data_PRJ
#
_chem_comp.id PRJ
_chem_comp.name '(2S,3aS,6R,7aS)-6-hydroxyoctahydro-1H-indole-2-carboxylic acid'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C9 H15 N O3'
_chem_comp.mon_nstd_parent_comp_id PRO
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-11-05
_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 185.220
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PRJ
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1A2C
_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
PRJ O O2 O 0 1 N N N Y N Y 15.522 -13.947 19.768 1.995 1.675 -0.223 O PRJ 1
PRJ N N5 N 0 1 N N N Y Y N 17.262 -14.761 21.976 0.419 0.071 1.214 N PRJ 2
PRJ C C7 C 0 1 N N N Y N Y 16.007 -13.108 20.529 2.501 0.610 0.044 C PRJ 3
PRJ CA C8 C 0 1 N N S Y N N 17.151 -13.511 21.311 1.665 -0.493 0.641 CA PRJ 4
PRJ CB C9 C 0 1 N N N N N N 18.536 -13.275 20.659 1.247 -1.489 -0.458 CB PRJ 5
PRJ CG C10 C 0 1 N N S N N N 19.539 -14.175 21.363 -0.307 -1.439 -0.472 CG PRJ 6
PRJ C11 C11 C 0 1 N N N N N N 20.841 -14.395 20.604 -0.702 -0.384 -1.507 C11 PRJ 7
PRJ C12 C12 C 0 1 N N N N N N 20.607 -15.131 19.215 -2.162 0.028 -1.332 C12 PRJ 8
PRJ C13 C13 C 0 1 N N R N N N 19.730 -16.368 19.498 -2.328 0.657 0.056 C13 PRJ 9
PRJ C14 C14 C 0 1 N N N N N N 18.328 -16.047 20.146 -2.020 -0.409 1.107 C14 PRJ 10
PRJ CD C15 C 0 1 N N S N N N 18.518 -15.334 21.587 -0.617 -0.947 0.953 CD PRJ 11
PRJ O2 OH2 O 0 1 N N N N N N 20.409 -17.461 20.107 -3.670 1.119 0.218 O2 PRJ 12
PRJ H HN5 H 0 1 N Y N Y Y N 17.233 -14.630 22.967 0.520 0.240 2.203 H PRJ 13
PRJ HA H8 H 0 1 N N N Y N N 16.865 -12.797 22.098 2.231 -1.008 1.417 HA PRJ 14
PRJ HB2 H9 H 0 1 N N N N N N 18.495 -13.521 19.588 1.645 -1.177 -1.424 HB2 PRJ 15
PRJ HB3 H9A H 0 1 N N N N N N 18.831 -12.221 20.771 1.593 -2.493 -0.212 HB3 PRJ 16
PRJ HG2 H10 H 0 1 N N N N N N 20.053 -13.845 22.278 -0.751 -2.414 -0.678 HG2 PRJ 17
PRJ H11 H11 H 0 1 N N N N N N 21.303 -13.416 20.409 -0.065 0.493 -1.387 H11 PRJ 18
PRJ H11A H11A H 0 0 N N N N N N 21.507 -15.015 21.222 -0.564 -0.793 -2.508 H11A PRJ 19
PRJ H12 H12 H 0 1 N N N N N N 20.100 -14.458 18.508 -2.432 0.754 -2.098 H12 PRJ 20
PRJ H12A H12A H 0 0 N N N N N N 21.569 -15.438 18.780 -2.802 -0.850 -1.414 H12A PRJ 21
PRJ H13 H13 H 0 1 N N N N N N 19.489 -16.734 18.489 -1.636 1.492 0.166 H13 PRJ 22
PRJ H14 H14 H 0 1 N N N N N N 17.770 -15.372 19.481 -2.128 0.027 2.100 H14 PRJ 23
PRJ H14A H14A H 0 0 N N N N N N 17.769 -16.985 20.279 -2.730 -1.230 1.001 H14A PRJ 24
PRJ HD2 H15 H 0 1 N N N N N N 18.860 -16.042 22.356 -0.472 -1.770 1.653 HD2 PRJ 25
PRJ HO2 HOH2 H 0 1 N N N N N N 19.799 -18.176 20.245 -3.937 1.786 -0.430 HO2 PRJ 26
PRJ OXT OXT O 0 1 N Y N Y N Y ? ? ? 3.807 0.410 -0.192 OXT PRJ 27
PRJ HXT HXT H 0 1 N Y N Y N Y ? ? ? 4.301 1.147 -0.576 HXT PRJ 28
#
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
PRJ O C DOUB N N 1
PRJ CA N SING N N 2
PRJ CD N SING N N 3
PRJ N H SING N N 4
PRJ C CA SING N N 5
PRJ CB CA SING N N 6
PRJ CA HA SING N N 7
PRJ CB CG SING N N 8
PRJ CB HB2 SING N N 9
PRJ CB HB3 SING N N 10
PRJ C11 CG SING N N 11
PRJ CG CD SING N N 12
PRJ CG HG2 SING N N 13
PRJ C12 C11 SING N N 14
PRJ C11 H11 SING N N 15
PRJ C11 H11A SING N N 16
PRJ C12 C13 SING N N 17
PRJ C12 H12 SING N N 18
PRJ C12 H12A SING N N 19
PRJ C13 O2 SING N N 20
PRJ C13 C14 SING N N 21
PRJ C13 H13 SING N N 22
PRJ C14 CD SING N N 23
PRJ C14 H14 SING N N 24
PRJ C14 H14A SING N N 25
PRJ CD HD2 SING N N 26
PRJ O2 HO2 SING N N 27
PRJ C OXT SING N N 28
PRJ OXT HXT SING N N 29
#
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
PRJ SMILES ACDLabs 12.01 'O=C(O)C1NC2CC(O)CCC2C1'
PRJ SMILES_CANONICAL CACTVS 3.370 'O[C@@H]1CC[C@H]2C[C@H](N[C@H]2C1)C(O)=O'
PRJ SMILES CACTVS 3.370 'O[CH]1CC[CH]2C[CH](N[CH]2C1)C(O)=O'
PRJ SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 'C1C[C@H](C[C@H]2[C@@H]1C[C@H](N2)C(=O)O)O'
PRJ SMILES 'OpenEye OEToolkits' 1.7.0 'C1CC(CC2C1CC(N2)C(=O)O)O'
PRJ InChI InChI 1.03 'InChI=1S/C9H15NO3/c11-6-2-1-5-3-8(9(12)13)10-7(5)4-6/h5-8,10-11H,1-4H2,(H,12,13)/t5-,6+,7-,8-/m0/s1'
PRJ InChIKey InChI 1.03 LKYGWJKCHDDFLW-YWIQKCBGSA-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
PRJ 'SYSTEMATIC NAME' ACDLabs 12.01 '(2S,3aS,6R,7aS)-6-hydroxyoctahydro-1H-indole-2-carboxylic acid'
PRJ 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 '(2S,3aS,6R,7aS)-6-hydroxy-2,3,3a,4,5,6,7,7a-octahydro-1H-indole-2-carboxylic 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
PRJ 'Other modification' 2010-11-05 ?
PRJ 'Other modification' 2010-12-07 RCSB
PRJ 'Modify descriptor' 2011-06-04 RCSB
PRJ 'Modify backbone' 2023-11-03 PDBE
PRJ 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PRJ
_pdbx_chem_comp_pcm.modified_residue_id PRO
_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 ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 1A2C
#
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
PRJ O O 12.247 1.595 1
PRJ N N 9.122 -0.912 2
PRJ C C 11.497 0.295 3
PRJ CA C 9.997 0.295 4
PRJ CB C 9.122 1.503 5
PRJ CG C 7.702 1.046 6
PRJ C11 C 6.404 1.796 7
PRJ C12 C 5.104 1.046 8
PRJ C13 C 5.104 -0.455 9
PRJ C14 C 6.404 -1.204 10
PRJ CD C 7.702 -0.455 11
PRJ O2 O 3.805 -1.204 12
PRJ OXT O 12.247 -1.004 13
#
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
PRJ O C DOUBLE NONE 1
PRJ CA N SINGLE NONE 2
PRJ CD N SINGLE NONE 3
PRJ CA C SINGLE BEGINWEDGE 4
PRJ CB CA SINGLE NONE 5
PRJ CB CG SINGLE NONE 6
PRJ C11 CG SINGLE NONE 7
PRJ CG CD SINGLE NONE 8
PRJ C12 C11 SINGLE NONE 9
PRJ C12 C13 SINGLE NONE 10
PRJ C13 O2 SINGLE BEGINDASH 11
PRJ C13 C14 SINGLE NONE 12
PRJ C14 CD SINGLE NONE 13
PRJ 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
PRJ MurckoScaffold S1 scaffold 'C1CC[C@@H]2NCC[C@@H]2C1' InChI=1S/C8H15N/c1-2-4-8-7(3-1)5-6-9-8/h7-9H,1-6H2/t7-,8-/m0/s1 PDELQDSYLBLPQO-YUMQZZPRSA-N
PRJ cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
PRJ peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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
PRJ N S1 1
PRJ CA S1 1
PRJ CB S1 1
PRJ CG S1 1
PRJ C11 S1 1
PRJ C12 S1 1
PRJ C13 S1 1
PRJ C14 S1 1
PRJ CD S1 1
PRJ CG F1 1
PRJ C11 F1 1
PRJ C12 F1 1
PRJ C13 F1 1
PRJ C14 F1 1
PRJ CD F1 1
PRJ O F2 1
PRJ C F2 1
PRJ CA F2 1
PRJ N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PRJ
_pdbe_chem_comp_rdkit_properties.exactmw 185.105
_pdbe_chem_comp_rdkit_properties.amw 185.223
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 28
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.889
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 98.253
_pdbe_chem_comp_rdkit_properties.tpsa 69.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.038
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.312
_pdbe_chem_comp_rdkit_properties.chi0v 6.172
_pdbe_chem_comp_rdkit_properties.chi1v 3.310
_pdbe_chem_comp_rdkit_properties.chi2v 1.430
_pdbe_chem_comp_rdkit_properties.chi3v 1.430
_pdbe_chem_comp_rdkit_properties.chi4v 0.909
_pdbe_chem_comp_rdkit_properties.chi0n 21.172
_pdbe_chem_comp_rdkit_properties.chi1n 10.573
_pdbe_chem_comp_rdkit_properties.chi2n 1.430
_pdbe_chem_comp_rdkit_properties.chi3n 1.430
_pdbe_chem_comp_rdkit_properties.chi4n 0.909
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.994
_pdbe_chem_comp_rdkit_properties.kappa2 3.270
_pdbe_chem_comp_rdkit_properties.kappa3 1.688
_pdbe_chem_comp_rdkit_properties.Phi 0.502
#
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
PRJ UniChem PDBe PRJ
PRJ UniChem PubChem 91034909
PRJ UniChem Nikkaji J1.256.055I
#
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
PRJ O 3.164 1.444 -0.828 ETKDGv3 1
PRJ N 0.912 1.268 0.840 ETKDGv3 2
PRJ C 3.217 0.766 0.234 ETKDGv3 3
PRJ CA 1.960 0.246 0.866 ETKDGv3 4
PRJ CB 1.423 -0.969 0.127 ETKDGv3 5
PRJ CG -0.066 -0.920 0.415 ETKDGv3 6
PRJ C11 -0.918 -1.569 -0.699 ETKDGv3 7
PRJ C12 -2.360 -1.065 -0.617 ETKDGv3 8
PRJ C13 -2.443 0.464 -0.852 ETKDGv3 9
PRJ C14 -1.129 1.216 -0.517 ETKDGv3 10
PRJ CD -0.368 0.574 0.655 ETKDGv3 11
PRJ O2 -3.528 1.012 -0.145 ETKDGv3 12
PRJ H 0.906 1.774 1.758 ETKDGv3 13
PRJ HA 2.175 -0.043 1.922 ETKDGv3 14
PRJ HB2 1.880 -1.910 0.503 ETKDGv3 15
PRJ HB3 1.616 -0.875 -0.965 ETKDGv3 16
PRJ HG2 -0.256 -1.469 1.366 ETKDGv3 17
PRJ H11 -0.514 -1.331 -1.708 ETKDGv3 18
PRJ H11A -0.902 -2.675 -0.580 ETKDGv3 19
PRJ H12 -2.771 -1.327 0.383 ETKDGv3 20
PRJ H12A -2.980 -1.591 -1.376 ETKDGv3 21
PRJ H13 -2.642 0.629 -1.934 ETKDGv3 22
PRJ H14 -0.471 1.209 -1.415 ETKDGv3 23
PRJ H14A -1.350 2.280 -0.283 ETKDGv3 24
PRJ HD2 -0.991 0.673 1.575 ETKDGv3 25
PRJ HO2 -3.327 0.930 0.823 ETKDGv3 26
PRJ OXT 4.451 0.464 0.802 ETKDGv3 27
PRJ HXT 5.311 0.794 0.381 ETKDGv3 28
#