data_9IJ
#
_chem_comp.id 9IJ
_chem_comp.name 2-cyano-L-phenylalanine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H10 N2 O2"
_chem_comp.mon_nstd_parent_comp_id PHE
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-10-18
_chem_comp.pdbx_modified_date 2023-11-03
_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 190.199
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9IJ
_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 7SJJ
_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
9IJ N N N 0 1 N N N Y Y N 8.929 0.932 -7.552 -1.120 0.956 -1.119 N 9IJ 1
9IJ CA CA C 0 1 N N S Y N N 9.648 0.715 -8.810 -1.402 -0.329 -0.465 CA 9IJ 2
9IJ C C C 0 1 N N N Y N Y 8.701 0.071 -9.813 -2.856 -0.385 -0.074 C 9IJ 3
9IJ CB CB C 0 1 N N N N N N 10.840 -0.203 -8.560 -0.532 -0.466 0.786 CB 9IJ 4
9IJ CG CG C 0 1 Y N N N N N 11.905 0.352 -7.649 0.919 -0.533 0.384 CG 9IJ 5
9IJ CD1 CD1 C 0 1 Y N N N N N 12.115 1.729 -7.463 1.536 -1.756 0.222 CD1 9IJ 6
9IJ CD2 CD2 C 0 1 Y N N N N N 12.792 -0.532 -7.022 1.641 0.643 0.168 CD2 9IJ 7
9IJ CE1 CE1 C 0 1 Y N N N N N 13.181 2.205 -6.703 2.868 -1.820 -0.147 CE1 9IJ 8
9IJ CE2 CE2 C 0 1 Y N N N N N 13.886 -0.047 -6.262 2.984 0.571 -0.205 CE2 9IJ 9
9IJ CZ CZ C 0 1 Y N N N N N 14.077 1.318 -6.116 3.590 -0.659 -0.357 CZ 9IJ 10
9IJ C01 C01 C 0 1 N N N N N N 12.567 -1.932 -7.140 1.005 1.916 0.327 C01 9IJ 11
9IJ N01 N01 N 0 1 N N N N N N 12.348 -3.062 -7.250 0.502 2.926 0.454 N01 9IJ 12
9IJ O O O 0 1 N N N Y N Y 8.180 -1.055 -9.533 -3.495 0.636 0.026 O 9IJ 13
9IJ H H H 0 1 N N N Y Y N 9.543 1.355 -6.885 -1.635 1.043 -1.983 H 9IJ 14
9IJ H2 H2 H 0 1 N Y N Y Y N 8.147 1.534 -7.715 -1.319 1.728 -0.501 H2 9IJ 15
9IJ HA HA H 0 1 N N N Y N N 10.006 1.674 -9.211 -1.179 -1.143 -1.154 HA 9IJ 16
9IJ HB2 HB2 H 0 1 N N N N N N 10.463 -1.134 -8.113 -0.689 0.396 1.434 HB2 9IJ 17
9IJ HB3 HB3 H 0 1 N N N N N N 11.306 -0.425 -9.531 -0.803 -1.377 1.319 HB3 9IJ 18
9IJ HD1 HD1 H 0 1 N N N N N N 11.435 2.433 -7.919 0.978 -2.667 0.385 HD1 9IJ 19
9IJ HE1 HE1 H 0 1 N N N N N N 13.312 3.269 -6.569 3.345 -2.780 -0.272 HE1 9IJ 20
9IJ HE2 HE2 H 0 1 N N N N N N 14.570 -0.741 -5.797 3.548 1.477 -0.373 HE2 9IJ 21
9IJ HZ HZ H 0 1 N N N N N N 14.917 1.691 -5.549 4.630 -0.716 -0.644 HZ 9IJ 22
9IJ OXT OXT O 0 1 N Y N Y N Y 8.490 0.676 -10.989 -3.442 -1.569 0.163 OXT 9IJ 23
9IJ HXT H1 H 0 1 N Y N Y N Y 7.920 0.137 -11.525 -4.377 -1.554 0.411 H1 9IJ 24
#
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
9IJ C O DOUB N N 1
9IJ C CA SING N N 2
9IJ CA CB SING N N 3
9IJ CA N SING N N 4
9IJ CB CG SING N N 5
9IJ CG CD1 DOUB Y N 6
9IJ CG CD2 SING Y N 7
9IJ CD1 CE1 SING Y N 8
9IJ N01 C01 TRIP N N 9
9IJ C01 CD2 SING N N 10
9IJ CD2 CE2 DOUB Y N 11
9IJ CE1 CZ DOUB Y N 12
9IJ CE2 CZ SING Y N 13
9IJ N H SING N N 14
9IJ N H2 SING N N 15
9IJ CA HA SING N N 16
9IJ CB HB2 SING N N 17
9IJ CB HB3 SING N N 18
9IJ CD1 HD1 SING N N 19
9IJ CE1 HE1 SING N N 20
9IJ CE2 HE2 SING N N 21
9IJ CZ HZ SING N N 22
9IJ C OXT SING N N 23
9IJ OXT HXT SING N N 24
#
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
9IJ SMILES ACDLabs 12.01 "NC(Cc1ccccc1C#N)C(=O)O"
9IJ InChI InChI 1.03 InChI=1S/C10H10N2O2/c11-6-8-4-2-1-3-7(8)5-9(12)10(13)14/h1-4,9H,5,12H2,(H,13,14)/t9-/m0/s1
9IJ InChIKey InChI 1.03 OCDHPLVCNWBKJN-VIFPVBQESA-N
9IJ SMILES_CANONICAL CACTVS 3.385 "N[C@@H](Cc1ccccc1C#N)C(O)=O"
9IJ SMILES CACTVS 3.385 "N[CH](Cc1ccccc1C#N)C(O)=O"
9IJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)C[C@@H](C(=O)O)N)C#N"
9IJ SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(c(c1)CC(C(=O)O)N)C#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
9IJ "SYSTEMATIC NAME" ACDLabs 12.01 2-cyano-L-phenylalanine
9IJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-3-(2-cyanophenyl)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
9IJ 'Create component' 2021-10-18 RCSB
9IJ 'Initial release' 2022-05-11 RCSB
9IJ 'Modify backbone' 2023-11-03 PDBE
#
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
9IJ N N 9.495 0.285 1
9IJ CA C 8.196 1.035 2
9IJ C C 8.196 2.535 3
9IJ CB C 6.897 0.285 4
9IJ CG C 6.897 -1.215 5
9IJ CD1 C 8.196 -1.965 6
9IJ CD2 C 5.598 -1.965 7
9IJ CE1 C 8.196 -3.465 8
9IJ CE2 C 5.598 -3.465 9
9IJ CZ C 6.897 -4.215 10
9IJ C01 C 4.299 -1.215 11
9IJ N01 N 3.000 -0.465 12
9IJ O O 9.495 3.285 13
9IJ OXT O 6.897 3.285 14
#
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
9IJ C O DOUBLE NONE 1
9IJ C CA SINGLE NONE 2
9IJ CA CB SINGLE NONE 3
9IJ CA N SINGLE BEGINWEDGE 4
9IJ CB CG SINGLE NONE 5
9IJ CG CD1 DOUBLE NONE 6
9IJ CG CD2 SINGLE NONE 7
9IJ CD1 CE1 SINGLE NONE 8
9IJ N01 C01 TRIPLE NONE 9
9IJ C01 CD2 SINGLE NONE 10
9IJ CD2 CE2 DOUBLE NONE 11
9IJ CE1 CZ DOUBLE NONE 12
9IJ CE2 CZ SINGLE NONE 13
9IJ C OXT SINGLE NONE 14
#
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
9IJ MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
9IJ peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
9IJ 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
9IJ CG S1 1
9IJ CD1 S1 1
9IJ CD2 S1 1
9IJ CE1 S1 1
9IJ CE2 S1 1
9IJ CZ S1 1
9IJ O F1 1
9IJ C F1 1
9IJ CA F1 1
9IJ N F1 1
9IJ CG F2 1
9IJ CD1 F2 1
9IJ CE1 F2 1
9IJ CZ F2 1
9IJ CE2 F2 1
9IJ CD2 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 9IJ
_pdbe_chem_comp_rdkit_properties.exactmw 190.074
_pdbe_chem_comp_rdkit_properties.amw 190.202
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_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 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 95.832
_pdbe_chem_comp_rdkit_properties.tpsa 87.110
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.403
_pdbe_chem_comp_rdkit_properties.CrippenMR 49.940
_pdbe_chem_comp_rdkit_properties.chi0v 6.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.355
_pdbe_chem_comp_rdkit_properties.chi2v 1.236
_pdbe_chem_comp_rdkit_properties.chi3v 1.236
_pdbe_chem_comp_rdkit_properties.chi4v 0.660
_pdbe_chem_comp_rdkit_properties.chi0n 16.711
_pdbe_chem_comp_rdkit_properties.chi1n 8.158
_pdbe_chem_comp_rdkit_properties.chi2n 1.236
_pdbe_chem_comp_rdkit_properties.chi3n 1.236
_pdbe_chem_comp_rdkit_properties.chi4n 0.660
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.860
_pdbe_chem_comp_rdkit_properties.kappa1 3.074
_pdbe_chem_comp_rdkit_properties.kappa2 4.397
_pdbe_chem_comp_rdkit_properties.kappa3 2.312
_pdbe_chem_comp_rdkit_properties.Phi 0.965
#
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
9IJ UniChem PDBe 9IJ
9IJ UniChem ZINC ZINC000002385773
9IJ UniChem eMolecules 6283256
9IJ UniChem Nikkaji J1.290.264F
9IJ UniChem 'EPA CompTox Dashboard' DTXSID80375804
9IJ UniChem ChemicalBook CB1188925
9IJ UniChem SureChEMBL SCHEMBL42647
9IJ UniChem PubChem 2761502
9IJ UniChem PubChem 7009702
9IJ UniChem ACTor 263396-42-5
#
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
9IJ N -1.267 -0.947 1.648 ETKDGv3 1
9IJ CA -1.493 0.176 0.733 ETKDGv3 2
9IJ C -2.962 0.485 0.619 ETKDGv3 3
9IJ CB -0.897 -0.127 -0.654 ETKDGv3 4
9IJ CG 0.605 -0.287 -0.586 ETKDGv3 5
9IJ CD1 1.143 -1.516 -0.471 ETKDGv3 6
9IJ CD2 1.510 0.904 -0.592 ETKDGv3 7
9IJ CE1 2.606 -1.690 -0.375 ETKDGv3 8
9IJ CE2 2.839 0.733 -0.500 ETKDGv3 9
9IJ CZ 3.410 -0.623 -0.390 ETKDGv3 10
9IJ C01 0.978 2.241 -0.692 ETKDGv3 11
9IJ N01 0.550 3.313 -0.772 ETKDGv3 12
9IJ O -3.769 -0.392 0.209 ETKDGv3 13
9IJ H -1.650 -0.695 2.589 ETKDGv3 14
9IJ H2 -1.792 -1.787 1.310 ETKDGv3 15
9IJ HA -0.982 1.073 1.148 ETKDGv3 16
9IJ HB2 -1.146 0.699 -1.355 ETKDGv3 17
9IJ HB3 -1.366 -1.045 -1.074 ETKDGv3 18
9IJ HD1 0.512 -2.396 -0.444 ETKDGv3 19
9IJ HE1 3.024 -2.684 -0.290 ETKDGv3 20
9IJ HE2 3.509 1.585 -0.504 ETKDGv3 21
9IJ HZ 4.483 -0.751 -0.318 ETKDGv3 22
9IJ OXT -3.430 1.750 0.961 ETKDGv3 23
9IJ HXT -4.414 1.978 0.887 ETKDGv3 24
#