data_OHU
#
_chem_comp.id OHU
_chem_comp.name "2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate)"
_chem_comp.type "DNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H13 N2 O9 P"
_chem_comp.mon_nstd_parent_comp_id DU
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-11-22
_chem_comp.pdbx_modified_date 2011-12-09
_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 324.181
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code OHU
_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 3VK7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
OHU P P P 0 1 N N N N N N 9.842 -26.234 84.395 4.279 -1.039 -0.070 P OHU 1
OHU N1 N1 N 0 1 N N N N N N 8.318 -22.055 79.567 -2.281 0.295 -0.409 N1 OHU 2
OHU C2 C2 C 0 1 N N N N N N 7.138 -22.459 80.246 -2.272 -0.157 0.858 C2 OHU 3
OHU O2 O2 O 0 1 N N N N N N 7.201 -23.000 81.372 -1.314 0.075 1.570 O2 OHU 4
OHU N3 N3 N 0 1 N N N N N N 5.920 -22.257 79.693 -3.308 -0.862 1.350 N3 OHU 5
OHU C4 C4 C 0 1 N N N N N N 5.803 -21.677 78.481 -4.379 -1.128 0.576 C4 OHU 6
OHU O4 O4 O 0 1 N N N N N N 4.675 -21.498 77.980 -5.316 -1.766 1.022 O4 OHU 7
OHU C5 C5 C 0 1 N N N N N N 7.027 -21.260 77.755 -4.405 -0.659 -0.763 C5 OHU 8
OHU O5 O5 O 0 1 N N N N N N 6.959 -20.671 76.528 -5.476 -0.915 -1.565 O5 OHU 9
OHU C6 C6 C 0 1 N N N N N N 8.253 -21.485 78.357 -3.351 0.047 -1.232 C6 OHU 10
OHU "C1'" "C1'" C 0 1 N N R N N N 9.660 -22.265 80.119 -1.141 1.065 -0.913 "C1'" OHU 11
OHU "C2'" "C2'" C 0 1 N N N N N N 9.882 -21.764 81.540 -1.030 2.398 -0.149 "C2'" OHU 12
OHU "C3'" "C3'" C 0 1 N N S N N N 11.064 -22.618 81.948 0.385 2.360 0.478 "C3'" OHU 13
OHU "O3'" "O3'" O 0 1 N N N N N N 12.232 -22.110 81.291 1.020 3.636 0.382 "O3'" OHU 14
OHU "C4'" "C4'" C 0 1 N N R N N N 10.708 -23.957 81.336 1.106 1.315 -0.412 "C4'" OHU 15
OHU "O4'" "O4'" O 0 1 N N N N N N 10.001 -23.655 80.132 0.078 0.338 -0.685 "O4'" OHU 16
OHU "C5'" "C5'" C 0 1 N N N N N N 9.772 -24.730 82.249 2.271 0.674 0.345 "C5'" OHU 17
OHU "O5'" "O5'" O 0 1 N N N N N N 10.548 -25.320 83.282 2.988 -0.196 -0.533 "O5'" OHU 18
OHU OP1 OP1 O 0 1 N N N N N N 10.706 -26.233 85.627 3.935 -1.856 1.115 OP1 OHU 19
OHU OP2 OP2 O 0 1 N N N N N N 9.503 -27.541 83.725 4.748 -2.005 -1.270 OP2 OHU 20
OHU OP3 OP3 O 0 1 N Y N N N N 8.481 -25.440 84.730 5.475 -0.028 0.304 OP3 OHU 21
OHU HN3 HN3 H 0 1 N N N N N N 5.098 -22.540 80.188 -3.283 -1.180 2.266 HN3 OHU 22
OHU HO5 HO5 H 0 1 N N N N N N 6.050 -20.593 76.264 -6.176 -1.426 -1.135 HO5 OHU 23
OHU H6 H6 H 0 1 N N N N N N 9.162 -21.199 77.848 -3.352 0.413 -2.248 H6 OHU 24
OHU "H1'" "H1'" H 0 1 N N N N N N 10.378 -21.739 79.473 -1.266 1.258 -1.979 "H1'" OHU 25
OHU "H2'" "H2'" H 0 1 N N N N N N 10.129 -20.692 81.560 -1.120 3.240 -0.835 "H2'" OHU 26
OHU "H2'A" "H2'A" H 0 0 N N N N N N 9.006 -21.950 82.179 -1.790 2.456 0.630 "H2'A" OHU 27
OHU "H3'" "H3'" H 0 1 N N N N N N 11.171 -22.679 83.041 0.343 2.025 1.514 "H3'" OHU 28
OHU "HO3'" "HO3'" H 0 0 N N N N N N 12.986 -22.634 81.535 0.555 4.343 0.850 "HO3'" OHU 29
OHU "H4'" "H4'" H 0 1 N N N N N N 11.618 -24.542 81.137 1.454 1.774 -1.338 "H4'" OHU 30
OHU "H5'" "H5'" H 0 1 N N N N N N 9.029 -24.047 82.685 2.940 1.454 0.709 "H5'" OHU 31
OHU "H5'A" "H5'A" H 0 0 N N N N N N 9.256 -25.515 81.676 1.885 0.102 1.188 "H5'A" OHU 32
OHU HOP2 HOP2 H 0 0 N N N N N N 9.909 -28.256 84.201 5.523 -2.544 -1.061 HOP2 OHU 33
OHU HOP3 HOP3 H 0 0 N Y N N N N 8.504 -25.137 85.630 5.752 0.540 -0.428 HOP3 OHU 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
OHU P "O5'" SING N N 1
OHU P OP1 DOUB N N 2
OHU P OP2 SING N N 3
OHU P OP3 SING N N 4
OHU N1 C2 SING N N 5
OHU N1 C6 SING N N 6
OHU N1 "C1'" SING N N 7
OHU C2 O2 DOUB N N 8
OHU C2 N3 SING N N 9
OHU N3 C4 SING N N 10
OHU C4 O4 DOUB N N 11
OHU C4 C5 SING N N 12
OHU C5 O5 SING N N 13
OHU C5 C6 DOUB N N 14
OHU "C1'" "C2'" SING N N 15
OHU "C1'" "O4'" SING N N 16
OHU "C2'" "C3'" SING N N 17
OHU "C3'" "O3'" SING N N 18
OHU "C3'" "C4'" SING N N 19
OHU "C4'" "O4'" SING N N 20
OHU "C4'" "C5'" SING N N 21
OHU "C5'" "O5'" SING N N 22
OHU N3 HN3 SING N N 23
OHU O5 HO5 SING N N 24
OHU C6 H6 SING N N 25
OHU "C1'" "H1'" SING N N 26
OHU "C2'" "H2'" SING N N 27
OHU "C2'" "H2'A" SING N N 28
OHU "C3'" "H3'" SING N N 29
OHU "O3'" "HO3'" SING N N 30
OHU "C4'" "H4'" SING N N 31
OHU "C5'" "H5'" SING N N 32
OHU "C5'" "H5'A" SING N N 33
OHU OP2 HOP2 SING N N 34
OHU OP3 HOP3 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
OHU SMILES ACDLabs 12.01 O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C(O)=C1)CC2O
OHU InChI InChI 1.03 InChI=1S/C9H13N2O9P/c12-4-1-7(20-6(4)3-19-21(16,17)18)11-2-5(13)8(14)10-9(11)15/h2,4,6-7,12-13H,1,3H2,(H,10,14,15)(H2,16,17,18)/t4-,6+,7+/m0/s1
OHU InChIKey InChI 1.03 ZQYXKIGZDRIQRE-UBKIQSJTSA-N
OHU SMILES_CANONICAL CACTVS 3.370 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(O)C(=O)NC2=O
OHU SMILES CACTVS 3.370 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(O)C(=O)NC2=O
OHU SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)O)COP(=O)(O)O)O
OHU SMILES "OpenEye OEToolkits" 1.7.6 C1C(C(OC1N2C=C(C(=O)NC2=O)O)COP(=O)(O)O)O
#
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
OHU "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate)"
OHU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-3-oxidanyl-5-[5-oxidanyl-2,4-bis(oxidanylidene)pyrimidin-1-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
OHU 'Create component' 2011-11-22 PDBJ
OHU 'Modify leaving atom flag' 2011-11-24 PDBJ
#
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
OHU P P 10.409 -4.683 1
OHU N1 N 6.404 1.396 2
OHU C2 C 7.702 2.146 3
OHU O2 O 9.002 1.396 4
OHU N3 N 7.702 3.646 5
OHU C4 C 6.404 4.396 6
OHU O4 O 6.404 5.896 7
OHU C5 C 5.104 3.646 8
OHU O5 O 3.805 4.396 9
OHU C6 C 5.104 2.146 10
OHU "C1'" C 6.404 -0.104 11
OHU "C2'" C 5.190 -0.986 12
OHU "C3'" C 5.654 -2.412 13
OHU "O3'" O 4.772 -3.626 14
OHU "C4'" C 7.154 -2.412 15
OHU "O4'" O 7.617 -0.986 16
OHU "C5'" C 8.035 -3.626 17
OHU "O5'" O 9.527 -3.469 18
OHU OP1 O 11.290 -5.896 19
OHU OP2 O 11.622 -3.801 20
OHU OP3 O 9.195 -5.564 21
#
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
OHU P "O5'" SINGLE NONE 1
OHU P OP1 DOUBLE NONE 2
OHU P OP2 SINGLE NONE 3
OHU P OP3 SINGLE NONE 4
OHU N1 C2 SINGLE NONE 5
OHU N1 C6 SINGLE NONE 6
OHU "C1'" N1 SINGLE BEGINDASH 7
OHU C2 O2 DOUBLE NONE 8
OHU C2 N3 SINGLE NONE 9
OHU N3 C4 SINGLE NONE 10
OHU C4 O4 DOUBLE NONE 11
OHU C4 C5 SINGLE NONE 12
OHU C5 O5 SINGLE NONE 13
OHU C5 C6 DOUBLE NONE 14
OHU "C1'" "C2'" SINGLE NONE 15
OHU "C1'" "O4'" SINGLE NONE 16
OHU "C2'" "C3'" SINGLE NONE 17
OHU "C3'" "O3'" SINGLE BEGINWEDGE 18
OHU "C3'" "C4'" SINGLE NONE 19
OHU "C4'" "O4'" SINGLE NONE 20
OHU "C4'" "C5'" SINGLE BEGINDASH 21
OHU "C5'" "O5'" 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
OHU MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
OHU 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
OHU 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
OHU 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
OHU N1 S1 1
OHU C2 S1 1
OHU O2 S1 1
OHU N3 S1 1
OHU C4 S1 1
OHU O4 S1 1
OHU C5 S1 1
OHU C6 S1 1
OHU "C1'" S1 1
OHU "C2'" S1 1
OHU "C3'" S1 1
OHU "C4'" S1 1
OHU "O4'" S1 1
OHU "C1'" F1 1
OHU "C2'" F1 1
OHU "C3'" F1 1
OHU "O3'" F1 1
OHU "C4'" F1 1
OHU "O4'" F1 1
OHU "C5'" F1 1
OHU "O5'" F1 1
OHU "O5'" F2 1
OHU P F2 1
OHU OP1 F2 1
OHU OP2 F2 1
OHU OP3 F2 1
OHU C5 F3 1
OHU C4 F3 1
OHU N3 F3 1
OHU C2 F3 1
OHU N1 F3 1
OHU C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id OHU
_pdbe_chem_comp_rdkit_properties.exactmw 324.036
_pdbe_chem_comp_rdkit_properties.amw 324.182
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 11
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_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 134.846
_pdbe_chem_comp_rdkit_properties.tpsa 171.310
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.663
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.123
_pdbe_chem_comp_rdkit_properties.chi0v 10.410
_pdbe_chem_comp_rdkit_properties.chi1v 6.238
_pdbe_chem_comp_rdkit_properties.chi2v 2.190
_pdbe_chem_comp_rdkit_properties.chi3v 2.190
_pdbe_chem_comp_rdkit_properties.chi4v 1.306
_pdbe_chem_comp_rdkit_properties.chi0n 22.516
_pdbe_chem_comp_rdkit_properties.chi1n 10.857
_pdbe_chem_comp_rdkit_properties.chi2n 1.875
_pdbe_chem_comp_rdkit_properties.chi3n 1.875
_pdbe_chem_comp_rdkit_properties.chi4n 1.111
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.490
_pdbe_chem_comp_rdkit_properties.kappa1 5.953
_pdbe_chem_comp_rdkit_properties.kappa2 5.716
_pdbe_chem_comp_rdkit_properties.kappa3 3.785
_pdbe_chem_comp_rdkit_properties.Phi 1.620
#
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
OHU UniChem PDBe OHU
OHU UniChem ZINC ZINC000013514788
OHU UniChem SureChEMBL SCHEMBL3265080
OHU UniChem PubChem 68573506
OHU UniChem BRENDA 110317
#
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
OHU P 3.617 1.507 -1.873 ETKDGv3 1
OHU N1 -1.883 0.430 0.967 ETKDGv3 2
OHU C2 -3.110 0.658 1.690 ETKDGv3 3
OHU O2 -3.132 0.639 2.950 ETKDGv3 4
OHU N3 -4.318 0.903 0.968 ETKDGv3 5
OHU C4 -4.300 0.879 -0.459 ETKDGv3 6
OHU O4 -5.359 1.100 -1.104 ETKDGv3 7
OHU C5 -3.039 0.589 -1.168 ETKDGv3 8
OHU O5 -3.002 0.531 -2.561 ETKDGv3 9
OHU C6 -1.914 0.374 -0.476 ETKDGv3 10
OHU "C1'" -0.633 0.132 1.686 ETKDGv3 11
OHU "C2'" -0.419 -1.378 1.788 ETKDGv3 12
OHU "C3'" 0.769 -1.629 0.904 ETKDGv3 13
OHU "O3'" 1.601 -2.615 1.456 ETKDGv3 14
OHU "C4'" 1.454 -0.269 0.876 ETKDGv3 15
OHU "O4'" 0.463 0.722 1.018 ETKDGv3 16
OHU "C5'" 2.232 -0.044 -0.424 ETKDGv3 17
OHU "O5'" 2.863 1.213 -0.371 ETKDGv3 18
OHU OP1 2.569 1.680 -2.951 ETKDGv3 19
OHU OP2 4.521 2.931 -1.758 ETKDGv3 20
OHU OP3 4.656 0.231 -2.280 ETKDGv3 21
OHU HN3 -5.209 1.089 1.481 ETKDGv3 22
OHU HO5 -3.830 0.685 -3.123 ETKDGv3 23
OHU H6 -1.006 0.152 -1.023 ETKDGv3 24
OHU "H1'" -0.670 0.565 2.709 ETKDGv3 25
OHU "H2'" -1.303 -1.962 1.450 ETKDGv3 26
OHU "H2'A" -0.189 -1.651 2.843 ETKDGv3 27
OHU "H3'" 0.411 -1.930 -0.110 ETKDGv3 28
OHU "HO3'" 2.232 -2.884 0.739 ETKDGv3 29
OHU "H4'" 2.159 -0.186 1.735 ETKDGv3 30
OHU "H5'" 1.518 -0.098 -1.278 ETKDGv3 31
OHU "H5'A" 2.993 -0.851 -0.521 ETKDGv3 32
OHU HOP2 5.173 2.757 -1.033 ETKDGv3 33
OHU HOP3 4.085 -0.431 -2.746 ETKDGv3 34
#