data_7D7
#
_chem_comp.id 7D7
_chem_comp.name "[(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)oxetane-2,3-diyl]dimethanol"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H13 N5 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms OXETANOCIN
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-10-07
_chem_comp.pdbx_modified_date 2020-06-17
_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 251.242
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 7D7
_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 5TK9
_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
7D7 O01 O1 O 0 1 N N N N N N -5.378 -20.510 -18.683 2.028 -1.178 -0.797 O01 7D7 1
7D7 C02 C1 C 0 1 N N S N N N -4.061 -20.561 -19.295 2.983 -0.189 -0.392 C02 7D7 2
7D7 C03 C2 C 0 1 N N N N N N -3.215 -21.815 -18.925 4.013 -0.713 0.611 C03 7D7 3
7D7 O04 O2 O 0 1 N N N N N N -2.746 -21.667 -17.561 5.080 -1.352 -0.093 O04 7D7 4
7D7 C05 C3 C 0 1 N N R N N N -3.686 -19.342 -18.574 1.835 0.589 0.265 C05 7D7 5
7D7 C06 C4 C 0 1 N N N N N N -3.259 -18.237 -19.563 1.906 2.106 0.079 C06 7D7 6
7D7 O07 O3 O 0 1 N N N N N N -4.334 -18.061 -20.505 2.754 2.670 1.081 O07 7D7 7
7D7 C08 C5 C 0 1 N N R N N N -5.067 -19.189 -18.112 1.031 -0.149 -0.812 C08 7D7 8
7D7 N09 N1 N 0 1 Y N N N N N -5.479 -19.188 -16.767 -0.282 -0.604 -0.348 N09 7D7 9
7D7 C10 C6 C 0 1 Y N N N N N -4.900 -19.982 -15.772 -0.572 -1.830 0.174 C10 7D7 10
7D7 N11 N2 N 0 1 Y N N N N N -5.554 -19.730 -14.597 -1.835 -1.894 0.482 N11 7D7 11
7D7 C12 C7 C 0 1 Y N N N N N -6.530 -18.795 -14.847 -2.434 -0.718 0.178 C12 7D7 12
7D7 C13 C8 C 0 1 Y N N N N N -7.494 -18.173 -13.984 -3.743 -0.218 0.286 C13 7D7 13
7D7 N14 N3 N 0 1 N N N N N N -7.553 -18.525 -12.556 -4.759 -1.000 0.806 N14 7D7 14
7D7 N15 N4 N 0 1 Y N N N N N -8.353 -17.261 -14.521 -3.982 1.024 -0.123 N15 7D7 15
7D7 C16 C9 C 0 1 Y N N N N N -8.303 -16.942 -15.846 -3.019 1.778 -0.621 C16 7D7 16
7D7 N17 N5 N 0 1 Y N N N N N -7.402 -17.510 -16.671 -1.779 1.352 -0.741 N17 7D7 17
7D7 C18 C10 C 0 1 Y N N N N N -6.488 -18.466 -16.171 -1.443 0.126 -0.353 C18 7D7 18
7D7 H1 H1 H 0 1 N N N N N N -4.093 -20.413 -20.384 3.441 0.339 -1.228 H1 7D7 19
7D7 H2 H2 H 0 1 N N N N N N -3.836 -22.719 -19.008 4.408 0.118 1.194 H2 7D7 20
7D7 H3 H3 H 0 1 N N N N N N -2.355 -21.897 -19.606 3.537 -1.432 1.278 H3 7D7 21
7D7 H4 H4 H 0 1 N N N N N N -2.227 -22.426 -17.320 5.771 -1.709 0.481 H4 7D7 22
7D7 H5 H5 H 0 1 N N N N N N -2.955 -19.501 -17.768 1.609 0.285 1.287 H5 7D7 23
7D7 H6 H6 H 0 1 N N N N N N -2.343 -18.539 -20.091 2.310 2.332 -0.908 H6 7D7 24
7D7 H7 H7 H 0 1 N N N N N N -3.077 -17.297 -19.021 0.906 2.530 0.168 H7 7D7 25
7D7 H8 H8 H 0 1 N N N N N N -4.101 -17.384 -21.130 2.846 3.630 1.024 H8 7D7 26
7D7 H9 H9 H 0 1 N N N N N N -5.576 -18.399 -18.684 0.979 0.390 -1.758 H9 7D7 27
7D7 H10 H10 H 0 1 N N N N N N -4.081 -20.673 -15.907 0.141 -2.629 0.312 H10 7D7 28
7D7 H11 H11 H 0 1 N N N N N N -8.283 -18.004 -12.114 -4.571 -1.905 1.102 H11 7D7 29
7D7 H12 H12 H 0 1 N N N N N N -7.737 -19.503 -12.461 -5.658 -0.644 0.876 H12 7D7 30
7D7 H13 H13 H 0 1 N N N N N N -9.000 -16.219 -16.242 -3.257 2.781 -0.941 H13 7D7 31
#
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
7D7 O07 C06 SING N N 1
7D7 C06 C05 SING N N 2
7D7 C02 C03 SING N N 3
7D7 C02 O01 SING N N 4
7D7 C02 C05 SING N N 5
7D7 C03 O04 SING N N 6
7D7 O01 C08 SING N N 7
7D7 C05 C08 SING N N 8
7D7 C08 N09 SING N N 9
7D7 N09 C18 SING Y N 10
7D7 N09 C10 SING Y N 11
7D7 N17 C18 DOUB Y N 12
7D7 N17 C16 SING Y N 13
7D7 C18 C12 SING Y N 14
7D7 C16 N15 DOUB Y N 15
7D7 C10 N11 DOUB Y N 16
7D7 C12 N11 SING Y N 17
7D7 C12 C13 DOUB Y N 18
7D7 N15 C13 SING Y N 19
7D7 C13 N14 SING N N 20
7D7 C02 H1 SING N N 21
7D7 C03 H2 SING N N 22
7D7 C03 H3 SING N N 23
7D7 O04 H4 SING N N 24
7D7 C05 H5 SING N N 25
7D7 C06 H6 SING N N 26
7D7 C06 H7 SING N N 27
7D7 O07 H8 SING N N 28
7D7 C08 H9 SING N N 29
7D7 C10 H10 SING N N 30
7D7 N14 H11 SING N N 31
7D7 N14 H12 SING N N 32
7D7 C16 H13 SING N N 33
#
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
7D7 SMILES ACDLabs 12.01 O1C(C(C1CO)CO)n2c3c(nc2)c(N)ncn3
7D7 InChI InChI 1.03 InChI=1S/C10H13N5O3/c11-8-7-9(13-3-12-8)15(4-14-7)10-5(1-16)6(2-17)18-10/h3-6,10,16-17H,1-2H2,(H2,11,12,13)/t5-,6-,10-/m1/s1
7D7 InChIKey InChI 1.03 LMJVXGOFWKVXAW-OXOINMOOSA-N
7D7 SMILES_CANONICAL CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@H]3CO
7D7 SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH]3CO
7D7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](O3)CO)CO)N
7D7 SMILES "OpenEye OEToolkits" 2.0.6 c1nc(c2c(n1)n(cn2)C3C(C(O3)CO)CO)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
7D7 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)oxetane-2,3-diyl]dimethanol"
7D7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},3~{R},4~{S})-2-(6-aminopurin-9-yl)-4-(hydroxymethyl)oxetan-3-yl]methanol"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
7D7 'Create component' 2016-10-07 RCSB
7D7 'Initial release' 2016-11-16 RCSB
7D7 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 7D7
_pdbx_chem_comp_synonyms.name OXETANOCIN
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 7D7
_pdbe_chem_comp_synonyms.name OXETANOCIN
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
7D7 O01 O 6.805 1.665 1
7D7 C02 C 8.143 2.344 2
7D7 C03 C 8.608 3.770 3
7D7 O04 O 7.607 4.886 4
7D7 C05 C 8.821 1.006 5
7D7 C06 C 10.247 0.540 6
7D7 O07 O 11.363 1.542 7
7D7 C08 C 7.483 0.328 8
7D7 N09 N 7.018 -1.098 9
7D7 C10 C 7.893 -2.305 10
7D7 N11 N 7.018 -3.512 11
7D7 C12 C 5.598 -3.055 12
7D7 C13 C 4.299 -3.805 13
7D7 N14 N 4.299 -5.305 14
7D7 N15 N 3.000 -3.055 15
7D7 C16 C 3.000 -1.555 16
7D7 N17 N 4.299 -0.805 17
7D7 C18 C 5.598 -1.555 18
#
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
7D7 O07 C06 SINGLE NONE 1
7D7 C05 C06 SINGLE BEGINWEDGE 2
7D7 C02 C03 SINGLE BEGINDASH 3
7D7 C02 O01 SINGLE NONE 4
7D7 C02 C05 SINGLE NONE 5
7D7 C03 O04 SINGLE NONE 6
7D7 O01 C08 SINGLE NONE 7
7D7 C05 C08 SINGLE NONE 8
7D7 C08 N09 SINGLE BEGINDASH 9
7D7 N09 C18 SINGLE NONE 10
7D7 N09 C10 SINGLE NONE 11
7D7 N17 C18 DOUBLE NONE 12
7D7 N17 C16 SINGLE NONE 13
7D7 C18 C12 SINGLE NONE 14
7D7 C16 N15 DOUBLE NONE 15
7D7 C10 N11 DOUBLE NONE 16
7D7 C12 N11 SINGLE NONE 17
7D7 C12 C13 DOUBLE NONE 18
7D7 N15 C13 SINGLE NONE 19
7D7 C13 N14 SINGLE NONE 20
#
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
7D7 MurckoScaffold S1 scaffold 'c1ncc2ncn([C@H]3CCO3)c2n1' InChI=1S/C8H8N4O/c1-2-13-7(1)12-5-11-6-3-9-4-10-8(6)12/h3-5,7H,1-2H2/t7-/m1/s1 ICZKJMQOSFUCKB-SSDOTTSWSA-N
7D7 adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
7D7 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
7D7 purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
7D7 pyrimidine F4 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
7D7 O01 S1 1
7D7 C02 S1 1
7D7 C05 S1 1
7D7 C08 S1 1
7D7 N09 S1 1
7D7 C10 S1 1
7D7 N11 S1 1
7D7 C12 S1 1
7D7 C13 S1 1
7D7 N15 S1 1
7D7 C16 S1 1
7D7 N17 S1 1
7D7 C18 S1 1
7D7 N15 F1 1
7D7 C13 F1 1
7D7 C12 F1 1
7D7 C18 F1 1
7D7 N17 F1 1
7D7 C16 F1 1
7D7 N09 F1 1
7D7 C10 F1 1
7D7 N11 F1 1
7D7 N14 F1 1
7D7 C12 F2 1
7D7 C18 F2 1
7D7 N09 F2 1
7D7 C10 F2 1
7D7 N11 F2 1
7D7 N11 F3 1
7D7 C10 F3 1
7D7 N09 F3 1
7D7 C18 F3 1
7D7 C12 F3 1
7D7 C13 F3 1
7D7 N15 F3 1
7D7 C16 F3 1
7D7 N17 F3 1
7D7 C12 F4 1
7D7 C18 F4 1
7D7 N17 F4 1
7D7 C16 F4 1
7D7 N15 F4 1
7D7 C13 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 7D7
_pdbe_chem_comp_rdkit_properties.exactmw 251.102
_pdbe_chem_comp_rdkit_properties.amw 251.246
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_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 120.606
_pdbe_chem_comp_rdkit_properties.tpsa 119.310
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.902
_pdbe_chem_comp_rdkit_properties.CrippenMR 58.277
_pdbe_chem_comp_rdkit_properties.chi0v 8.461
_pdbe_chem_comp_rdkit_properties.chi1v 4.553
_pdbe_chem_comp_rdkit_properties.chi2v 2.247
_pdbe_chem_comp_rdkit_properties.chi3v 2.247
_pdbe_chem_comp_rdkit_properties.chi4v 1.439
_pdbe_chem_comp_rdkit_properties.chi0n 21.461
_pdbe_chem_comp_rdkit_properties.chi1n 10.763
_pdbe_chem_comp_rdkit_properties.chi2n 2.247
_pdbe_chem_comp_rdkit_properties.chi3n 2.247
_pdbe_chem_comp_rdkit_properties.chi4n 1.439
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.770
_pdbe_chem_comp_rdkit_properties.kappa1 3.860
_pdbe_chem_comp_rdkit_properties.kappa2 4.159
_pdbe_chem_comp_rdkit_properties.kappa3 1.465
_pdbe_chem_comp_rdkit_properties.Phi 0.892
#
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
7D7 UniChem ChEMBL CHEMBL116430
7D7 UniChem PDBe 7D7
7D7 UniChem ChEBI 86012
7D7 UniChem SureChEMBL SCHEMBL3417634
7D7 UniChem NMRShiftDB 70108890
7D7 UniChem ACTor 103913-16-2
7D7 UniChem Nikkaji J81.908E
7D7 UniChem 'EPA CompTox Dashboard' DTXSID70146141
7D7 UniChem MetaboLights MTBLC86012
7D7 UniChem PubChem 72214
7D7 UniChem 'PubChem TPHARMA' 15196742
#
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
7D7 O01 -1.278 0.410 -1.295 ETKDGv3 1
7D7 C02 -2.470 0.401 -0.544 ETKDGv3 2
7D7 C03 -2.648 1.714 0.229 ETKDGv3 3
7D7 O04 -2.964 2.756 -0.654 ETKDGv3 4
7D7 C05 -2.002 -0.755 0.324 ETKDGv3 5
7D7 C06 -2.811 -2.042 0.128 ETKDGv3 6
7D7 O07 -2.155 -3.103 0.764 ETKDGv3 7
7D7 C08 -0.762 -0.670 -0.549 ETKDGv3 8
7D7 N09 0.422 -0.266 0.206 ETKDGv3 9
7D7 C10 1.017 -1.019 1.286 ETKDGv3 10
7D7 N11 2.291 -0.799 1.484 ETKDGv3 11
7D7 C12 2.663 0.146 0.492 ETKDGv3 12
7D7 C13 3.865 0.612 0.156 ETKDGv3 13
7D7 N14 5.040 0.273 0.893 ETKDGv3 14
7D7 N15 3.946 1.459 -1.013 ETKDGv3 15
7D7 C16 2.883 1.723 -1.738 ETKDGv3 16
7D7 N17 1.595 1.167 -1.381 ETKDGv3 17
7D7 C18 1.530 0.452 -0.300 ETKDGv3 18
7D7 H1 -3.348 0.165 -1.187 ETKDGv3 19
7D7 H2 -3.485 1.596 0.949 ETKDGv3 20
7D7 H3 -1.729 1.963 0.808 ETKDGv3 21
7D7 H4 -2.115 3.021 -1.095 ETKDGv3 22
7D7 H5 -1.835 -0.490 1.392 ETKDGv3 23
7D7 H6 -2.936 -2.272 -0.955 ETKDGv3 24
7D7 H7 -3.817 -1.902 0.581 ETKDGv3 25
7D7 H8 -2.722 -3.904 0.618 ETKDGv3 26
7D7 H9 -0.567 -1.558 -1.193 ETKDGv3 27
7D7 H10 0.461 -1.734 1.878 ETKDGv3 28
7D7 H11 5.968 0.645 0.595 ETKDGv3 29
7D7 H12 4.991 -0.344 1.735 ETKDGv3 30
7D7 H13 2.972 2.353 -2.612 ETKDGv3 31
#