data_D4V
#
_chem_comp.id D4V
_chem_comp.name 3-methylpyridin-2-ol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H7 N O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
"(R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-18
_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 109.126
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D4V
_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 6BB7
_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
D4V C4 C1 C 0 1 Y N N N N N -3.939 28.578 54.553 1.842 0.650 -0.000 C4 D4V 1
D4V C5 C2 C 0 1 Y N N N N N -1.678 27.766 54.946 -0.464 0.687 0.018 C5 D4V 2
D4V C3 C3 C 0 1 Y N N N N N -4.342 27.274 54.133 1.860 -0.730 -0.014 C3 D4V 3
D4V C2 C4 C 0 1 Y N N N N N -3.397 26.193 54.118 0.657 -1.424 -0.011 C2 D4V 4
D4V C1 C5 C 0 1 Y N N N N N -2.092 26.402 54.519 -0.522 -0.701 0.005 C1 D4V 5
D4V O O1 O 0 1 N N N N N N -0.389 28.017 55.324 -1.613 1.407 0.035 O D4V 6
D4V C C6 C 0 1 N N N N N N -1.091 25.263 54.506 -1.852 -1.410 0.009 C D4V 7
D4V N N1 N 0 1 Y N N N N N -2.578 28.806 54.953 0.701 1.312 0.015 N D4V 8
D4V H5 H1 H 0 1 N N N N N N -4.653 29.388 54.570 2.775 1.195 0.002 H5 D4V 9
D4V H4 H2 H 0 1 N N N N N N -5.362 27.100 53.825 2.798 -1.264 -0.027 H4 D4V 10
D4V H3 H3 H 0 1 N N N N N N -3.708 25.212 53.792 0.643 -2.504 -0.022 H3 D4V 11
D4V H1 H4 H 0 1 N N N N N N -0.593 25.223 53.526 -2.164 -1.590 1.038 H1 D4V 12
D4V H2 H5 H 0 1 N N N N N N -0.339 25.427 55.292 -2.595 -0.790 -0.493 H2 D4V 13
D4V H H6 H 0 1 N N N N N N -1.614 24.313 54.691 -1.759 -2.361 -0.514 H D4V 14
D4V H7 H7 H 0 1 N N N N N N -0.298 28.935 55.551 -1.954 1.625 -0.843 H7 D4V 15
#
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
D4V C2 C3 SING Y N 1
D4V C2 C1 DOUB Y N 2
D4V C3 C4 DOUB Y N 3
D4V C C1 SING N N 4
D4V C1 C5 SING Y N 5
D4V C4 N SING Y N 6
D4V C5 N DOUB Y N 7
D4V C5 O SING N N 8
D4V C4 H5 SING N N 9
D4V C3 H4 SING N N 10
D4V C2 H3 SING N N 11
D4V C H1 SING N N 12
D4V C H2 SING N N 13
D4V C H SING N N 14
D4V O H7 SING N N 15
#
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
D4V SMILES ACDLabs 12.01 c1nc(O)c(cc1)C
D4V InChI InChI 1.03 InChI=1S/C6H7NO/c1-5-3-2-4-7-6(5)8/h2-4H,1H3,(H,7,8)
D4V InChIKey InChI 1.03 MVKDNXIKAWKCCS-UHFFFAOYSA-N
D4V SMILES_CANONICAL CACTVS 3.385 Cc1cccnc1O
D4V SMILES CACTVS 3.385 Cc1cccnc1O
D4V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 Cc1cccnc1O
D4V SMILES "OpenEye OEToolkits" 2.0.6 Cc1cccnc1O
#
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
D4V "SYSTEMATIC NAME" ACDLabs 12.01 3-methylpyridin-2-ol
D4V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 3-methylpyridin-2-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D4V 'Create component' 2017-10-18 RCSB
D4V 'Initial release' 2018-10-17 RCSB
D4V 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id D4V
_pdbx_chem_comp_synonyms.name
"(R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id D4V
_pdbe_chem_comp_synonyms.name
'(R)-N-[2-[1-(AMINOIMINOMETHYL)-3-PIPERIDINYL]-1-OXOETHYL]-4-(PHENYLETHYNYL)-L-PHENYLALANINE METHYL ESTER'
_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
D4V C4 C 6.897 -0.285 1
D4V C5 C 4.299 -0.285 2
D4V C3 C 6.897 1.215 3
D4V C2 C 5.598 1.965 4
D4V C1 C 4.299 1.215 5
D4V O O 3.000 -1.035 6
D4V C C 3.000 1.965 7
D4V N N 5.598 -1.035 8
#
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
D4V C2 C3 SINGLE NONE 1
D4V C2 C1 DOUBLE NONE 2
D4V C3 C4 DOUBLE NONE 3
D4V C C1 SINGLE NONE 4
D4V C1 C5 SINGLE NONE 5
D4V C4 N SINGLE NONE 6
D4V C5 N DOUBLE NONE 7
D4V C5 O SINGLE NONE 8
#
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
D4V MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
D4V pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
D4V C4 S1 1
D4V C5 S1 1
D4V C3 S1 1
D4V C2 S1 1
D4V C1 S1 1
D4V N S1 1
D4V C4 F1 1
D4V C3 F1 1
D4V C2 F1 1
D4V C1 F1 1
D4V C5 F1 1
D4V N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id D4V
_pdbe_chem_comp_rdkit_properties.exactmw 109.053
_pdbe_chem_comp_rdkit_properties.amw 109.128
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.167
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 57.732
_pdbe_chem_comp_rdkit_properties.tpsa 33.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.579
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.763
_pdbe_chem_comp_rdkit_properties.chi0v 3.855
_pdbe_chem_comp_rdkit_properties.chi1v 1.901
_pdbe_chem_comp_rdkit_properties.chi2v 0.615
_pdbe_chem_comp_rdkit_properties.chi3v 0.615
_pdbe_chem_comp_rdkit_properties.chi4v 0.279
_pdbe_chem_comp_rdkit_properties.chi0n 10.855
_pdbe_chem_comp_rdkit_properties.chi1n 5.310
_pdbe_chem_comp_rdkit_properties.chi2n 0.615
_pdbe_chem_comp_rdkit_properties.chi3n 0.615
_pdbe_chem_comp_rdkit_properties.chi4n 0.279
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.050
_pdbe_chem_comp_rdkit_properties.kappa1 1.264
_pdbe_chem_comp_rdkit_properties.kappa2 1.820
_pdbe_chem_comp_rdkit_properties.kappa3 0.780
_pdbe_chem_comp_rdkit_properties.Phi 0.288
#
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
D4V UniChem ChEMBL CHEMBL4548076
D4V UniChem PDBe D4V
D4V UniChem ChEBI 194930
D4V UniChem ZINC ZINC000008580061
D4V UniChem eMolecules 836540
D4V UniChem fdasrs VM19FN4HHV
D4V UniChem SureChEMBL SCHEMBL146698
D4V UniChem NMRShiftDB 20027333
D4V UniChem NMRShiftDB 20165640
D4V UniChem ACTor 1003-56-1
D4V UniChem Nikkaji J110.367I
D4V UniChem 'EPA CompTox Dashboard' DTXSID50143118
D4V UniChem ChemicalBook CB7415881
D4V UniChem ChemicalBook CB9302897
D4V UniChem eMolecules 523993
D4V UniChem 'PubChem TPHARMA' 17499758
D4V UniChem PubChem 70481
D4V UniChem Mcule MCULE-8735614074
#
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
D4V C4 2.174 -0.759 0.279 ETKDGv3 1
D4V C5 -0.148 -1.216 -0.110 ETKDGv3 2
D4V C3 1.968 0.559 0.342 ETKDGv3 3
D4V C2 0.603 1.088 0.170 ETKDGv3 4
D4V C1 -0.425 0.248 -0.047 ETKDGv3 5
D4V O -1.166 -2.142 -0.332 ETKDGv3 6
D4V C -1.820 0.778 -0.223 ETKDGv3 7
D4V N 1.071 -1.650 0.046 ETKDGv3 8
D4V H5 3.171 -1.161 0.403 ETKDGv3 9
D4V H4 2.795 1.235 0.517 ETKDGv3 10
D4V H3 0.447 2.158 0.223 ETKDGv3 11
D4V H1 -1.856 1.886 -0.149 ETKDGv3 12
D4V H2 -2.480 0.357 0.564 ETKDGv3 13
D4V H -2.206 0.485 -1.222 ETKDGv3 14
D4V H7 -2.131 -1.867 -0.460 ETKDGv3 15
#