data_HD3
#
_chem_comp.id HD3
_chem_comp.name
2-azanyl-7-[(2R,3R,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3H-pyrrolo[2,3-d]pyrimidin-4-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H14 N4 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-12-18
_chem_comp.pdbx_modified_date 2022-01-28
_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 282.253
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HD3
_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 7DOW
_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
HD3 C05 C1 C 0 1 Y N N N N N -49.749 -16.897 -3.432 2.290 1.192 0.185 C05 HD3 1
HD3 C06 C2 C 0 1 N N N N N N -50.712 -16.499 -2.308 3.682 0.951 0.187 C06 HD3 2
HD3 C01 C3 C 0 1 Y N N N N N -49.687 -16.518 -4.747 1.450 2.354 0.468 C01 HD3 3
HD3 C02 C4 C 0 1 Y N N N N N -48.595 -17.183 -5.328 0.177 1.962 0.290 C02 HD3 4
HD3 C04 C5 C 0 1 Y N N N N N -48.709 -17.791 -3.198 1.418 0.149 -0.156 C04 HD3 5
HD3 C12 C6 C 0 1 N N R N N N -46.898 -18.760 -4.622 -1.067 -0.124 -0.366 C12 HD3 6
HD3 C09 C7 C 0 1 N N N N N N -49.456 -18.022 -0.754 3.223 -1.263 -0.469 C09 HD3 7
HD3 C13 C8 C 0 1 N N R N N N -45.472 -17.939 -4.321 -1.524 -0.904 0.894 C13 HD3 8
HD3 C14 C9 C 0 1 N N S N N N -44.591 -18.865 -4.421 -3.039 -1.087 0.630 C14 HD3 9
HD3 C15 C10 C 0 1 N N R N N N -45.329 -20.165 -3.881 -3.379 0.011 -0.396 C15 HD3 10
HD3 C17 C11 C 0 1 N N N N N N -44.851 -20.523 -2.651 -4.463 0.932 0.168 C17 HD3 11
HD3 N03 N1 N 0 1 Y N N N N N -48.032 -17.937 -4.382 0.149 0.643 -0.085 N03 HD3 12
HD3 N08 N2 N 0 1 N N N N N N -50.543 -17.072 -1.000 4.117 -0.286 -0.144 N08 HD3 13
HD3 N10 N3 N 0 1 N N N N N N -48.531 -18.387 -1.827 1.927 -1.051 -0.472 N10 HD3 14
HD3 N11 N4 N 0 1 N N N N N N -49.278 -18.588 0.560 3.693 -2.509 -0.801 N11 HD3 15
HD3 O07 O1 O 0 1 N N N N N N -51.588 -15.743 -2.523 4.470 1.834 0.478 O07 HD3 16
HD3 O16 O2 O 0 1 N N N N N N -46.838 -19.770 -3.812 -2.176 0.761 -0.634 O16 HD3 17
HD3 O18 O3 O 0 1 N N N N N N -45.696 -19.986 -1.647 -4.855 1.875 -0.831 O18 HD3 18
HD3 O19 O4 O 0 1 N N N N N N -44.228 -19.089 -5.841 -3.298 -2.381 0.082 O19 HD3 19
HD3 O20 O5 O 0 1 N N N N N N -45.264 -16.874 -5.302 -0.864 -2.169 0.978 O20 HD3 20
HD3 H1 H1 H 0 1 N N N N N N -50.356 -15.833 -5.246 1.786 3.336 0.765 H1 HD3 21
HD3 H2 H2 H 0 1 N N N N N N -48.270 -17.099 -6.354 -0.691 2.591 0.421 H2 HD3 22
HD3 H3 H3 H 0 1 N N N N N N -46.873 -19.072 -5.677 -0.906 -0.805 -1.201 H3 HD3 23
HD3 H4 H4 H 0 1 N N N N N N -45.541 -17.514 -3.309 -1.355 -0.318 1.797 H4 HD3 24
HD3 H5 H5 H 0 1 N N N N N N -43.689 -18.688 -3.817 -3.606 -0.940 1.549 H5 HD3 25
HD3 H6 H6 H 0 1 N N N N N N -45.204 -20.972 -4.618 -3.723 -0.443 -1.325 H6 HD3 26
HD3 H7 H7 H 0 1 N N N N N N -44.833 -21.620 -2.568 -5.327 0.337 0.465 H7 HD3 27
HD3 H8 H8 H 0 1 N N N N N N -43.832 -20.129 -2.524 -4.073 1.464 1.036 H8 HD3 28
HD3 H9 H9 H 0 1 N N N N N N -51.167 -16.822 -0.259 5.068 -0.478 -0.152 H9 HD3 29
HD3 H10 H10 H 0 1 N N N N N N -48.527 -19.225 0.732 4.647 -2.683 -0.803 H10 HD3 30
HD3 H11 H11 H 0 1 N N N N N N -49.906 -18.344 1.299 3.071 -3.216 -1.035 H11 HD3 31
HD3 H12 H12 H 0 1 N N N N N N -45.367 -20.233 -0.791 -5.541 2.492 -0.543 H12 HD3 32
HD3 H13 H13 H 0 1 N N N N N N -43.575 -19.777 -5.897 -4.232 -2.550 -0.102 H13 HD3 33
HD3 H14 H14 H 0 1 N N N N N N -44.450 -16.422 -5.112 -1.117 -2.694 1.749 H14 HD3 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
HD3 O19 C14 SING N N 1
HD3 C02 C01 DOUB Y N 2
HD3 C02 N03 SING Y N 3
HD3 O20 C13 SING N N 4
HD3 C01 C05 SING Y N 5
HD3 C12 N03 SING N N 6
HD3 C12 C13 SING N N 7
HD3 C12 O16 SING N N 8
HD3 C14 C13 SING N N 9
HD3 C14 C15 SING N N 10
HD3 N03 C04 SING Y N 11
HD3 C15 O16 SING N N 12
HD3 C15 C17 SING N N 13
HD3 C05 C04 DOUB Y N 14
HD3 C05 C06 SING N N 15
HD3 C04 N10 SING N N 16
HD3 C17 O18 SING N N 17
HD3 O07 C06 DOUB N N 18
HD3 C06 N08 SING N N 19
HD3 N10 C09 DOUB N N 20
HD3 N08 C09 SING N N 21
HD3 C09 N11 SING N N 22
HD3 C01 H1 SING N N 23
HD3 C02 H2 SING N N 24
HD3 C12 H3 SING N N 25
HD3 C13 H4 SING N N 26
HD3 C14 H5 SING N N 27
HD3 C15 H6 SING N N 28
HD3 C17 H7 SING N N 29
HD3 C17 H8 SING N N 30
HD3 N08 H9 SING N N 31
HD3 N11 H10 SING N N 32
HD3 N11 H11 SING N N 33
HD3 O18 H12 SING N N 34
HD3 O19 H13 SING N N 35
HD3 O20 H14 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
HD3 InChI InChI 1.03 InChI=1S/C11H14N4O5/c12-11-13-8-4(9(19)14-11)1-2-15(8)10-7(18)6(17)5(3-16)20-10/h1-2,5-7,10,16-18H,3H2,(H3,12,13,14,19)/t5-,6-,7-,10-/m1/s1
HD3 InChIKey InChI 1.03 JRYMOPZHXMVHTA-DAGMQNCNSA-N
HD3 SMILES_CANONICAL CACTVS 3.385 NC1=Nc2n(ccc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O
HD3 SMILES CACTVS 3.385 NC1=Nc2n(ccc2C(=O)N1)[CH]3O[CH](CO)[CH](O)[CH]3O
HD3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
HD3 SMILES "OpenEye OEToolkits" 2.0.7 c1cn(c2c1C(=O)NC(=N2)N)C3C(C(C(O3)CO)O)O
#
_pdbx_chem_comp_identifier.comp_id HD3
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
2-azanyl-7-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-3~{H}-pyrrolo[2,3-d]pyrimidin-4-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
HD3 'Create component' 2020-12-18 PDBJ
HD3 'Initial release' 2022-02-02 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
HD3 C05 C 7.702 2.839 1
HD3 C06 C 6.404 3.589 2
HD3 C01 C 9.122 3.296 3
HD3 C02 C 9.997 2.089 4
HD3 C04 C 7.702 1.339 5
HD3 C12 C 9.588 -0.544 6
HD3 C09 C 5.104 1.339 7
HD3 C13 C 8.708 -1.759 8
HD3 C14 C 9.592 -2.971 9
HD3 C15 C 11.018 -2.505 10
HD3 C17 C 12.233 -3.385 11
HD3 N03 N 9.122 0.882 12
HD3 N08 N 5.104 2.839 13
HD3 N10 N 6.404 0.589 14
HD3 N11 N 3.805 0.589 15
HD3 O07 O 6.404 5.089 16
HD3 O16 O 11.015 -1.005 17
HD3 O18 O 13.602 -2.772 18
HD3 O19 O 9.131 -4.399 19
HD3 O20 O 7.208 -1.762 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
HD3 C14 O19 SINGLE BEGINWEDGE 1
HD3 C02 C01 DOUBLE NONE 2
HD3 C02 N03 SINGLE NONE 3
HD3 C13 O20 SINGLE BEGINWEDGE 4
HD3 C01 C05 SINGLE NONE 5
HD3 C12 N03 SINGLE BEGINDASH 6
HD3 C12 C13 SINGLE NONE 7
HD3 C12 O16 SINGLE NONE 8
HD3 C14 C13 SINGLE NONE 9
HD3 C14 C15 SINGLE NONE 10
HD3 N03 C04 SINGLE NONE 11
HD3 C15 O16 SINGLE NONE 12
HD3 C15 C17 SINGLE BEGINDASH 13
HD3 C05 C04 DOUBLE NONE 14
HD3 C05 C06 SINGLE NONE 15
HD3 C04 N10 SINGLE NONE 16
HD3 C17 O18 SINGLE NONE 17
HD3 O07 C06 DOUBLE NONE 18
HD3 C06 N08 SINGLE NONE 19
HD3 N10 C09 DOUBLE NONE 20
HD3 N08 C09 SINGLE NONE 21
HD3 C09 N11 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
HD3 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1ccn2[C@H]1CCCO1' InChI=1S/C10H11N3O2/c14-10-7-3-4-13(8-2-1-5-15-8)9(7)11-6-12-10/h3-4,6,8H,1-2,5H2,(H,11,12,14)/t8-/m1/s1 KMILJNWZZSWZDI-MRVPVSSYSA-N
HD3 pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
HD3 pyrrole F2 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N
HD3 ribose F3 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
HD3 C05 S1 1
HD3 C06 S1 1
HD3 C01 S1 1
HD3 C02 S1 1
HD3 C04 S1 1
HD3 C12 S1 1
HD3 C09 S1 1
HD3 C13 S1 1
HD3 C14 S1 1
HD3 C15 S1 1
HD3 N03 S1 1
HD3 N08 S1 1
HD3 N10 S1 1
HD3 O07 S1 1
HD3 O16 S1 1
HD3 C05 F1 1
HD3 C04 F1 1
HD3 N10 F1 1
HD3 C09 F1 1
HD3 N08 F1 1
HD3 C06 F1 1
HD3 C02 F2 1
HD3 C01 F2 1
HD3 C05 F2 1
HD3 C04 F2 1
HD3 N03 F2 1
HD3 C13 F3 1
HD3 C14 F3 1
HD3 C15 F3 1
HD3 O16 F3 1
HD3 C12 F3 1
HD3 C17 F3 1
HD3 O18 F3 1
HD3 O19 F3 1
HD3 O20 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HD3
_pdbe_chem_comp_rdkit_properties.exactmw 282.096
_pdbe_chem_comp_rdkit_properties.amw 282.256
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_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 0.455
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 131.892
_pdbe_chem_comp_rdkit_properties.tpsa 146.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.991
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.854
_pdbe_chem_comp_rdkit_properties.chi0v 9.330
_pdbe_chem_comp_rdkit_properties.chi1v 5.014
_pdbe_chem_comp_rdkit_properties.chi2v 2.451
_pdbe_chem_comp_rdkit_properties.chi3v 2.451
_pdbe_chem_comp_rdkit_properties.chi4v 1.605
_pdbe_chem_comp_rdkit_properties.chi0n 23.330
_pdbe_chem_comp_rdkit_properties.chi1n 11.580
_pdbe_chem_comp_rdkit_properties.chi2n 2.451
_pdbe_chem_comp_rdkit_properties.chi3n 2.451
_pdbe_chem_comp_rdkit_properties.chi4n 1.605
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.940
_pdbe_chem_comp_rdkit_properties.kappa1 4.531
_pdbe_chem_comp_rdkit_properties.kappa2 4.561
_pdbe_chem_comp_rdkit_properties.kappa3 1.794
_pdbe_chem_comp_rdkit_properties.Phi 1.033
#
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
HD3 UniChem ChEMBL CHEMBL519587
HD3 UniChem PDBe HD3
HD3 UniChem 'PubChem DOTF' 24714745
HD3 UniChem ZINC ZINC000005425329
HD3 UniChem SureChEMBL SCHEMBL1738311
HD3 UniChem 'PubChem TPHARMA' 143485955
HD3 UniChem PubChem 135410907
HD3 UniChem Nikkaji J358.008C
HD3 UniChem 'PubChem TPHARMA' 16535522
HD3 UniChem ACTor 62160-23-0
#
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
HD3 C05 2.295 -1.485 0.459 ETKDGv3 1
HD3 C06 3.731 -1.500 0.715 ETKDGv3 2
HD3 C01 1.237 -2.427 0.804 ETKDGv3 3
HD3 C02 0.095 -1.865 0.408 ETKDGv3 4
HD3 C04 1.742 -0.439 -0.109 ETKDGv3 5
HD3 C12 -0.645 0.469 -0.423 ETKDGv3 6
HD3 C09 3.788 0.768 -0.307 ETKDGv3 7
HD3 C13 -1.720 0.043 -1.413 ETKDGv3 8
HD3 C14 -2.936 0.788 -0.913 ETKDGv3 9
HD3 C15 -2.642 0.958 0.584 ETKDGv3 10
HD3 C17 -3.405 -0.069 1.429 ETKDGv3 11
HD3 N03 0.334 -0.598 -0.217 ETKDGv3 12
HD3 N08 4.478 -0.344 0.309 ETKDGv3 13
HD3 N10 2.495 0.720 -0.499 ETKDGv3 14
HD3 N11 4.519 1.927 -0.705 ETKDGv3 15
HD3 O07 4.294 -2.479 1.272 ETKDGv3 16
HD3 O16 -1.254 0.802 0.806 ETKDGv3 17
HD3 O18 -3.100 0.113 2.784 ETKDGv3 18
HD3 O19 -3.092 2.038 -1.548 ETKDGv3 19
HD3 O20 -1.370 0.405 -2.724 ETKDGv3 20
HD3 H1 1.340 -3.372 1.320 ETKDGv3 21
HD3 H2 -0.886 -2.292 0.567 ETKDGv3 22
HD3 H3 -0.128 1.376 -0.809 ETKDGv3 23
HD3 H4 -1.904 -1.055 -1.348 ETKDGv3 24
HD3 H5 -3.856 0.189 -1.098 ETKDGv3 25
HD3 H6 -2.947 1.974 0.920 ETKDGv3 26
HD3 H7 -4.499 0.065 1.275 ETKDGv3 27
HD3 H8 -3.121 -1.099 1.116 ETKDGv3 28
HD3 H9 5.510 -0.305 0.465 ETKDGv3 29
HD3 H10 5.551 1.979 -0.556 ETKDGv3 30
HD3 H11 4.030 2.736 -1.149 ETKDGv3 31
HD3 H12 -3.611 -0.580 3.277 ETKDGv3 32
HD3 H13 -2.280 2.582 -1.368 ETKDGv3 33
HD3 H14 -2.040 -0.021 -3.320 ETKDGv3 34
#