA3 C5M H72 SING N N 37
TA3 C5M H73 SING N N 38
TA3 C6 H6 SING N N 39
#
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
TA3 SMILES ACDLabs 10.04 O=C2N1CC(C1N2C3OC(C(O)C3)COP(=O)(O)O)C
TA3 SMILES_CANONICAL CACTVS 3.341 C[C@@H]1CN2[C@H]1N([C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)C2=O
TA3 SMILES CACTVS 3.341 C[CH]1CN2[CH]1N([CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)C2=O
TA3 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H]1CN2[C@H]1N(C2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O
TA3 SMILES "OpenEye OEToolkits" 1.5.0 CC1CN2C1N(C2=O)C3CC(C(O3)COP(=O)(O)O)O
TA3 InChI InChI 1.03 InChI=1S/C10H17N2O7P/c1-5-3-11-9(5)12(10(11)14)8-2-6(13)7(19-8)4-18-20(15,16)17/h5-9,13H,2-4H2,1H3,(H2,15,16,17)/t5-,6+,7-,8-,9+/m1/s1
TA3 InChIKey InChI 1.03 TXQJFYDCAIBOMW-WUNNTHRKSA-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
TA3 "SYSTEMATIC NAME" ACDLabs 10.04 (4S,5R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-1,3-diazabicyclo[2.2.0]hexan-2-one
TA3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-[(3R,4S)-3-methyl-6-oxo-1,5-diazabicyclo[2.2.0]hexan-5-yl]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
TA3 'Create component' 2006-10-16 RCSB
TA3 'Modify descriptor' 2011-06-04 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
TA3 OP3 O 8.772 -5.293 1
TA3 P P 8.537 -3.812 2
TA3 OP1 O 10.018 -3.577 3
TA3 OP2 O 7.055 -4.047 4
TA3 "O5'" O 8.302 -2.331 5
TA3 "C5'" C 9.468 -1.387 6
TA3 "C4'" C 9.233 0.095 7
TA3 "O4'" O 7.897 0.776 8
TA3 "C3'" C 10.294 1.156 9
TA3 "O3'" O 11.776 0.921 10
TA3 "C2'" C 9.613 2.492 11
TA3 "C1'" C 8.132 2.257 12
TA3 N1 N 7.071 3.318 13
TA3 C2 C 7.071 4.818 14
TA3 O2 O 8.132 5.879 15
TA3 N3 N 5.571 4.818 16
TA3 C4 C 4.058 4.824 17
TA3 C5 C 4.058 3.312 18
TA3 C5M C 3.000 2.249 19
TA3 C6 C 5.571 3.318 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
TA3 OP3 P DOUBLE NONE 1
TA3 P OP2 SINGLE NONE 2
TA3 P "O5'" SINGLE NONE 3
TA3 P OP1 SINGLE NONE 4
TA3 "O5'" "C5'" SINGLE NONE 5
TA3 "C4'" "C5'" SINGLE BEGINWEDGE 6
TA3 "C4'" "O4'" SINGLE NONE 7
TA3 "C4'" "C3'" SINGLE NONE 8
TA3 "O4'" "C1'" SINGLE NONE 9
TA3 "C3'" "C2'" SINGLE NONE 10
TA3 "C3'" "O3'" SINGLE BEGINDASH 11
TA3 "C2'" "C1'" SINGLE NONE 12
TA3 "C1'" N1 SINGLE BEGINWEDGE 13
TA3 N1 C2 SINGLE NONE 14
TA3 N1 C6 SINGLE NONE 15
TA3 C2 O2 DOUBLE NONE 16
TA3 C2 N3 SINGLE NONE 17
TA3 N3 C4 SINGLE NONE 18
TA3 N3 C6 SINGLE NONE 19
TA3 C4 C5 SINGLE NONE 20
TA3 C5 C5M SINGLE BEGINDASH 21
TA3 C5 C6 SINGLE NONE 22
#
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
TA3 MurckoScaffold S1 scaffold 'O=C1N2CC[C@@H]2N1[C@H]1CCCO1' InChI=1S/C8H12N2O2/c11-8-9-4-3-6(9)10(8)7-2-1-5-12-7/h6-7H,1-5H2/t6-,7+/m0/s1 NEKRFZWPHHZXPA-NKWVEPMBSA-N
TA3 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
TA3 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
#
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
TA3 "C4'" S1 1
TA3 "O4'" S1 1
TA3 "C3'" S1 1
TA3 "C2'" S1 1
TA3 "C1'" S1 1
TA3 N1 S1 1
TA3 C2 S1 1
TA3 O2 S1 1
TA3 N3 S1 1
TA3 C4 S1 1
TA3 C5 S1 1
TA3 C6 S1 1
TA3 "C1'" F1 1
TA3 "C2'" F1 1
TA3 "C3'" F1 1
TA3 "O3'" F1 1
TA3 "C4'" F1 1
TA3 "O4'" F1 1
TA3 "C5'" F1 1
TA3 "O5'" F1 1
TA3 OP1 F2 1
TA3 P F2 1
TA3 OP3 F2 1
TA3 OP2 F2 1
TA3 "O5'" F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id TA3
_pdbe_chem_comp_rdkit_properties.exactmw 308.077
_pdbe_chem_comp_rdkit_properties.amw 308.227
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_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 138.991
_pdbe_chem_comp_rdkit_properties.tpsa 119.770
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.715
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.174
_pdbe_chem_comp_rdkit_properties.chi0v 10.094
_pdbe_chem_comp_rdkit_properties.chi1v 6.303
_pdbe_chem_comp_rdkit_properties.chi2v 2.647
_pdbe_chem_comp_rdkit_properties.chi3v 2.647
_pdbe_chem_comp_rdkit_properties.chi4v 1.736
_pdbe_chem_comp_rdkit_properties.chi0n 26.199
_pdbe_chem_comp_rdkit_properties.chi1n 13.067
_pdbe_chem_comp_rdkit_properties.chi2n 2.332
_pdbe_chem_comp_rdkit_properties.chi3n 2.332
_pdbe_chem_comp_rdkit_properties.chi4n 1.541
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.700
_pdbe_chem_comp_rdkit_properties.kappa1 4.406
_pdbe_chem_comp_rdkit_properties.kappa2 4.655
_pdbe_chem_comp_rdkit_properties.kappa3 2.240
_pdbe_chem_comp_rdkit_properties.Phi 1.026
#
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
TA3 UniChem PDBe TA3
TA3 UniChem ZINC ZINC000098209439
TA3 UniChem PubChem 137350042
#
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
TA3 OP3 2.568 -3.675 0.871 ETKDGv3 1
TA3 P 2.899 -2.791 -0.310 ETKDGv3 2
TA3 OP1 2.377 -3.554 -1.729 ETKDGv3 3
TA3 OP2 4.574 -2.549 -0.366 ETKDGv3 4
TA3 "O5'" 2.101 -1.298 -0.116 ETKDGv3 5
TA3 "C5'" 2.412 -0.479 -1.219 ETKDGv3 6
TA3 "C4'" 1.734 0.888 -1.058 ETKDGv3 7
TA3 "O4'" 0.335 0.708 -0.981 ETKDGv3 8
TA3 "C3'" 2.226 1.631 0.194 ETKDGv3 9
TA3 "O3'" 2.475 2.981 -0.104 ETKDGv3 10
TA3 "C2'" 1.058 1.529 1.131 ETKDGv3 11
TA3 "C1'" -0.114 1.349 0.189 ETKDGv3 12
TA3 N1 -1.158 0.550 0.814 ETKDGv3 13
TA3 C2 -1.336 -0.848 1.254 ETKDGv3 14
TA3 O2 -0.596 -1.866 1.249 ETKDGv3 15
TA3 N3 -2.707 -0.569 1.760 ETKDGv3 16
TA3 C4 -3.467 -0.918 0.514 ETKDGv3 17
TA3 C5 -3.395 0.451 -0.096 ETKDGv3 18
TA3 C5M -4.713 1.228 -0.067 ETKDGv3 19
TA3 C6 -2.527 0.699 1.120 ETKDGv3 20
TA3 HO1P 2.999 -3.239 -2.433 ETKDGv3 21
TA3 HO2P 4.954 -3.449 -0.531 ETKDGv3 22
TA3 "H5'" 2.035 -0.935 -2.162 ETKDGv3 23
TA3 "H5''" 3.511 -0.319 -1.305 ETKDGv3 24
TA3 "H4'" 1.961 1.486 -1.968 ETKDGv3 25
TA3 "H3'" 3.132 1.169 0.654 ETKDGv3 26
TA3 "HO3'" 3.357 3.011 -0.559 ETKDGv3 27
TA3 "H2'" 1.182 0.634 1.781 ETKDGv3 28
TA3 "H2''" 0.940 2.433 1.768 ETKDGv3 29
TA3 "H1'" -0.531 2.343 -0.085 ETKDGv3 30
TA3 H41 -4.508 -1.204 0.783 ETKDGv3 31
TA3 H42 -3.040 -1.727 -0.134 ETKDGv3 32
TA3 H5 -2.858 0.486 -1.070 ETKDGv3 33
TA3 H71 -5.406 0.808 -0.827 ETKDGv3 34
TA3 H72 -5.198 1.174 0.932 ETKDGv3 35
TA3 H73 -4.518 2.293 -0.313 ETKDGv3 36
TA3 H6 -2.761 1.569 1.774 ETKDGv3 37
#