data_VVC
#
_chem_comp.id VVC
_chem_comp.name "4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-one"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H13 N3 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-04-05
_chem_comp.pdbx_modified_date 2023-12-15
_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 251.239
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VVC
_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 8OOJ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
VVC C4 C1 C 0 1 N N N N N N -25.456 -50.376 -8.102 -2.935 1.585 0.179 C4 VVC 1
VVC C5 C2 C 0 1 N N R N N N -26.978 -47.461 -8.972 -0.134 -0.716 -0.215 C5 VVC 2
VVC C6 C3 C 0 1 N N N N N N -24.706 -46.460 -8.930 2.135 -1.203 -0.990 C6 VVC 3
VVC C11 C4 C 0 1 N N S N N N -27.449 -49.697 -9.576 -2.002 -0.460 1.328 C11 VVC 4
VVC C7 C5 C 0 1 N N N N N N -23.859 -45.419 -8.892 3.463 -0.937 -0.992 C7 VVC 5
VVC C8 C6 C 0 1 N N N N N N -24.424 -44.113 -8.949 3.951 0.113 -0.187 C8 VVC 6
VVC C9 C7 C 0 1 N N N N N N -26.595 -45.000 -8.999 1.801 0.551 0.537 C9 VVC 7
VVC C10 C8 C 0 1 N N N N N N -26.923 -48.396 -10.183 -0.608 -1.114 1.201 C10 VVC 8
VVC N1 N1 N 0 1 N N N N N N -26.057 -46.290 -8.990 1.306 -0.447 -0.216 N1 VVC 9
VVC N2 N2 N 0 1 N N N N N N -23.635 -43.037 -8.897 5.295 0.405 -0.171 N2 VVC 10
VVC C3 C9 C 0 1 N N R N N N -26.802 -49.667 -8.178 -2.206 0.256 -0.026 C3 VVC 11
VVC N3 N3 N 0 1 N N N N N N -25.758 -43.936 -8.976 3.106 0.817 0.554 N3 VVC 12
VVC C1 C10 C 0 1 N N N N N N -28.321 -50.639 -6.242 -3.562 -1.290 -1.690 C1 VVC 13
VVC C2 C11 C 0 1 N N N N N N -27.683 -50.230 -7.144 -2.960 -0.604 -0.952 C2 VVC 14
VVC O1 O1 O 0 1 N N N N N N -24.460 -49.933 -9.050 -3.217 2.175 -1.092 O1 VVC 15
VVC O2 O2 O 0 1 N N N N N N -26.618 -48.284 -7.873 -0.870 0.487 -0.525 O2 VVC 16
VVC O3 O3 O 0 1 N N N N N N -27.823 -44.875 -9.051 1.043 1.224 1.216 O3 VVC 17
VVC O4 O4 O 0 1 N N N N N N -28.866 -49.789 -9.497 -3.007 -1.457 1.524 O4 VVC 18
VVC H1 H1 H 0 1 N N N N N N -25.629 -51.449 -8.271 -3.869 1.408 0.712 H1 VVC 19
VVC H2 H2 H 0 1 N N N N N N -25.051 -50.224 -7.091 -2.306 2.259 0.761 H2 VVC 20
VVC H3 H3 H 0 1 N N N N N N -28.011 -47.104 -8.853 -0.374 -1.503 -0.930 H3 VVC 21
VVC H4 H4 H 0 1 N N N N N N -24.305 -47.463 -8.912 1.737 -2.001 -1.598 H4 VVC 22
VVC H5 H5 H 0 1 N N N N N N -27.038 -50.548 -10.140 -2.015 0.260 2.147 H5 VVC 23
VVC H6 H6 H 0 1 N N N N N N -22.791 -45.566 -8.821 4.138 -1.520 -1.601 H6 VVC 24
VVC H7 H7 H 0 1 N N N N N N -25.895 -48.512 -10.557 -0.685 -2.198 1.287 H7 VVC 25
VVC H8 H8 H 0 1 N N N N N N -27.571 -48.040 -10.997 0.071 -0.717 1.956 H8 VVC 26
VVC H9 H9 H 0 1 N N N N N N -24.038 -42.122 -8.879 5.910 -0.112 -0.714 H9 VVC 27
VVC H10 H10 H 0 1 N N N N N N -22.641 -43.146 -8.876 5.628 1.127 0.384 H10 VVC 28
VVC H11 H11 H 0 1 N N N N N N -28.895 -51.007 -5.430 -4.100 -1.904 -2.351 H11 VVC 29
VVC H12 H12 H 0 1 N N N N N N -23.660 -50.431 -8.926 -3.679 3.022 -1.038 H12 VVC 30
VVC H13 H13 H 0 1 N N N N N N -29.109 -50.622 -9.111 -2.927 -1.938 2.359 H13 VVC 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
VVC C10 C11 SING N N 1
VVC C10 C5 SING N N 2
VVC C11 O4 SING N N 3
VVC C11 C3 SING N N 4
VVC O3 C9 DOUB N N 5
VVC O1 C4 SING N N 6
VVC C9 N1 SING N N 7
VVC C9 N3 SING N N 8
VVC N1 C5 SING N N 9
VVC N1 C6 SING N N 10
VVC N3 C8 DOUB N N 11
VVC C5 O2 SING N N 12
VVC C8 N2 SING N N 13
VVC C8 C7 SING N N 14
VVC C6 C7 DOUB N N 15
VVC C3 C4 SING N N 16
VVC C3 O2 SING N N 17
VVC C3 C2 SING N N 18
VVC C2 C1 TRIP N N 19
VVC C4 H1 SING N N 20
VVC C4 H2 SING N N 21
VVC C5 H3 SING N N 22
VVC C6 H4 SING N N 23
VVC C11 H5 SING N N 24
VVC C7 H6 SING N N 25
VVC C10 H7 SING N N 26
VVC C10 H8 SING N N 27
VVC N2 H9 SING N N 28
VVC N2 H10 SING N N 29
VVC C1 H11 SING N N 30
VVC O1 H12 SING N N 31
VVC O4 H13 SING N N 32
#
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
VVC InChI InChI 1.06 "InChI=1S/C11H13N3O4/c1-2-11(6-15)7(16)5-9(18-11)14-4-3-8(12)13-10(14)17/h1,3-4,7,9,15-16H,5-6H2,(H2,12,13,17)/t7-,9+,11+/m0/s1"
VVC InChIKey InChI 1.06 MSPJPGIGNWYLAC-JVUFJMBOSA-N
VVC SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@](CO)(O2)C#C"
VVC SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[C](CO)(O2)C#C"
VVC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C#C[C@]1([C@H](C[C@@H](O1)N2C=CC(=NC2=O)N)O)CO"
VVC SMILES "OpenEye OEToolkits" 2.0.7 "C#CC1(C(CC(O1)N2C=CC(=NC2=O)N)O)CO"
#
_pdbx_chem_comp_identifier.comp_id VVC
_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
"4-azanyl-1-[(2~{R},4~{S},5~{R})-5-ethynyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]pyrimidin-2-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
VVC 'Create component' 2023-04-05 PDBE
VVC 'Initial release' 2023-12-20 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
VVC C4 C 6.738 -4.297 1
VVC C5 C 7.488 -0.488 2
VVC C6 C 6.189 1.762 3
VVC C11 C 8.238 -2.797 4
VVC C7 C 6.189 3.262 5
VVC C8 C 7.488 4.012 6
VVC C9 C 8.787 1.762 7
VVC C10 C 8.701 -1.370 8
VVC N1 N 7.488 1.012 9
VVC N2 N 7.488 5.512 10
VVC C3 C 6.738 -2.797 11
VVC N3 N 8.787 3.262 12
VVC C1 C 3.884 -3.724 13
VVC C2 C 5.311 -3.260 14
VVC O1 O 5.439 -5.047 15
VVC O2 O 6.274 -1.370 16
VVC O3 O 10.086 1.012 17
VVC O4 O 9.119 -4.010 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
VVC C10 C11 SINGLE NONE 1
VVC C10 C5 SINGLE NONE 2
VVC C11 O4 SINGLE BEGINDASH 3
VVC C11 C3 SINGLE NONE 4
VVC O3 C9 DOUBLE NONE 5
VVC O1 C4 SINGLE NONE 6
VVC C9 N1 SINGLE NONE 7
VVC C9 N3 SINGLE NONE 8
VVC C5 N1 SINGLE BEGINWEDGE 9
VVC N1 C6 SINGLE NONE 10
VVC N3 C8 DOUBLE NONE 11
VVC C5 O2 SINGLE NONE 12
VVC C8 N2 SINGLE NONE 13
VVC C8 C7 SINGLE NONE 14
VVC C6 C7 DOUBLE NONE 15
VVC C3 C4 SINGLE BEGINWEDGE 16
VVC C3 O2 SINGLE NONE 17
VVC C3 C2 SINGLE NONE 18
VVC C2 C1 TRIPLE NONE 19
#
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
VVC MurckoScaffold S1 scaffold 'O=c1ncccn1[C@H]1CCCO1' InChI=1S/C8H10N2O2/c11-8-9-4-2-5-10(8)7-3-1-6-12-7/h2,4-5,7H,1,3,6H2/t7-/m1/s1 AKXKPKRAUWTVBW-SSDOTTSWSA-N
VVC 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
VVC pyrimidine F2 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
VVC C5 S1 1
VVC C6 S1 1
VVC C11 S1 1
VVC C7 S1 1
VVC C8 S1 1
VVC C9 S1 1
VVC C10 S1 1
VVC N1 S1 1
VVC C3 S1 1
VVC N3 S1 1
VVC O2 S1 1
VVC O3 S1 1
VVC C5 F1 1
VVC C10 F1 1
VVC C11 F1 1
VVC O4 F1 1
VVC C3 F1 1
VVC O2 F1 1
VVC C4 F1 1
VVC O1 F1 1
VVC C7 F2 1
VVC C8 F2 1
VVC N3 F2 1
VVC C9 F2 1
VVC N1 F2 1
VVC C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VVC
_pdbe_chem_comp_rdkit_properties.exactmw 251.091
_pdbe_chem_comp_rdkit_properties.amw 251.242
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.455
_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 121.386
_pdbe_chem_comp_rdkit_properties.tpsa 110.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.011
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.589
_pdbe_chem_comp_rdkit_properties.chi0v 8.475
_pdbe_chem_comp_rdkit_properties.chi1v 4.362
_pdbe_chem_comp_rdkit_properties.chi2v 1.985
_pdbe_chem_comp_rdkit_properties.chi3v 1.985
_pdbe_chem_comp_rdkit_properties.chi4v 1.138
_pdbe_chem_comp_rdkit_properties.chi0n 21.475
_pdbe_chem_comp_rdkit_properties.chi1n 10.573
_pdbe_chem_comp_rdkit_properties.chi2n 1.985
_pdbe_chem_comp_rdkit_properties.chi3n 1.985
_pdbe_chem_comp_rdkit_properties.chi4n 1.138
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.880
_pdbe_chem_comp_rdkit_properties.kappa1 4.062
_pdbe_chem_comp_rdkit_properties.kappa2 4.418
_pdbe_chem_comp_rdkit_properties.kappa3 1.863
_pdbe_chem_comp_rdkit_properties.Phi 0.997
#
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
VVC UniChem ChEMBL CHEMBL322215
VVC UniChem ZINC ZINC000003993852
VVC UniChem SureChEMBL SCHEMBL938876
VVC UniChem 'PubChem TPHARMA' 14749858
VVC UniChem Nikkaji J1.159.041A
VVC UniChem PubChem 9794951
VVC UniChem 'PubChem TPHARMA' 14774337
#
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
VVC C4 -1.463 1.593 -1.761 ETKDGv3 1
VVC C5 -0.502 -0.512 0.625 ETKDGv3 2
VVC C6 1.564 -0.636 -0.839 ETKDGv3 3
VVC C11 -1.814 1.438 0.745 ETKDGv3 4
VVC C7 2.839 -0.991 -1.019 ETKDGv3 5
VVC C8 3.568 -1.721 0.040 ETKDGv3 6
VVC C9 1.621 -1.649 1.410 ETKDGv3 7
VVC C10 -0.511 0.875 1.239 ETKDGv3 8
VVC N1 0.875 -0.969 0.382 ETKDGv3 9
VVC N2 4.928 -2.103 -0.166 ETKDGv3 10
VVC C3 -1.990 0.714 -0.608 ETKDGv3 11
VVC N3 2.982 -2.014 1.164 ETKDGv3 12
VVC C1 -4.562 0.120 -1.090 ETKDGv3 13
VVC C2 -3.407 0.388 -0.873 ETKDGv3 14
VVC O1 -1.501 0.884 -2.971 ETKDGv3 15
VVC O2 -1.244 -0.488 -0.577 ETKDGv3 16
VVC O3 1.094 -1.923 2.521 ETKDGv3 17
VVC O4 -2.843 1.107 1.647 ETKDGv3 18
VVC H1 -2.083 2.515 -1.850 ETKDGv3 19
VVC H2 -0.415 1.902 -1.550 ETKDGv3 20
VVC H3 -1.016 -1.218 1.316 ETKDGv3 21
VVC H4 1.055 -0.095 -1.626 ETKDGv3 22
VVC H5 -1.754 2.547 0.624 ETKDGv3 23
VVC H6 3.341 -0.737 -1.944 ETKDGv3 24
VVC H7 -0.454 0.836 2.349 ETKDGv3 25
VVC H8 0.333 1.485 0.848 ETKDGv3 26
VVC H9 5.453 -2.617 0.577 ETKDGv3 27
VVC H10 5.416 -1.875 -1.061 ETKDGv3 28
VVC H11 -5.576 -0.115 -1.280 ETKDGv3 29
VVC H12 -1.146 1.501 -3.663 ETKDGv3 30
VVC H13 -2.788 1.757 2.395 ETKDGv3 31
#