data_MPD
#
_chem_comp.id MPD
_chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H14 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 118.174
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MPD
_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 ?
_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
MPD C1 C1 C 0 1 N N N N N N -2.503 -3.420 8.511 -1.297 -0.463 -1.462 C1 MPD 1
MPD C2 C2 C 0 1 N N N N N N -2.962 -4.044 9.830 -1.118 -0.087 0.010 C2 MPD 2
MPD O2 O2 O 0 1 N N N N N N -2.698 -5.408 9.790 -1.061 1.336 0.134 O2 MPD 3
MPD CM CM C 0 1 N N N N N N -4.456 -3.762 9.953 -2.300 -0.622 0.820 CM MPD 4
MPD C3 C3 C 0 1 N N N N N N -2.278 -3.458 11.042 0.181 -0.698 0.539 C3 MPD 5
MPD C4 C4 C 0 1 N N S N N N -2.192 -4.181 12.269 1.363 -0.162 -0.272 C4 MPD 6
MPD O4 O4 O 0 1 N N N N N N -1.996 -5.510 12.308 1.491 1.245 -0.055 O4 MPD 7
MPD C5 C5 C 0 1 N N N N N N -1.655 -3.474 13.505 2.647 -0.865 0.173 C5 MPD 8
MPD H11 H11 H 0 1 N N N N N N -2.705 -2.339 8.526 -0.455 -0.082 -2.040 H11 MPD 9
MPD H12 H12 H 0 1 N N N N N N -1.424 -3.589 8.381 -1.341 -1.548 -1.557 H12 MPD 10
MPD H13 H13 H 0 1 N N N N N N -3.050 -3.883 7.677 -2.223 -0.028 -1.839 H13 MPD 11
MPD HO2 HO2 H 0 1 N N N N N N -2.978 -5.809 10.604 -0.948 1.647 1.043 HO2 MPD 12
MPD HM1 HM1 H 0 1 N N N N N N -4.835 -4.193 10.891 -2.344 -1.707 0.725 HM1 MPD 13
MPD HM2 HM2 H 0 1 N N N N N N -4.625 -2.675 9.955 -2.173 -0.354 1.869 HM2 MPD 14
MPD HM3 HM3 H 0 1 N N N N N N -4.986 -4.214 9.101 -3.226 -0.187 0.444 HM3 MPD 15
MPD H31 H31 H 0 1 N N N N N N -1.239 -3.269 10.735 0.308 -0.429 1.587 H31 MPD 16
MPD H32 H32 H 0 1 N N N N N N -2.830 -2.536 11.278 0.137 -1.783 0.444 H32 MPD 17
MPD H4 H4 H 0 1 N N N N N N -3.290 -4.137 12.316 1.193 -0.352 -1.332 H4 MPD 18
MPD HO4 HO4 H 0 1 N N N N N N -1.969 -5.800 13.212 1.645 1.488 0.868 HO4 MPD 19
MPD H51 H51 H 0 1 N N N N N N -1.657 -4.171 14.356 2.549 -1.939 0.007 H51 MPD 20
MPD H52 H52 H 0 1 N N N N N N -0.627 -3.131 13.314 3.489 -0.484 -0.405 H52 MPD 21
MPD H53 H53 H 0 1 N N N N N N -2.293 -2.609 13.738 2.817 -0.675 1.232 H53 MPD 22
#
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
MPD C1 C2 SING N N 1
MPD C1 H11 SING N N 2
MPD C1 H12 SING N N 3
MPD C1 H13 SING N N 4
MPD C2 O2 SING N N 5
MPD C2 CM SING N N 6
MPD C2 C3 SING N N 7
MPD O2 HO2 SING N N 8
MPD CM HM1 SING N N 9
MPD CM HM2 SING N N 10
MPD CM HM3 SING N N 11
MPD C3 C4 SING N N 12
MPD C3 H31 SING N N 13
MPD C3 H32 SING N N 14
MPD C4 O4 SING N N 15
MPD C4 C5 SING N N 16
MPD C4 H4 SING N N 17
MPD O4 HO4 SING N N 18
MPD C5 H51 SING N N 19
MPD C5 H52 SING N N 20
MPD C5 H53 SING N N 21
#
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
MPD SMILES ACDLabs 11.02 OC(C)CC(O)(C)C
MPD SMILES_CANONICAL CACTVS 3.352 C[C@H](O)CC(C)(C)O
MPD SMILES CACTVS 3.352 C[CH](O)CC(C)(C)O
MPD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C[C@@H](CC(C)(C)O)O
MPD SMILES "OpenEye OEToolkits" 1.7.0 CC(CC(C)(C)O)O
MPD InChI InChI 1.03 InChI=1S/C6H14O2/c1-5(7)4-6(2,3)8/h5,7-8H,4H2,1-3H3/t5-/m0/s1
MPD InChIKey InChI 1.03 SVTBMSDMJJWYQN-YFKPBYRVSA-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
MPD "SYSTEMATIC NAME" ACDLabs 11.02 (4S)-2-methylpentane-2,4-diol
MPD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 (4S)-2-methylpentane-2,4-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
MPD 'Create component' 1999-07-08 RCSB
MPD 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id MPD
_pdbe_chem_comp_drugbank_details.drugbank_id DB03564
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name (4r)-2-Methylpentane-2,4-Diol
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id MPD
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03564
_pdbe_chem_comp_drugbank_classification.parent 'Tertiary alcohols'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organooxygen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic oxygen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as tertiary alcohols. These are compounds in which a hydroxy group, -OH, is attached to a saturated carbon atom R3COH (R not H ).'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
MPD DB03564 'Xylose isomerase' 'Streptomyces rubiginosus' P24300 unknown 1
MPD DB03564 '1-pyrroline-5-carboxylate dehydrogenase' 'Thermus thermophilus' P83849 unknown 2
#
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
MPD C1 C 3.805 -0.649 1
MPD C2 C 5.104 0.101 2
MPD O2 O 4.354 1.399 3
MPD CM C 5.854 -1.198 4
MPD C3 C 6.404 0.851 5
MPD C4 C 7.702 0.101 6
MPD O4 O 9.002 0.851 7
MPD C5 C 7.702 -1.399 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
MPD C1 C2 SINGLE NONE 1
MPD C2 O2 SINGLE NONE 2
MPD C2 CM SINGLE NONE 3
MPD C2 C3 SINGLE NONE 4
MPD C3 C4 SINGLE NONE 5
MPD C4 O4 SINGLE NONE 6
MPD C4 C5 SINGLE BEGINWEDGE 7
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id MPD
_pdbe_chem_comp_rdkit_properties.exactmw 118.099
_pdbe_chem_comp_rdkit_properties.amw 118.176
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 69.995
_pdbe_chem_comp_rdkit_properties.tpsa 40.460
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.528
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.596
_pdbe_chem_comp_rdkit_properties.chi0v 3.816
_pdbe_chem_comp_rdkit_properties.chi1v 1.658
_pdbe_chem_comp_rdkit_properties.chi2v 0.290
_pdbe_chem_comp_rdkit_properties.chi3v 0.290
_pdbe_chem_comp_rdkit_properties.chi4v 0.160
_pdbe_chem_comp_rdkit_properties.chi0n 17.816
_pdbe_chem_comp_rdkit_properties.chi1n 8.475
_pdbe_chem_comp_rdkit_properties.chi2n 0.290
_pdbe_chem_comp_rdkit_properties.chi3n 0.290
_pdbe_chem_comp_rdkit_properties.chi4n 0.160
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.867
_pdbe_chem_comp_rdkit_properties.kappa2 2.464
_pdbe_chem_comp_rdkit_properties.kappa3 5.920
_pdbe_chem_comp_rdkit_properties.Phi 0.267
#
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
MPD UniChem DrugBank DB03564
MPD UniChem PDBe MPD
MPD UniChem ChEBI 44224
MPD UniChem ZINC ZINC000000388075
MPD UniChem ChemicalBook CB23051551
MPD UniChem 'Probes And Drugs' PD006810
MPD UniChem Nikkaji J766.306D
MPD UniChem SureChEMBL SCHEMBL335683
MPD UniChem PubChem 5288834
MPD UniChem NMRShiftDB 60070954
#
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
MPD C1 -2.136 0.844 -0.875 ETKDGv3 1
MPD C2 -1.153 0.166 0.102 ETKDGv3 2
MPD O2 -1.290 0.751 1.376 ETKDGv3 3
MPD CM -1.527 -1.322 0.216 ETKDGv3 4
MPD C3 0.301 0.346 -0.427 ETKDGv3 5
MPD C4 1.397 -0.215 0.506 ETKDGv3 6
MPD O4 1.459 -1.612 0.377 ETKDGv3 7
MPD C5 2.762 0.380 0.148 ETKDGv3 8
MPD H11 -2.085 0.366 -1.877 ETKDGv3 9
MPD H12 -1.894 1.922 -0.988 ETKDGv3 10
MPD H13 -3.177 0.765 -0.495 ETKDGv3 11
MPD HO2 -1.046 1.711 1.300 ETKDGv3 12
MPD HM1 -2.606 -1.434 0.457 ETKDGv3 13
MPD HM2 -0.960 -1.809 1.036 ETKDGv3 14
MPD HM3 -1.321 -1.856 -0.737 ETKDGv3 15
MPD H31 0.398 -0.127 -1.430 ETKDGv3 16
MPD H32 0.479 1.435 -0.571 ETKDGv3 17
MPD H4 1.164 0.065 1.560 ETKDGv3 18
MPD HO4 1.919 -1.956 1.187 ETKDGv3 19
MPD H51 3.024 0.141 -0.906 ETKDGv3 20
MPD H52 3.545 -0.040 0.814 ETKDGv3 21
MPD H53 2.749 1.483 0.279 ETKDGv3 22
#