data_QD7
#
_chem_comp.id QD7
_chem_comp.name "(R)-(3-aminopropyl)methylphosphinic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H12 N O2 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-10-16
_chem_comp.pdbx_modified_date 2020-06-05
_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 137.117
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code QD7
_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 6UO9
_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
QD7 CAB C1 C 0 1 N N N N N N 125.101 128.265 202.627 2.787 0.575 -0.183 CAB QD7 1
QD7 CAC C2 C 0 1 N N N N N N 126.325 129.147 202.561 1.454 -0.132 0.071 CAC QD7 2
QD7 CAD C3 C 0 1 N N N N N N 126.738 129.551 203.958 0.302 0.818 -0.262 CAD QD7 3
QD7 CAG C4 C 0 1 N N N N N N 127.579 132.174 203.325 -2.656 1.153 -0.212 CAG QD7 4
QD7 NAA N1 N 0 1 N N N N N N 124.718 127.921 201.257 3.894 -0.338 0.136 NAA QD7 5
QD7 OAF O1 O 0 1 N N N N N N 128.832 130.786 205.198 -1.443 -1.257 -0.983 OAF QD7 6
QD7 OAH O2 O 0 1 N N N N N N 129.127 129.969 202.785 -1.320 -0.530 1.431 OAH QD7 7
QD7 PAE P1 P 0 1 N N N N N N 128.158 130.538 203.752 -1.286 -0.024 0.040 PAE QD7 8
QD7 H1 H1 H 0 1 N N N N N N 124.279 128.804 203.121 2.849 0.869 -1.230 H1 QD7 9
QD7 H2 H2 H 0 1 N N N N N N 125.331 127.349 203.192 2.854 1.461 0.448 H2 QD7 10
QD7 H3 H3 H 0 1 N N N N N N 127.147 128.596 202.082 1.388 -1.018 -0.560 H3 QD7 11
QD7 H4 H4 H 0 1 N N N N N N 126.095 130.048 201.973 1.392 -0.426 1.118 H4 QD7 12
QD7 H5 H5 H 0 1 N N N N N N 125.937 130.126 204.445 0.369 1.705 0.369 H5 QD7 13
QD7 H6 H6 H 0 1 N N N N N N 126.971 128.662 204.563 0.364 1.112 -1.309 H6 QD7 14
QD7 H7 H7 H 0 1 N N N N N N 126.868 132.523 204.088 -2.550 1.988 0.481 H7 QD7 15
QD7 H8 H8 H 0 1 N N N N N N 128.434 132.865 203.278 -2.631 1.525 -1.237 H8 QD7 16
QD7 H9 H9 H 0 1 N N N N N N 127.079 132.142 202.346 -3.605 0.649 -0.032 H9 QD7 17
QD7 H10 H10 H 0 1 N N N N N N 123.907 127.336 201.274 3.818 -1.196 -0.389 H10 QD7 18
QD7 H11 H11 H 0 1 N N N N N N 124.514 128.757 200.748 4.786 0.106 -0.023 H11 QD7 19
QD7 H13 H13 H 0 1 N N N N N N 129.744 130.520 205.173 -2.267 -1.752 -0.880 H13 QD7 20
#
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
QD7 NAA CAB SING N N 1
QD7 CAC CAB SING N N 2
QD7 CAC CAD SING N N 3
QD7 OAH PAE DOUB N N 4
QD7 CAG PAE SING N N 5
QD7 PAE CAD SING N N 6
QD7 PAE OAF SING N N 7
QD7 CAB H1 SING N N 8
QD7 CAB H2 SING N N 9
QD7 CAC H3 SING N N 10
QD7 CAC H4 SING N N 11
QD7 CAD H5 SING N N 12
QD7 CAD H6 SING N N 13
QD7 CAG H7 SING N N 14
QD7 CAG H8 SING N N 15
QD7 CAG H9 SING N N 16
QD7 NAA H10 SING N N 17
QD7 NAA H11 SING N N 18
QD7 OAF H13 SING N N 19
#
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
QD7 SMILES ACDLabs 12.01 C(CCP(C)(O)=O)N
QD7 InChI InChI 1.03 InChI=1S/C4H12NO2P/c1-8(6,7)4-2-3-5/h2-5H2,1H3,(H,6,7)
QD7 InChIKey InChI 1.03 NHVRIDDXGZPJTJ-UHFFFAOYSA-N
QD7 SMILES_CANONICAL CACTVS 3.385 C[P](O)(=O)CCCN
QD7 SMILES CACTVS 3.385 C[P](O)(=O)CCCN
QD7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CP(=O)(CCCN)O
QD7 SMILES "OpenEye OEToolkits" 2.0.7 CP(=O)(CCCN)O
#
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
QD7 "SYSTEMATIC NAME" ACDLabs 12.01 "(R)-(3-aminopropyl)methylphosphinic acid"
QD7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-azanylpropyl(methyl)phosphinic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
QD7 'Create component' 2019-10-16 RCSB
QD7 'Initial release' 2020-06-10 RCSB
#
_pdbe_chem_comp_synonyms.comp_id QD7
_pdbe_chem_comp_synonyms.name CGP-35024
_pdbe_chem_comp_synonyms.provenance ChEMBL
_pdbe_chem_comp_synonyms.type 'Research Code'
#
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
QD7 CAB C 9.002 0.750 1
QD7 CAC C 7.702 0.000 2
QD7 CAD C 6.404 0.750 3
QD7 CAG C 5.854 -1.299 4
QD7 NAA N 10.301 0.000 5
QD7 OAF O 4.354 1.299 6
QD7 OAH O 3.805 -0.750 7
QD7 PAE P 5.104 0.000 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
QD7 NAA CAB SINGLE NONE 1
QD7 CAC CAB SINGLE NONE 2
QD7 CAC CAD SINGLE NONE 3
QD7 OAH PAE DOUBLE NONE 4
QD7 PAE CAG SINGLE BEGINWEDGE 5
QD7 PAE CAD SINGLE NONE 6
QD7 PAE OAF SINGLE NONE 7
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id QD7
_pdbe_chem_comp_rdkit_properties.exactmw 137.061
_pdbe_chem_comp_rdkit_properties.amw 137.119
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_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 66.407
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.235
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.288
_pdbe_chem_comp_rdkit_properties.chi0v 4.605
_pdbe_chem_comp_rdkit_properties.chi1v 3.161
_pdbe_chem_comp_rdkit_properties.chi2v 0.665
_pdbe_chem_comp_rdkit_properties.chi3v 0.665
_pdbe_chem_comp_rdkit_properties.chi4v 0.296
_pdbe_chem_comp_rdkit_properties.chi0n 15.711
_pdbe_chem_comp_rdkit_properties.chi1n 7.339
_pdbe_chem_comp_rdkit_properties.chi2n 0.259
_pdbe_chem_comp_rdkit_properties.chi3n 0.259
_pdbe_chem_comp_rdkit_properties.chi4n 0.099
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.150
_pdbe_chem_comp_rdkit_properties.kappa1 1.136
_pdbe_chem_comp_rdkit_properties.kappa2 3.230
_pdbe_chem_comp_rdkit_properties.kappa3 6.150
_pdbe_chem_comp_rdkit_properties.Phi 0.459
#
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
QD7 UniChem ChEMBL CHEMBL112710
QD7 UniChem PDBe QD7
QD7 UniChem 'Guide to Pharmacology' 1080
QD7 UniChem ZINC ZINC000020028798
QD7 UniChem ACTor 127729-35-5
QD7 UniChem Nikkaji J364.038H
QD7 UniChem BindingDb 24185
QD7 UniChem 'Probes And Drugs' PD050301
QD7 UniChem eMolecules 1934249
QD7 UniChem SureChEMBL SCHEMBL341867
QD7 UniChem 'PubChem TPHARMA' 15219048
QD7 UniChem PubChem 28559746
QD7 UniChem PubChem 5230
QD7 UniChem Mcule MCULE-1158131505
QD7 UniChem ACTor 130434-62-7
#
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
QD7 CAB -2.393 -0.416 -0.328 ETKDGv3 1
QD7 CAC -1.107 0.295 0.116 ETKDGv3 2
QD7 CAD 0.122 -0.574 -0.158 ETKDGv3 3
QD7 CAG 3.071 -0.782 0.002 ETKDGv3 4
QD7 NAA -3.572 0.408 -0.070 ETKDGv3 5
QD7 OAF 1.794 1.737 -0.473 ETKDGv3 6
QD7 OAH 1.587 0.549 1.853 ETKDGv3 7
QD7 PAE 1.643 0.276 0.367 ETKDGv3 8
QD7 H1 -2.342 -0.641 -1.416 ETKDGv3 9
QD7 H2 -2.499 -1.378 0.219 ETKDGv3 10
QD7 H3 -1.168 0.517 1.204 ETKDGv3 11
QD7 H4 -1.010 1.256 -0.437 ETKDGv3 12
QD7 H5 0.196 -0.794 -1.245 ETKDGv3 13
QD7 H6 0.040 -1.533 0.397 ETKDGv3 14
QD7 H7 2.970 -1.742 0.548 ETKDGv3 15
QD7 H8 3.116 -0.980 -1.088 ETKDGv3 16
QD7 H9 4.002 -0.271 0.323 ETKDGv3 17
QD7 H10 -3.617 0.623 0.953 ETKDGv3 18
QD7 H11 -3.470 1.314 -0.582 ETKDGv3 19
QD7 H13 2.638 2.135 -0.141 ETKDGv3 20
#