data_NAL
#
_chem_comp.id NAL
_chem_comp.name 'BETA-(2-NAPHTHYL)-ALANINE'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C13 H13 N O2'
_chem_comp.mon_nstd_parent_comp_id ALA
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2024-09-27
_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 215.248
_chem_comp.one_letter_code A
_chem_comp.three_letter_code NAL
_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 2ITK
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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
NAL C1 C1 C 0 1 Y N N N N N 40.838 28.486 22.485 -0.616 0.617 -0.580 C1 NAL 1
NAL C2 C2 C 0 1 Y N N N N N 39.512 28.736 22.947 0.209 -0.463 -0.507 C2 NAL 2
NAL C3 C3 C 0 1 Y N N N N N 38.444 28.060 22.265 -0.277 -1.713 -0.129 C3 NAL 3
NAL C4 C4 C 0 1 Y N N N N N 38.645 27.166 21.158 -1.592 -1.890 0.178 C4 NAL 4
NAL C4A C4A C 0 1 Y N N N N N 39.985 26.941 20.710 -2.474 -0.799 0.113 C4A NAL 5
NAL C5 C5 C 0 1 Y N N N N N 40.308 26.077 19.612 -3.837 -0.943 0.422 C5 NAL 6
NAL C6 C6 C 0 1 Y N N N N N 41.647 25.860 19.177 -4.662 0.137 0.348 C6 NAL 7
NAL C7 C7 C 0 1 Y N N N N N 42.712 26.529 19.849 -4.176 1.387 -0.030 C7 NAL 8
NAL C8 C8 C 0 1 Y N N N N N 42.483 27.414 20.956 -2.862 1.564 -0.337 C8 NAL 9
NAL C8A C8A C 0 1 Y N N N N N 41.111 27.613 21.374 -1.978 0.474 -0.266 C8A NAL 10
NAL C9 C9 C 0 1 N N N N N N 39.099 29.637 24.117 1.670 -0.304 -0.839 C9 NAL 11
NAL CA CA C 0 1 N N S Y N N 39.037 28.749 25.417 2.446 0.058 0.429 CA NAL 12
NAL C C C 0 1 N N N Y N Y 39.308 29.631 26.639 3.921 0.096 0.122 C NAL 13
NAL N N N 0 1 N N N Y Y N 37.817 27.857 25.721 2.011 1.377 0.908 N NAL 14
NAL O O O 0 1 N N N Y N Y 38.129 30.095 27.173 4.471 1.155 -0.068 O NAL 15
NAL OXT OXT O 0 1 N Y N Y N Y 40.467 29.850 27.268 4.623 -1.046 0.059 OXT NAL 16
NAL H1 H1 H 0 1 N N N N N N 41.665 28.968 22.986 -0.225 1.580 -0.874 H1 NAL 17
NAL H3 H3 H 0 1 N N N N N N 37.433 28.233 22.603 0.399 -2.553 -0.078 H3 NAL 18
NAL H4 H4 H 0 1 N N N N N N 37.809 26.678 20.678 -1.954 -2.865 0.468 H4 NAL 19
NAL H5 H5 H 0 1 N N N N N N 39.506 25.572 19.095 -4.228 -1.906 0.716 H5 NAL 20
NAL H6 H6 H 0 1 N N N N N N 41.853 25.198 18.349 -5.710 0.023 0.586 H6 NAL 21
NAL H7 H7 H 0 1 N N N N N N 43.725 26.364 19.514 -4.852 2.227 -0.081 H7 NAL 22
NAL H8 H8 H 0 1 N N N N N N 43.301 27.911 21.457 -2.500 2.539 -0.629 H8 NAL 23
NAL H91 H91 H 0 1 N N N N N N 39.835 30.444 24.248 2.054 -1.240 -1.245 H91 NAL 24
NAL H92 H92 H 0 1 N N N N N N 38.113 30.082 23.919 1.791 0.488 -1.578 H92 NAL 25
NAL HA HA H 0 1 N N N Y N N 39.807 27.998 25.189 2.254 -0.690 1.198 HA NAL 26
NAL H H H 0 1 N N N Y Y N 37.964 27.374 26.584 2.462 1.611 1.780 H NAL 27
NAL H2 H2 H 0 1 N Y N Y Y N 36.998 28.426 25.793 2.179 2.088 0.212 H2 NAL 28
NAL HXT HXT H 0 1 N Y N Y N Y 40.307 30.338 28.067 5.566 -0.971 -0.140 HXT NAL 29
#
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
NAL C6 C5 DOUB Y N 1
NAL C6 C7 SING Y N 2
NAL C5 C4A SING Y N 3
NAL C7 C8 DOUB Y N 4
NAL C4A C4 DOUB Y N 5
NAL C4A C8A SING Y N 6
NAL C8 C8A SING Y N 7
NAL C4 C3 SING Y N 8
NAL C8A C1 DOUB Y N 9
NAL C3 C2 DOUB Y N 10
NAL C1 C2 SING Y N 11
NAL C2 C9 SING N N 12
NAL C9 CA SING N N 13
NAL CA N SING N N 14
NAL CA C SING N N 15
NAL C O DOUB N N 16
NAL C OXT SING N N 17
NAL C1 H1 SING N N 18
NAL C3 H3 SING N N 19
NAL C4 H4 SING N N 20
NAL C5 H5 SING N N 21
NAL C6 H6 SING N N 22
NAL C7 H7 SING N N 23
NAL C8 H8 SING N N 24
NAL C9 H91 SING N N 25
NAL C9 H92 SING N N 26
NAL CA HA SING N N 27
NAL N H SING N N 28
NAL N H2 SING N N 29
NAL OXT HXT SING N N 30
#
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
NAL SMILES ACDLabs 12.01 'O=C(O)C(N)Cc2ccc1c(cccc1)c2'
NAL SMILES_CANONICAL CACTVS 3.370 'N[C@@H](Cc1ccc2ccccc2c1)C(O)=O'
NAL SMILES CACTVS 3.370 'N[CH](Cc1ccc2ccccc2c1)C(O)=O'
NAL SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'c1ccc2cc(ccc2c1)C[C@@H](C(=O)O)N'
NAL SMILES 'OpenEye OEToolkits' 1.7.0 'c1ccc2cc(ccc2c1)CC(C(=O)O)N'
NAL InChI InChI 1.03 'InChI=1S/C13H13NO2/c14-12(13(15)16)8-9-5-6-10-3-1-2-4-11(10)7-9/h1-7,12H,8,14H2,(H,15,16)/t12-/m0/s1'
NAL InChIKey InChI 1.03 JPZXHKDZASGCLU-LBPRGKRZSA-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
NAL 'SYSTEMATIC NAME' ACDLabs 12.01 '(2S)-2-amino-3-(naphthalen-2-yl)propanoic acid (non-preferred name)'
NAL 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 '(2S)-2-azanyl-3-naphthalen-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
NAL 'Create component' 1999-07-08 RCSB
NAL 'Modify aromatic_flag' 2011-06-04 RCSB
NAL 'Modify descriptor' 2011-06-04 RCSB
NAL 'Modify backbone' 2023-11-03 PDBE
NAL 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id NAL
_pdbx_chem_comp_pcm.modified_residue_id ?
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id NAL
_pdbe_chem_comp_drugbank_details.drugbank_id DB01766
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Beta-(2-Naphthyl)-Alanine
_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 NAL
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01766
_pdbe_chem_comp_drugbank_classification.parent Naphthalenes
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Naphthalenes
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as naphthalenes. These are compounds containing a naphthalene moiety, which consists of two fused benzene rings.'
#
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
NAL DB01766 'Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1' Humans Q13526 yes 1
NAL DB01766 Prothrombin Humans P00734 yes 2
NAL DB01766 'Tyrosine--tRNA ligase, cytoplasmic' Humans P54577 unknown 3
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
NAL C1 C 10.301 -0.776 1
NAL C2 C 9.002 -0.026 2
NAL C3 C 9.002 1.474 3
NAL C4 C 10.301 2.224 4
NAL C4A C 11.600 1.474 5
NAL C5 C 12.941 2.276 6
NAL C6 C 14.300 1.505 7
NAL C7 C 14.300 -0.057 8
NAL C8 C 12.941 -0.828 9
NAL C8A C 11.600 -0.026 10
NAL C9 C 7.702 -0.776 11
NAL CA C 6.404 -0.026 12
NAL C C 5.104 -0.776 13
NAL N N 6.404 1.474 14
NAL O O 3.805 -0.026 15
NAL OXT O 5.104 -2.276 16
#
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
NAL C6 C5 DOUBLE NONE 1
NAL C6 C7 SINGLE NONE 2
NAL C5 C4A SINGLE NONE 3
NAL C7 C8 DOUBLE NONE 4
NAL C4A C4 DOUBLE NONE 5
NAL C4A C8A SINGLE NONE 6
NAL C8 C8A SINGLE NONE 7
NAL C4 C3 SINGLE NONE 8
NAL C8A C1 DOUBLE NONE 9
NAL C3 C2 DOUBLE NONE 10
NAL C1 C2 SINGLE NONE 11
NAL C2 C9 SINGLE NONE 12
NAL C9 CA SINGLE NONE 13
NAL CA N SINGLE BEGINWEDGE 14
NAL CA C SINGLE NONE 15
NAL C O DOUBLE NONE 16
NAL C OXT SINGLE NONE 17
#
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
NAL MurckoScaffold S1 scaffold c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
NAL napthalene F1 fragment c1ccc2ccccc2c1 InChI=1S/C10H8/c1-2-6-10-8-4-3-7-9(10)5-1/h1-8H UFWIBTONFRDIAS-UHFFFAOYSA-N
NAL peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
NAL phenyl F3 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
NAL C1 S1 1
NAL C2 S1 1
NAL C3 S1 1
NAL C4 S1 1
NAL C4A S1 1
NAL C5 S1 1
NAL C6 S1 1
NAL C7 S1 1
NAL C8 S1 1
NAL C8A S1 1
NAL C2 F1 1
NAL C3 F1 1
NAL C4 F1 1
NAL C4A F1 1
NAL C8A F1 1
NAL C1 F1 1
NAL C8 F1 1
NAL C7 F1 1
NAL C6 F1 1
NAL C5 F1 1
NAL O F2 1
NAL C F2 1
NAL CA F2 1
NAL N F2 1
NAL C1 F3 1
NAL C8A F3 1
NAL C4A F3 1
NAL C4 F3 1
NAL C3 F3 1
NAL C2 F3 1
NAL C4A F3 2
NAL C5 F3 2
NAL C6 F3 2
NAL C7 F3 2
NAL C8 F3 2
NAL C8A F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id NAL
_pdbe_chem_comp_rdkit_properties.exactmw 215.095
_pdbe_chem_comp_rdkit_properties.amw 215.252
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.154
_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 111.971
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.311
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.791
_pdbe_chem_comp_rdkit_properties.chi0v 7.764
_pdbe_chem_comp_rdkit_properties.chi1v 4.132
_pdbe_chem_comp_rdkit_properties.chi2v 1.687
_pdbe_chem_comp_rdkit_properties.chi3v 1.687
_pdbe_chem_comp_rdkit_properties.chi4v 1.013
_pdbe_chem_comp_rdkit_properties.chi0n 20.764
_pdbe_chem_comp_rdkit_properties.chi1n 10.435
_pdbe_chem_comp_rdkit_properties.chi2n 1.687
_pdbe_chem_comp_rdkit_properties.chi3n 1.687
_pdbe_chem_comp_rdkit_properties.chi4n 1.013
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.870
_pdbe_chem_comp_rdkit_properties.kappa1 3.078
_pdbe_chem_comp_rdkit_properties.kappa2 4.327
_pdbe_chem_comp_rdkit_properties.kappa3 2.201
_pdbe_chem_comp_rdkit_properties.Phi 0.833
#
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
NAL UniChem DrugBank DB01766
NAL UniChem ChEBI 44170
NAL UniChem ZINC ZINC000000128256
NAL UniChem eMolecules 592711
NAL UniChem fdasrs W425Q6KV9R
NAL UniChem ACTor 58438-03-2
NAL UniChem Nikkaji J353.121J
NAL UniChem BRENDA 144708
NAL UniChem BRENDA 175733
NAL UniChem BRENDA 203527
NAL UniChem BRENDA 224778
NAL UniChem ChemicalBook CB5853881
NAL UniChem 'Probes And Drugs' PD008440
NAL UniChem SureChEMBL SCHEMBL93303
NAL UniChem 'PubChem TPHARMA' 15195828
NAL UniChem PubChem 185915
NAL UniChem PubChem 6927613
#
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
NAL C1 0.409 -0.533 -0.780 ETKDGv3 1
NAL C2 -0.386 0.653 -0.371 ETKDGv3 2
NAL C3 0.215 1.655 0.296 ETKDGv3 3
NAL C4 1.660 1.590 0.603 ETKDGv3 4
NAL C4A 2.377 0.522 0.226 ETKDGv3 5
NAL C5 3.820 0.415 0.515 ETKDGv3 6
NAL C6 4.505 -0.670 0.129 ETKDGv3 7
NAL C7 3.848 -1.785 -0.592 ETKDGv3 8
NAL C8 2.543 -1.756 -0.889 ETKDGv3 9
NAL C8A 1.719 -0.594 -0.498 ETKDGv3 10
NAL C9 -1.865 0.699 -0.656 ETKDGv3 11
NAL CA -2.683 0.192 0.545 ETKDGv3 12
NAL C -4.157 0.368 0.290 ETKDGv3 13
NAL N -2.369 -1.210 0.830 ETKDGv3 14
NAL O -4.718 -0.244 -0.659 ETKDGv3 15
NAL OXT -4.903 1.214 1.104 ETKDGv3 16
NAL H1 -0.076 -1.348 -1.305 ETKDGv3 17
NAL H3 -0.352 2.519 0.621 ETKDGv3 18
NAL H4 2.126 2.411 1.135 ETKDGv3 19
NAL H5 4.333 1.211 1.041 ETKDGv3 20
NAL H6 5.563 -0.737 0.347 ETKDGv3 21
NAL H7 4.442 -2.642 -0.885 ETKDGv3 22
NAL H8 2.096 -2.590 -1.417 ETKDGv3 23
NAL H91 -2.162 1.745 -0.894 ETKDGv3 24
NAL H92 -2.092 0.087 -1.556 ETKDGv3 25
NAL HA -2.411 0.802 1.435 ETKDGv3 26
NAL H -2.912 -1.512 1.672 ETKDGv3 27
NAL H2 -2.674 -1.809 0.028 ETKDGv3 28
NAL HXT -5.895 1.346 0.946 ETKDGv3 29
#