data_NPX
#
_chem_comp.id NPX
_chem_comp.name "(2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H14 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms (R)-Naproxen
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-10-04
_chem_comp.pdbx_modified_date 2021-03-01
_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 230.259
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NPX
_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 2VDB
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
NPX C1 C1 C 0 1 Y N N N N N 15.312 -5.298 28.011 -3.398 -0.235 -0.054 C1 NPX 1
NPX O2 O2 O 0 1 N N N N N N 16.079 -6.434 27.907 -4.687 -0.659 -0.119 O2 NPX 2
NPX C2 C2 C 0 1 Y N N N N N 15.594 -4.172 27.235 -3.111 1.126 -0.202 C2 NPX 3
NPX C3 C3 C 0 1 Y N N N N N 14.810 -3.027 27.347 -1.831 1.581 -0.141 C3 NPX 4
NPX C4 C4 C 0 1 Y N N N N N 13.729 -2.989 28.233 -0.778 0.674 0.073 C4 NPX 5
NPX C5 C5 C 0 1 Y N N N N N 13.425 -4.188 29.060 -1.066 -0.705 0.224 C5 NPX 6
NPX C6 C6 C 0 1 Y N N N N N 14.240 -5.305 28.918 -2.399 -1.142 0.162 C6 NPX 7
NPX C7 C7 C 0 1 Y N N N N N 12.921 -1.861 28.370 0.556 1.111 0.141 C7 NPX 8
NPX C8 C8 C 0 1 Y N N N N N 11.849 -1.856 29.275 1.551 0.206 0.350 C8 NPX 9
NPX C9 C9 C 0 1 N N R N N N 10.994 -0.626 29.355 2.981 0.678 0.422 C9 NPX 10
NPX C10 C10 C 0 1 N N N N N N 9.520 -1.028 29.283 3.568 0.317 1.788 C10 NPX 11
NPX C13 C13 C 0 1 Y N N N N N 12.348 -4.154 29.947 -0.012 -1.610 0.439 C13 NPX 12
NPX C11 C11 C 0 1 Y N N N N N 11.566 -2.996 30.043 1.268 -1.151 0.498 C11 NPX 13
NPX C12 C12 C 0 1 N N N N N N 17.007 -6.625 26.851 -5.687 0.336 -0.340 C12 NPX 14
NPX O O O 0 1 N N N N N N 11.469 1.472 30.312 5.094 0.281 -0.791 O NPX 15
NPX OXT OXT O 0 1 N N N N N N 11.079 -0.177 31.699 3.253 -0.769 -1.418 OXT NPX 16
NPX C15 C15 C 0 1 N N N N N N 11.200 0.274 30.544 3.786 0.010 -0.663 C15 NPX 17
NPX H2 H2 H 0 1 N N N N N N 16.424 -4.189 26.545 -3.917 1.825 -0.368 H2 NPX 18
NPX H6 H6 H 0 1 N N N N N N 14.047 -6.187 29.511 -2.634 -2.190 0.280 H6 NPX 19
NPX H121 H121 H 0 0 N N N N N N 17.504 -7.599 26.971 -6.669 -0.135 -0.371 H121 NPX 20
NPX H122 H122 H 0 0 N N N N N N 16.476 -6.600 25.888 -5.660 1.066 0.469 H122 NPX 21
NPX H123 H123 H 0 0 N N N N N N 17.760 -5.824 26.876 -5.496 0.839 -1.289 H123 NPX 22
NPX H3 H3 H 0 1 N N N N N N 15.039 -2.161 26.744 -1.624 2.635 -0.258 H3 NPX 23
NPX H7 H7 H 0 1 N N N N N N 13.122 -0.983 27.774 0.791 2.159 0.027 H7 NPX 24
NPX H13 H13 H 0 1 N N N N N N 12.119 -5.016 30.556 -0.216 -2.664 0.555 H13 NPX 25
NPX H9 H9 H 0 1 N N N N N N 11.315 -0.021 28.494 3.014 1.758 0.286 H9 NPX 26
NPX H11 H11 H 0 1 N N N N N N 10.727 -2.980 30.723 2.076 -1.848 0.663 H11 NPX 27
NPX H101 H101 H 0 0 N N N N N N 8.891 -0.128 29.341 4.602 0.658 1.840 H101 NPX 28
NPX H102 H102 H 0 0 N N N N N N 9.328 -1.548 28.333 2.986 0.800 2.573 H102 NPX 29
NPX H103 H103 H 0 0 N N N N N N 9.281 -1.697 30.123 3.535 -0.764 1.924 H103 NPX 30
NPX H H H 0 1 N N N N N N 11.558 1.942 31.133 5.568 -0.172 -1.502 H NPX 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
NPX C1 O2 SING N N 1
NPX C1 C2 SING Y N 2
NPX C1 C6 DOUB Y N 3
NPX O2 C12 SING N N 4
NPX C2 C3 DOUB Y N 5
NPX C3 C4 SING Y N 6
NPX C4 C5 DOUB Y N 7
NPX C4 C7 SING Y N 8
NPX C5 C6 SING Y N 9
NPX C5 C13 SING Y N 10
NPX C7 C8 DOUB Y N 11
NPX C8 C9 SING N N 12
NPX C8 C11 SING Y N 13
NPX C9 C10 SING N N 14
NPX C9 C15 SING N N 15
NPX C13 C11 DOUB Y N 16
NPX O C15 SING N N 17
NPX OXT C15 DOUB N N 18
NPX C2 H2 SING N N 19
NPX C6 H6 SING N N 20
NPX C12 H121 SING N N 21
NPX C12 H122 SING N N 22
NPX C12 H123 SING N N 23
NPX C3 H3 SING N N 24
NPX C7 H7 SING N N 25
NPX C13 H13 SING N N 26
NPX C9 H9 SING N N 27
NPX C11 H11 SING N N 28
NPX C10 H101 SING N N 29
NPX C10 H102 SING N N 30
NPX C10 H103 SING N N 31
NPX O H 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
NPX SMILES ACDLabs 12.01 O=C(O)C(c1ccc2c(c1)ccc(OC)c2)C
NPX InChI InChI 1.03 InChI=1S/C14H14O3/c1-9(14(15)16)10-3-4-12-8-13(17-2)6-5-11(12)7-10/h3-9H,1-2H3,(H,15,16)/t9-/m1/s1
NPX InChIKey InChI 1.03 CMWTZPSULFXXJA-SECBINFHSA-N
NPX SMILES_CANONICAL CACTVS 3.370 COc1ccc2cc(ccc2c1)[C@@H](C)C(O)=O
NPX SMILES CACTVS 3.370 COc1ccc2cc(ccc2c1)[CH](C)C(O)=O
NPX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C[C@H](c1ccc2cc(ccc2c1)OC)C(=O)O
NPX SMILES "OpenEye OEToolkits" 1.7.2 CC(c1ccc2cc(ccc2c1)OC)C(=O)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
NPX "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-(6-methoxynaphthalen-2-yl)propanoic acid"
NPX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(2R)-2-(6-methoxynaphthalen-2-yl)propanoic 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
NPX 'Create component' 2007-10-04 EBI
NPX 'Modify aromatic_flag' 2011-06-04 RCSB
NPX 'Modify descriptor' 2011-06-04 RCSB
NPX 'Modify synonyms' 2011-11-03 RCSB
NPX 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id NPX
_pdbx_chem_comp_synonyms.name (R)-Naproxen
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id NPX
_pdbe_chem_comp_synonyms.name (R)-Naproxen
_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
NPX C1 C 13.001 1.505 1
NPX O2 O 14.297 2.260 2
NPX C2 C 13.001 -0.057 3
NPX C3 C 11.642 -0.828 4
NPX C4 C 10.301 -0.026 5
NPX C5 C 10.301 1.474 6
NPX C6 C 11.642 2.276 7
NPX C7 C 9.002 -0.776 8
NPX C8 C 7.702 -0.026 9
NPX C9 C 6.404 -0.776 10
NPX C10 C 6.404 -2.276 11
NPX C13 C 9.002 2.224 12
NPX C11 C 7.702 1.474 13
NPX C12 C 15.599 1.515 14
NPX O O 3.805 -0.776 15
NPX OXT O 5.104 1.474 16
NPX C15 C 5.104 -0.026 17
#
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
NPX C1 O2 SINGLE NONE 1
NPX C1 C2 DOUBLE NONE 2
NPX C1 C6 SINGLE NONE 3
NPX O2 C12 SINGLE NONE 4
NPX C2 C3 SINGLE NONE 5
NPX C3 C4 DOUBLE NONE 6
NPX C4 C5 SINGLE NONE 7
NPX C4 C7 SINGLE NONE 8
NPX C5 C6 DOUBLE NONE 9
NPX C5 C13 SINGLE NONE 10
NPX C7 C8 DOUBLE NONE 11
NPX C8 C9 SINGLE NONE 12
NPX C8 C11 SINGLE NONE 13
NPX C9 C10 SINGLE BEGINWEDGE 14
NPX C9 C15 SINGLE NONE 15
NPX C13 C11 DOUBLE NONE 16
NPX O C15 SINGLE NONE 17
NPX OXT C15 DOUBLE NONE 18
#
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
NPX MurckoScaffold S1 scaffold c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
NPX napthalene F1 fragment c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
NPX phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
NPX C1 S1 1
NPX C2 S1 1
NPX C3 S1 1
NPX C4 S1 1
NPX C5 S1 1
NPX C6 S1 1
NPX C7 S1 1
NPX C8 S1 1
NPX C13 S1 1
NPX C11 S1 1
NPX C1 F1 1
NPX C2 F1 1
NPX C3 F1 1
NPX C4 F1 1
NPX C5 F1 1
NPX C6 F1 1
NPX C13 F1 1
NPX C11 F1 1
NPX C8 F1 1
NPX C7 F1 1
NPX C1 F2 1
NPX C2 F2 1
NPX C3 F2 1
NPX C4 F2 1
NPX C5 F2 1
NPX C6 F2 1
NPX C4 F2 2
NPX C5 F2 2
NPX C13 F2 2
NPX C11 F2 2
NPX C8 F2 2
NPX C7 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id NPX
_pdbe_chem_comp_rdkit_properties.exactmw 230.094
_pdbe_chem_comp_rdkit_properties.amw 230.263
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.214
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 119.398
_pdbe_chem_comp_rdkit_properties.tpsa 46.530
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.091
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.469
_pdbe_chem_comp_rdkit_properties.chi0v 8.225
_pdbe_chem_comp_rdkit_properties.chi1v 4.316
_pdbe_chem_comp_rdkit_properties.chi2v 1.908
_pdbe_chem_comp_rdkit_properties.chi3v 1.908
_pdbe_chem_comp_rdkit_properties.chi4v 1.136
_pdbe_chem_comp_rdkit_properties.chi0n 22.225
_pdbe_chem_comp_rdkit_properties.chi1n 11.225
_pdbe_chem_comp_rdkit_properties.chi2n 1.908
_pdbe_chem_comp_rdkit_properties.chi3n 1.908
_pdbe_chem_comp_rdkit_properties.chi4n 1.136
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.030
_pdbe_chem_comp_rdkit_properties.kappa1 3.253
_pdbe_chem_comp_rdkit_properties.kappa2 4.454
_pdbe_chem_comp_rdkit_properties.kappa3 2.228
_pdbe_chem_comp_rdkit_properties.Phi 0.852
#
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
NPX UniChem ChEMBL CHEMBL1618254
NPX UniChem PDBe NPX
NPX UniChem ChEBI 94583
NPX UniChem ZINC ZINC000000113439
NPX UniChem fdasrs 484XV9323P
NPX UniChem LINCS LSM-5472
NPX UniChem Nikkaji J242.711G
NPX UniChem BindingDb 50533571
NPX UniChem BRENDA 134002
NPX UniChem ChemicalBook CB2753351
NPX UniChem 'Probes And Drugs' PD087093
NPX UniChem eMolecules 522636
NPX UniChem SureChEMBL SCHEMBL42434
NPX UniChem 'PubChem TPHARMA' 14798154
NPX UniChem PubChem 169118
NPX UniChem Mcule MCULE-2427044065
NPX UniChem ACTor 31482-07-2
#
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
NPX C1 3.119 0.276 1.170 ETKDGv3 1
NPX O2 4.501 0.274 1.403 ETKDGv3 2
NPX C2 2.319 0.876 2.065 ETKDGv3 3
NPX C3 0.855 0.906 1.865 ETKDGv3 4
NPX C4 0.315 0.330 0.781 ETKDGv3 5
NPX C5 1.187 -0.336 -0.214 ETKDGv3 6
NPX C6 2.517 -0.363 -0.033 ETKDGv3 7
NPX C7 -1.142 0.338 0.546 ETKDGv3 8
NPX C8 -1.666 -0.245 -0.553 ETKDGv3 9
NPX C9 -3.163 -0.244 -0.797 ETKDGv3 10
NPX C10 -3.903 -1.056 0.274 ETKDGv3 11
NPX C13 0.553 -0.957 -1.390 ETKDGv3 12
NPX C11 -0.776 -0.913 -1.545 ETKDGv3 13
NPX C12 5.452 -0.328 0.532 ETKDGv3 14
NPX O -4.084 1.851 0.253 ETKDGv3 15
NPX OXT -3.734 1.740 -2.012 ETKDGv3 16
NPX C15 -3.690 1.163 -0.892 ETKDGv3 17
NPX H2 2.742 1.345 2.944 ETKDGv3 18
NPX H6 3.148 -0.852 -0.764 ETKDGv3 19
NPX H121 5.253 -1.417 0.443 ETKDGv3 20
NPX H122 6.469 -0.185 0.951 ETKDGv3 21
NPX H123 5.409 0.152 -0.469 ETKDGv3 22
NPX H3 0.230 1.396 2.602 ETKDGv3 23
NPX H7 -1.789 0.821 1.268 ETKDGv3 24
NPX H13 1.160 -1.454 -2.137 ETKDGv3 25
NPX H9 -3.374 -0.742 -1.769 ETKDGv3 26
NPX H11 -1.210 -1.381 -2.420 ETKDGv3 27
NPX H101 -4.990 -1.085 0.043 ETKDGv3 28
NPX H102 -3.766 -0.615 1.284 ETKDGv3 29
NPX H103 -3.522 -2.099 0.288 ETKDGv3 30
NPX H -4.422 2.804 0.196 ETKDGv3 31
#