data_8DA
#
_chem_comp.id 8DA
_chem_comp.name 8-OXODEOXYADENOSINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H15 N5 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-08-08
_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 269.257
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 8DA
_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 N
_chem_comp.pdbx_model_coordinates_db_code 2A5C
_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
8DA O19 O19 O 0 1 N N N N N N 2.879 9.862 22.351 -3.476 -2.764 -0.625 O19 8DA 1
8DA "C5'" C5* C 0 1 N N N N N N 1.574 10.107 21.832 -3.514 -1.720 0.350 "C5'" 8DA 2
8DA "C4'" C4* C 0 1 N N S N N N 1.209 11.604 21.870 -2.961 -0.432 -0.261 "C4'" 8DA 3
8DA "C3'" C3* C 0 1 N N R N N N -0.265 11.670 21.941 -3.107 0.741 0.734 "C3'" 8DA 4
8DA "O3'" O3* O 0 1 N N N N N N -0.355 12.911 21.260 -4.266 1.519 0.428 "O3'" 8DA 5
8DA "O4'" O4* O 0 1 N N N N N N 1.631 12.242 23.074 -1.538 -0.550 -0.488 "O4'" 8DA 6
8DA "C1'" C1* C 0 1 N N S N N N 0.566 12.600 23.959 -1.054 0.808 -0.576 "C1'" 8DA 7
8DA "C2'" C2* C 0 1 N N N N N N -0.706 12.165 23.285 -1.824 1.576 0.522 "C2'" 8DA 8
8DA N9 N9 N 0 1 N N N N N N 0.711 12.126 25.364 0.387 0.854 -0.314 N9 8DA 9
8DA C4 C4 C 0 1 N N N N N N 1.630 11.352 25.941 1.190 -0.235 -0.082 C4 8DA 10
8DA N3 N3 N 0 1 N N N N N N 2.773 10.707 25.352 0.911 -1.511 0.049 N3 8DA 11
8DA C5 C5 C 0 1 N N N N N N 1.353 11.209 27.389 2.524 0.260 0.001 C5 8DA 12
8DA N7 N7 N 0 1 N N N N N N 0.222 11.922 27.641 2.432 1.652 -0.036 N7 8DA 13
8DA C8 C8 C 0 1 N N N N N N -0.083 12.437 26.411 1.139 1.972 -0.263 C8 8DA 14
8DA O18 O18 O 0 1 N N N N N N -1.121 13.186 26.247 0.715 3.104 -0.402 O18 8DA 15
8DA C6 C6 C 0 1 N N N N N N 2.262 10.401 28.111 3.591 -0.583 0.112 C6 8DA 16
8DA N6 N6 N 0 1 N N N N N N 2.049 10.230 29.443 4.874 -0.125 0.312 N6 8DA 17
8DA N1 N1 N 0 1 N N N N N N 3.336 9.807 27.489 3.293 -1.937 0.004 N1 8DA 18
8DA C2 C2 C 0 1 N N N N N N 3.574 9.973 26.162 1.985 -2.432 0.444 C2 8DA 19
8DA H19 H19 H 0 1 N N N N N N 3.500 9.808 21.634 -3.833 -3.557 -0.200 H19 8DA 20
8DA "H5'1" 1H5* H 0 0 N N N N N N 0.851 9.564 22.458 -2.908 -2.004 1.210 "H5'1" 8DA 21
8DA "H5'2" 2H5* H 0 0 N N N N N N 1.541 9.764 20.788 -4.544 -1.558 0.669 "H5'2" 8DA 22
8DA "H4'" H4* H 0 1 N N N N N N 1.676 12.086 20.998 -3.475 -0.204 -1.195 "H4'" 8DA 23
8DA "H3'" H3* H 0 1 N N N N N N -0.777 10.742 21.646 -3.157 0.370 1.757 "H3'" 8DA 24
8DA H1 H1 H 0 1 N N N N N N -0.375 13.619 21.893 -4.271 2.267 1.040 H1 8DA 25
8DA "H1'" H1* H 0 1 N N N N N N 0.571 13.689 24.116 -1.274 1.227 -1.557 "H1'" 8DA 26
8DA "H2'1" 1H2* H 0 0 N N N N N N -1.240 11.393 23.859 -1.239 1.617 1.441 "H2'1" 8DA 27
8DA "H2'2" 2H2* H 0 0 N N N N N N -1.412 13.003 23.188 -2.074 2.581 0.181 "H2'2" 8DA 28
8DA HN7 HN7 H 0 1 N N N N N N -0.264 12.040 28.507 3.164 2.278 0.082 HN7 8DA 29
8DA HN61 1HN6 H 0 0 N N N N N N 1.515 10.998 29.796 5.044 0.827 0.379 HN61 8DA 30
8DA HN62 2HN6 H 0 0 N N N N N N 2.928 10.188 29.919 5.607 -0.756 0.391 HN62 8DA 31
8DA HN1 HN1 H 0 1 N N N N N N 4.146 10.163 27.954 3.950 -2.553 -0.357 HN1 8DA 32
8DA H21 1H2 H 0 1 N N N N N N 4.498 10.569 26.169 1.985 -2.535 1.529 H21 8DA 33
8DA H22 2H2 H 0 1 N N N N N N 3.559 8.958 25.738 1.804 -3.407 -0.007 H22 8DA 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
8DA O19 "C5'" SING N N 1
8DA O19 H19 SING N N 2
8DA "C5'" "C4'" SING N N 3
8DA "C5'" "H5'1" SING N N 4
8DA "C5'" "H5'2" SING N N 5
8DA "C4'" "C3'" SING N N 6
8DA "C4'" "O4'" SING N N 7
8DA "C4'" "H4'" SING N N 8
8DA "C3'" "O3'" SING N N 9
8DA "C3'" "C2'" SING N N 10
8DA "C3'" "H3'" SING N N 11
8DA "O3'" H1 SING N N 12
8DA "O4'" "C1'" SING N N 13
8DA "C1'" "C2'" SING N N 14
8DA "C1'" N9 SING N N 15
8DA "C1'" "H1'" SING N N 16
8DA "C2'" "H2'1" SING N N 17
8DA "C2'" "H2'2" SING N N 18
8DA N9 C4 SING N N 19
8DA N9 C8 SING N N 20
8DA C4 N3 DOUB N N 21
8DA C4 C5 SING N N 22
8DA N3 C2 SING N N 23
8DA C5 N7 SING N N 24
8DA C5 C6 DOUB N N 25
8DA N7 C8 SING N N 26
8DA N7 HN7 SING N N 27
8DA C8 O18 DOUB N N 28
8DA C6 N6 SING N N 29
8DA C6 N1 SING N N 30
8DA N6 HN61 SING N N 31
8DA N6 HN62 SING N N 32
8DA N1 C2 SING N N 33
8DA N1 HN1 SING N N 34
8DA C2 H21 SING N N 35
8DA C2 H22 SING N N 36
#
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
8DA SMILES ACDLabs 10.04 O=C2NC1=C(N)NCN=C1N2C3OC(C(O)C3)CO
8DA SMILES_CANONICAL CACTVS 3.341 NC1=C2NC(=O)N([C@@H]3C[C@@H](O)[C@H](CO)O3)C2=NCN1
8DA SMILES CACTVS 3.341 NC1=C2NC(=O)N([CH]3C[CH](O)[CH](CO)O3)C2=NCN1
8DA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@H]([C@@H](O[C@@H]1N2C3=NCNC(=C3NC2=O)N)CO)O
8DA SMILES "OpenEye OEToolkits" 1.5.0 C1C(C(OC1N2C3=NCNC(=C3NC2=O)N)CO)O
8DA InChI InChI 1.03 InChI=1S/C10H15N5O4/c11-8-7-9(13-3-12-8)15(10(18)14-7)6-1-4(17)5(2-16)19-6/h4-6,12,16-17H,1-3,11H2,(H,14,18)/t4-,5+,6+/m1/s1
8DA InChIKey InChI 1.03 KTCVXRUKSBTHOG-SRQIZXRXSA-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
8DA "SYSTEMATIC NAME" ACDLabs 10.04 6-amino-9-(2-deoxy-beta-L-erythro-pentofuranosyl)-1,2,7,9-tetrahydro-8H-purin-8-one
8DA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 6-amino-9-[(2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,7-dihydro-1H-purin-8-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
8DA 'Create component' 2005-08-08 RCSB
8DA '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
8DA O19 O 12.303 -3.252 1
8DA "C5'" C 10.934 -3.865 2
8DA "C4'" C 9.719 -2.985 3
8DA "C3'" C 8.293 -3.451 4
8DA "O3'" O 7.832 -4.879 5
8DA "O4'" O 9.716 -1.485 6
8DA "C1'" C 8.289 -1.024 7
8DA "C2'" C 7.409 -2.239 8
8DA N9 N 7.823 0.402 9
8DA C4 C 6.404 0.859 10
8DA N3 N 5.104 0.109 11
8DA C5 C 6.404 2.359 12
8DA N7 N 7.823 2.816 13
8DA C8 C 8.698 1.609 14
8DA O18 O 10.198 1.609 15
8DA C6 C 5.104 3.109 16
8DA N6 N 5.104 4.609 17
8DA N1 N 3.805 2.359 18
8DA C2 C 3.805 0.859 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
8DA O19 "C5'" SINGLE NONE 1
8DA "C4'" "C5'" SINGLE BEGINWEDGE 2
8DA "C4'" "C3'" SINGLE NONE 3
8DA "C4'" "O4'" SINGLE NONE 4
8DA "C3'" "O3'" SINGLE BEGINDASH 5
8DA "C3'" "C2'" SINGLE NONE 6
8DA "O4'" "C1'" SINGLE NONE 7
8DA "C1'" "C2'" SINGLE NONE 8
8DA "C1'" N9 SINGLE BEGINWEDGE 9
8DA N9 C4 SINGLE NONE 10
8DA N9 C8 SINGLE NONE 11
8DA C4 N3 DOUBLE NONE 12
8DA C4 C5 SINGLE NONE 13
8DA N3 C2 SINGLE NONE 14
8DA C5 N7 SINGLE NONE 15
8DA C5 C6 DOUBLE NONE 16
8DA N7 C8 SINGLE NONE 17
8DA C8 O18 DOUBLE NONE 18
8DA C6 N6 SINGLE NONE 19
8DA C6 N1 SINGLE NONE 20
8DA N1 C2 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
8DA MurckoScaffold S1 scaffold 'O=c1[nH]c2c(n1[C@@H]1CCCO1)=NCNC=2' InChI=1S/C9H12N4O2/c14-9-12-6-4-10-5-11-8(6)13(9)7-2-1-3-15-7/h4,7,10H,1-3,5H2,(H,12,14)/t7-/m0/s1 PDSHZHBVDOJKGU-ZETCQYMHSA-N
8DA 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
8DA imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-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
8DA "C4'" S1 1
8DA "C3'" S1 1
8DA "O4'" S1 1
8DA "C1'" S1 1
8DA "C2'" S1 1
8DA N9 S1 1
8DA C4 S1 1
8DA N3 S1 1
8DA C5 S1 1
8DA N7 S1 1
8DA C8 S1 1
8DA O18 S1 1
8DA C6 S1 1
8DA N1 S1 1
8DA C2 S1 1
8DA "C1'" F1 1
8DA "C2'" F1 1
8DA "C3'" F1 1
8DA "O3'" F1 1
8DA "C4'" F1 1
8DA "O4'" F1 1
8DA "C5'" F1 1
8DA O19 F1 1
8DA C4 F2 1
8DA C5 F2 1
8DA N7 F2 1
8DA C8 F2 1
8DA N9 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 8DA
_pdbe_chem_comp_rdkit_properties.exactmw 269.112
_pdbe_chem_comp_rdkit_properties.amw 269.261
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_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 128.052
_pdbe_chem_comp_rdkit_properties.tpsa 137.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.279
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.375
_pdbe_chem_comp_rdkit_properties.chi0v 8.869
_pdbe_chem_comp_rdkit_properties.chi1v 4.757
_pdbe_chem_comp_rdkit_properties.chi2v 2.267
_pdbe_chem_comp_rdkit_properties.chi3v 2.267
_pdbe_chem_comp_rdkit_properties.chi4v 1.492
_pdbe_chem_comp_rdkit_properties.chi0n 23.869
_pdbe_chem_comp_rdkit_properties.chi1n 11.862
_pdbe_chem_comp_rdkit_properties.chi2n 2.267
_pdbe_chem_comp_rdkit_properties.chi3n 2.267
_pdbe_chem_comp_rdkit_properties.chi4n 1.492
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 3.840
_pdbe_chem_comp_rdkit_properties.kappa2 4.368
_pdbe_chem_comp_rdkit_properties.kappa3 1.823
_pdbe_chem_comp_rdkit_properties.Phi 0.883
#
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
8DA UniChem PDBe 8DA
8DA UniChem ZINC ZINC000103530118
#
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
8DA O19 4.563 1.491 -1.781 ETKDGv3 1
8DA "C5'" 3.258 0.983 -1.886 ETKDGv3 2
8DA "C4'" 3.110 -0.298 -1.052 ETKDGv3 3
8DA "C3'" 3.160 -0.025 0.451 ETKDGv3 4
8DA "O3'" 3.770 -1.107 1.107 ETKDGv3 5
8DA "O4'" 1.876 -0.907 -1.365 ETKDGv3 6
8DA "C1'" 1.039 -0.830 -0.229 ETKDGv3 7
8DA "C2'" 1.706 0.052 0.816 ETKDGv3 8
8DA N9 -0.281 -0.305 -0.599 ETKDGv3 9
8DA C4 -1.372 -0.087 0.293 ETKDGv3 10
8DA N3 -1.306 -0.066 1.587 ETKDGv3 11
8DA C5 -2.613 -0.060 -0.428 ETKDGv3 12
8DA N7 -2.358 -0.264 -1.812 ETKDGv3 13
8DA C8 -0.939 -0.444 -1.870 ETKDGv3 14
8DA O18 -0.335 -0.727 -2.939 ETKDGv3 15
8DA C6 -3.781 -0.056 0.208 ETKDGv3 16
8DA N6 -5.027 -0.125 -0.492 ETKDGv3 17
8DA N1 -3.757 -0.025 1.646 ETKDGv3 18
8DA C2 -2.507 0.142 2.415 ETKDGv3 19
8DA H19 4.536 2.234 -1.124 ETKDGv3 20
8DA "H5'1" 3.069 0.739 -2.953 ETKDGv3 21
8DA "H5'2" 2.497 1.740 -1.581 ETKDGv3 22
8DA "H4'" 3.930 -0.994 -1.340 ETKDGv3 23
8DA "H3'" 3.691 0.924 0.699 ETKDGv3 24
8DA H1 3.960 -0.807 2.034 ETKDGv3 25
8DA "H1'" 0.916 -1.857 0.180 ETKDGv3 26
8DA "H2'1" 1.358 1.106 0.721 ETKDGv3 27
8DA "H2'2" 1.510 -0.308 1.850 ETKDGv3 28
8DA HN7 -3.041 -0.408 -2.588 ETKDGv3 29
8DA HN61 -5.924 -0.150 0.041 ETKDGv3 30
8DA HN62 -5.074 -0.131 -1.535 ETKDGv3 31
8DA HN1 -4.662 -0.021 2.168 ETKDGv3 32
8DA H21 -2.479 1.170 2.834 ETKDGv3 33
8DA H22 -2.494 -0.579 3.259 ETKDGv3 34
#