data_DX
#
_chem_comp.id DX
_chem_comp.name
"[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type "DNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C10 H13 N4 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-07-19
_chem_comp.pdbx_modified_date 2018-03-02
_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 348.206
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DX
_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 5KWC
_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
DX P P1 P 0 1 N N N N N N -20.111 20.147 2.417 4.861 -1.083 -0.285 P DX 1
DX OP1 O1 O 0 1 N N N N N N -20.996 21.318 2.666 4.848 -1.705 1.058 OP1 DX 2
DX "O5'" O2 O 0 1 N N N N N N -18.570 20.629 2.360 3.488 -0.274 -0.515 "O5'" DX 3
DX "C5'" C1 C 0 1 N N N N N N -17.798 21.052 3.523 3.023 0.740 0.378 "C5'" DX 4
DX "C4'" C2 C 0 1 N N R N N N -17.002 22.341 3.333 1.695 1.301 -0.135 "C4'" DX 5
DX "C3'" C3 C 0 1 N N S N N N -17.641 23.488 2.542 1.216 2.459 0.768 "C3'" DX 6
DX "O3'" O3 O 0 1 N N N N N N -17.348 24.801 3.022 1.557 3.720 0.189 "O3'" DX 7
DX "C2'" C4 C 0 1 N N N N N N -16.934 23.488 1.208 -0.318 2.285 0.820 "C2'" DX 8
DX "C1'" C5 C 0 1 N N R N N N -15.625 22.762 1.426 -0.585 1.042 -0.058 "C1'" DX 9
DX "O4'" O4 O 0 1 N N N N N N -15.731 22.095 2.686 0.657 0.302 -0.040 "O4'" DX 10
DX N9 N1 N 0 1 N N N N N N -15.401 21.688 0.475 -1.667 0.237 0.513 N9 DX 11
DX C4 C6 C 0 1 N N N N N N -15.743 21.586 -0.859 -2.879 0.007 -0.058 C4 DX 12
DX N5 N2 N 0 1 N N N N N N -15.278 20.341 -1.242 -3.590 -0.792 0.791 N5 DX 13
DX C7 C7 C 0 1 N N N N N N -14.664 19.678 -0.192 -2.795 -1.051 1.896 C7 DX 14
DX C8 C8 C 0 1 N N N N N N -14.763 20.514 0.801 -1.633 -0.429 1.726 C8 DX 15
DX N3 N3 N 0 1 N N N N N N -16.388 22.502 -1.620 -3.417 0.405 -1.202 N3 DX 16
DX C2 C9 C 0 1 N N N N N N -16.563 22.090 -2.865 -4.655 0.030 -1.533 C2 DX 17
DX O2 O5 O 0 1 N N N N N N -17.183 22.873 -3.758 -5.138 0.402 -2.588 O2 DX 18
DX N1 N4 N 0 1 N N N N N N -16.136 20.873 -3.332 -5.372 -0.759 -0.710 N1 DX 19
DX C6 C10 C 0 1 N N N N N N -15.470 19.913 -2.574 -4.840 -1.173 0.458 C6 DX 20
DX O6 O6 O 0 1 N N N N N N -15.119 18.838 -3.081 -5.482 -1.885 1.206 O6 DX 21
DX OP2 O7 O 0 1 N N N N N N -20.257 18.961 3.312 6.106 -0.069 -0.395 OP2 DX 22
DX H2 H2 H 0 1 N N N N N N -18.496 21.202 4.360 2.878 0.312 1.370 H2 DX 23
DX H3 H3 H 0 1 N N N N N N -17.091 20.248 3.774 3.759 1.541 0.433 H3 DX 24
DX H4 H4 H 0 1 N N N N N N -16.792 22.733 4.339 1.801 1.642 -1.165 H4 DX 25
DX H5 H5 H 0 1 N N N N N N -18.721 23.320 2.417 1.647 2.369 1.765 H5 DX 26
DX H6 H6 H 0 1 N N N N N N -17.749 24.924 3.875 1.280 4.483 0.715 H6 DX 27
DX H7 H7 H 0 1 N N N N N N -16.747 24.520 0.875 -0.647 2.106 1.844 H7 DX 28
DX H8 H8 H 0 1 N N N N N N -17.540 22.964 0.455 -0.818 3.160 0.405 H8 DX 29
DX H9 H9 H 0 1 N N N N N N -14.789 23.477 1.419 -0.831 1.342 -1.076 H9 DX 30
DX H10 H10 H 0 1 N N N N N N -14.210 18.698 -0.196 -3.072 -1.655 2.747 H10 DX 31
DX H11 H11 H 0 1 N N N N N N -14.380 20.305 1.789 -0.802 -0.444 2.416 H11 DX 32
DX H13 H13 H 0 1 N N N N N N -16.317 20.658 -4.292 -6.271 -1.028 -0.956 H13 DX 33
DX H14 H14 H 0 1 N N N N N N -20.936 19.130 3.955 6.177 0.376 -1.250 H14 DX 34
DX OP3 O8 O 0 1 N Y N N N N -20.411 19.666 0.934 5.003 -2.230 -1.406 OP3 DX 35
DX H1 H1 H 0 1 N N N N N N -21.076 20.224 0.548 5.809 -2.759 -1.328 H1 DX 36
#
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
DX O2 C2 DOUB N N 1
DX N1 C2 SING N N 2
DX N1 C6 SING N N 3
DX O6 C6 DOUB N N 4
DX C2 N3 SING N N 5
DX C6 N5 SING N N 6
DX N3 C4 DOUB N N 7
DX N5 C4 SING N N 8
DX N5 C7 SING N N 9
DX C4 N9 SING N N 10
DX C7 C8 DOUB N N 11
DX N9 C8 SING N N 12
DX N9 "C1'" SING N N 13
DX "C2'" "C1'" SING N N 14
DX "C2'" "C3'" SING N N 15
DX "C1'" "O4'" SING N N 16
DX "O5'" P SING N N 17
DX "O5'" "C5'" SING N N 18
DX P OP1 DOUB N N 19
DX P OP2 SING N N 20
DX "C3'" "O3'" SING N N 21
DX "C3'" "C4'" SING N N 22
DX "O4'" "C4'" SING N N 23
DX "C4'" "C5'" SING N N 24
DX "C5'" H2 SING N N 25
DX "C5'" H3 SING N N 26
DX "C4'" H4 SING N N 27
DX "C3'" H5 SING N N 28
DX "O3'" H6 SING N N 29
DX "C2'" H7 SING N N 30
DX "C2'" H8 SING N N 31
DX "C1'" H9 SING N N 32
DX C7 H10 SING N N 33
DX C8 H11 SING N N 34
DX N1 H13 SING N N 35
DX OP2 H14 SING N N 36
DX P OP3 SING N N 37
DX OP3 H1 SING N N 38
#
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
DX InChI InChI 1.03 InChI=1S/C10H13N4O8P/c15-5-3-7(22-6(5)4-21-23(18,19)20)13-1-2-14-9(13)11-8(16)12-10(14)17/h1-2,5-7,15H,3-4H2,(H,12,16,17)(H2,18,19,20)/t5-,6+,7+/m0/s1
DX InChIKey InChI 1.03 MIJXVMWIKXUKNK-RRKCRQDMSA-N
DX SMILES_CANONICAL CACTVS 3.385 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23
DX SMILES CACTVS 3.385 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23
DX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 C1[C@@H]([C@H](O[C@H]1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O
DX SMILES "OpenEye OEToolkits" 2.0.5 C1C(C(OC1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O
#
_pdbx_chem_comp_identifier.comp_id DX
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.5
_pdbx_chem_comp_identifier.identifier
"[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-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
DX 'Create component' 2016-07-19 RCSB
DX 'Initial release' 2018-03-07 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
DX P P 14.012 -3.763 1
DX OP1 O 15.227 -4.642 2
DX "O5'" O 12.797 -2.883 3
DX "C5'" C 11.428 -3.496 4
DX "C4'" C 10.213 -2.616 5
DX "C3'" C 8.787 -3.082 6
DX "O3'" O 8.326 -4.510 7
DX "C2'" C 7.903 -1.870 8
DX "C1'" C 8.783 -0.655 9
DX "O4'" O 10.210 -1.116 10
DX N9 N 8.316 0.771 11
DX C4 C 6.897 1.228 12
DX N5 N 6.897 2.728 13
DX C7 C 8.316 3.185 14
DX C8 C 9.192 1.978 15
DX N3 N 5.598 0.478 16
DX C2 C 4.299 1.228 17
DX O2 O 3.000 0.478 18
DX N1 N 4.299 2.728 19
DX C6 C 5.598 3.478 20
DX O6 O 5.598 4.978 21
DX OP2 O 14.891 -2.548 22
DX OP3 O 13.132 -4.978 23
#
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
DX O2 C2 DOUBLE NONE 1
DX N1 C2 SINGLE NONE 2
DX N1 C6 SINGLE NONE 3
DX O6 C6 DOUBLE NONE 4
DX C2 N3 SINGLE NONE 5
DX C6 N5 SINGLE NONE 6
DX N3 C4 DOUBLE NONE 7
DX N5 C4 SINGLE NONE 8
DX N5 C7 SINGLE NONE 9
DX C4 N9 SINGLE NONE 10
DX C7 C8 DOUBLE NONE 11
DX N9 C8 SINGLE NONE 12
DX "C1'" N9 SINGLE BEGINDASH 13
DX "C2'" "C1'" SINGLE NONE 14
DX "C2'" "C3'" SINGLE NONE 15
DX "C1'" "O4'" SINGLE NONE 16
DX "O5'" P SINGLE NONE 17
DX "O5'" "C5'" SINGLE NONE 18
DX P OP1 DOUBLE NONE 19
DX P OP2 SINGLE NONE 20
DX "C3'" "O3'" SINGLE BEGINWEDGE 21
DX "C3'" "C4'" SINGLE NONE 22
DX "O4'" "C4'" SINGLE NONE 23
DX "C4'" "C5'" SINGLE BEGINDASH 24
DX P OP3 SINGLE NONE 25
#
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
DX MurckoScaffold S1 scaffold 'O=c1nc2n([C@H]3CCCO3)ccn2c(=O)[nH]1' InChI=1S/C9H10N4O3/c14-7-10-8-12(6-2-1-5-16-6)3-4-13(8)9(15)11-7/h3-4,6H,1-2,5H2,(H,11,14,15)/t6-/m1/s1 ZJGKECRFTXRWLY-ZCFIWIBFSA-N
DX 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
DX imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
DX phosphate F3 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
DX "C4'" S1 1
DX "C3'" S1 1
DX "C2'" S1 1
DX "C1'" S1 1
DX "O4'" S1 1
DX N9 S1 1
DX C4 S1 1
DX N5 S1 1
DX C7 S1 1
DX C8 S1 1
DX N3 S1 1
DX C2 S1 1
DX O2 S1 1
DX N1 S1 1
DX C6 S1 1
DX O6 S1 1
DX "C1'" F1 1
DX "C2'" F1 1
DX "C3'" F1 1
DX "O3'" F1 1
DX "C4'" F1 1
DX "O4'" F1 1
DX "C5'" F1 1
DX "O5'" F1 1
DX C7 F2 1
DX C8 F2 1
DX N9 F2 1
DX C4 F2 1
DX N5 F2 1
DX "O5'" F3 1
DX P F3 1
DX OP1 F3 1
DX OP2 F3 1
DX H2 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DX
_pdbe_chem_comp_rdkit_properties.exactmw 348.047
_pdbe_chem_comp_rdkit_properties.amw 348.208
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 12
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 11
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 13
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 145.302
_pdbe_chem_comp_rdkit_properties.tpsa 168.380
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.472
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.716
_pdbe_chem_comp_rdkit_properties.chi0v 11.396
_pdbe_chem_comp_rdkit_properties.chi1v 6.902
_pdbe_chem_comp_rdkit_properties.chi2v 2.645
_pdbe_chem_comp_rdkit_properties.chi3v 2.645
_pdbe_chem_comp_rdkit_properties.chi4v 1.701
_pdbe_chem_comp_rdkit_properties.chi0n 23.502
_pdbe_chem_comp_rdkit_properties.chi1n 11.613
_pdbe_chem_comp_rdkit_properties.chi2n 2.330
_pdbe_chem_comp_rdkit_properties.chi3n 2.330
_pdbe_chem_comp_rdkit_properties.chi4n 1.506
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.820
_pdbe_chem_comp_rdkit_properties.kappa1 6.589
_pdbe_chem_comp_rdkit_properties.kappa2 5.671
_pdbe_chem_comp_rdkit_properties.kappa3 3.268
_pdbe_chem_comp_rdkit_properties.Phi 1.625
#
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
DX UniChem PDBe DX
DX UniChem PubChem 137349212
#
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
DX P -4.613 -1.027 0.449 ETKDGv3 1
DX OP1 -4.462 -1.949 1.639 ETKDGv3 2
DX "O5'" -3.633 0.354 0.651 ETKDGv3 3
DX "C5'" -2.286 -0.058 0.678 ETKDGv3 4
DX "C4'" -1.378 1.169 0.834 ETKDGv3 5
DX "C3'" -1.436 2.087 -0.391 ETKDGv3 6
DX "O3'" -1.366 3.429 0.020 ETKDGv3 7
DX "C2'" -0.194 1.710 -1.149 ETKDGv3 8
DX "C1'" 0.727 1.208 -0.051 ETKDGv3 9
DX "O4'" -0.048 0.734 1.027 ETKDGv3 10
DX N9 1.606 0.144 -0.537 ETKDGv3 11
DX C4 2.941 -0.097 -0.111 ETKDGv3 12
DX N5 3.338 -1.423 -0.371 ETKDGv3 13
DX C7 2.175 -2.050 -0.894 ETKDGv3 14
DX C8 1.186 -1.157 -0.986 ETKDGv3 15
DX N3 3.662 0.718 0.601 ETKDGv3 16
DX C2 4.940 0.288 1.108 ETKDGv3 17
DX O2 5.664 1.098 1.743 ETKDGv3 18
DX N1 5.380 -1.070 0.913 ETKDGv3 19
DX C6 4.532 -1.961 0.184 ETKDGv3 20
DX O6 4.831 -3.176 0.039 ETKDGv3 21
DX OP2 -4.181 -1.850 -0.966 ETKDGv3 22
DX H2 -2.104 -0.731 1.547 ETKDGv3 23
DX H3 -2.009 -0.589 -0.261 ETKDGv3 24
DX H4 -1.703 1.724 1.743 ETKDGv3 25
DX H5 -2.351 1.921 -1.008 ETKDGv3 26
DX H6 -1.609 3.981 -0.768 ETKDGv3 27
DX H7 -0.438 0.905 -1.875 ETKDGv3 28
DX H8 0.249 2.571 -1.697 ETKDGv3 29
DX H9 1.343 2.062 0.309 ETKDGv3 30
DX H10 2.093 -3.104 -1.126 ETKDGv3 31
DX H11 0.179 -1.395 -1.301 ETKDGv3 32
DX H13 6.288 -1.401 1.310 ETKDGv3 33
DX H14 -4.840 -2.585 -1.043 ETKDGv3 34
DX OP3 -6.229 -0.539 0.334 ETKDGv3 35
DX H1 -6.254 0.059 -0.455 ETKDGv3 36
#