data_P1V
#
_chem_comp.id P1V
_chem_comp.name '(2~{S})-2-azanyl-6-(5-methyl-1~{H}-1,2,4-triazol-3-yl)hexanoic acid'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C9 H16 N4 O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-29
_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 212.249
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code P1V
_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 8B5C
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_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
P1V C4 C4 C 0 1 N N N N N N -15.627 10.409 -7.763 1.467 -0.253 1.192 C4 P1V 1
P1V C5 C5 C 0 1 N N N N N N -15.383 9.939 -6.342 0.352 0.106 0.208 C5 P1V 2
P1V C6 C6 C 0 1 N N N N N N -16.575 10.223 -5.455 -1.006 -0.211 0.837 C6 P1V 3
P1V C7 C7 C 0 1 N N N N N N -16.461 9.530 -4.113 -2.121 0.149 -0.147 C7 P1V 4
P1V N1 N1 N 0 1 Y N N N N N -12.523 10.727 -9.457 4.635 1.058 -0.054 N1 P1V 5
P1V N2 N2 N 0 1 Y N N N N N -13.551 11.276 -8.763 3.437 1.199 0.665 N2 P1V 6
P1V C3 C3 C 0 1 N N N N N N -11.799 8.479 -10.272 5.720 -0.811 -1.392 C3 P1V 7
P1V N3 N3 N 0 1 Y N N N N N -13.852 9.100 -8.973 3.530 -0.779 -0.167 N3 P1V 8
P1V N N N 0 1 N N N Y Y N -16.907 11.625 -2.932 -3.596 -1.618 0.691 N P1V 9
P1V CA CA C 0 1 N N S Y N N -17.327 10.207 -3.061 -3.479 -0.168 0.483 CA P1V 10
P1V C C C 0 1 N N N Y N Y -17.199 9.451 -1.740 -4.580 0.298 -0.435 C P1V 11
P1V O O O 0 1 N N N Y N Y -17.405 8.223 -1.780 -5.146 -0.494 -1.150 O P1V 12
P1V C1 C1 C 0 1 Y N N N N N -12.722 9.422 -9.586 4.635 -0.192 -0.548 C1 P1V 13
P1V C2 C2 C 0 1 Y N N N N N -14.357 10.273 -8.505 2.804 0.060 0.572 C2 P1V 14
P1V H1 H1 H 0 1 N N N N N N -15.948 11.461 -7.760 1.346 0.328 2.106 H1 P1V 15
P1V H17 H2 H 0 1 N N N N N N -16.404 9.790 -8.234 1.415 -1.316 1.428 H2 P1V 16
P1V H3 H3 H 0 1 N N N N N N -15.193 8.855 -6.351 0.404 1.169 -0.028 H3 P1V 17
P1V H4 H4 H 0 1 N N N N N N -14.504 10.462 -5.938 0.473 -0.475 -0.706 H4 P1V 18
P1V H5 H5 H 0 1 N N N N N N -16.644 11.308 -5.290 -1.058 -1.273 1.073 H5 P1V 19
P1V H6 H6 H 0 1 N N N N N N -17.486 9.870 -5.961 -1.127 0.371 1.752 H6 P1V 20
P1V H7 H7 H 0 1 N N N N N N -16.783 8.484 -4.222 -2.069 1.212 -0.382 H7 P1V 21
P1V H8 H8 H 0 1 N N N N N N -15.412 9.558 -3.784 -2.000 -0.433 -1.061 H8 P1V 22
P1V H9 H9 H 0 1 N N N N N N -11.736 11.229 -9.816 5.324 1.731 -0.175 H9 P1V 23
P1V H10 H10 H 0 1 N N N N N N -12.196 7.456 -10.196 6.452 -1.294 -0.745 H10 P1V 24
P1V H11 H11 H 0 1 N N N N N N -11.709 8.760 -11.332 5.282 -1.550 -2.062 H11 P1V 25
P1V H12 H12 H 0 1 N N N N N N -10.809 8.524 -9.796 6.211 -0.034 -1.979 H12 P1V 26
P1V H H13 H 0 1 N N N Y Y N -17.471 12.079 -2.242 -4.457 -1.847 1.164 H13 P1V 27
P1V H2 H14 H 0 1 N Y N Y Y N -15.947 11.664 -2.656 -3.521 -2.116 -0.184 H14 P1V 28
P1V HA H16 H 0 1 N N N Y N N -18.376 10.168 -3.389 -3.563 0.344 1.441 H16 P1V 29
P1V OXT O1 O 0 1 N Y N Y N Y -16.885 10.124 -0.643 -4.930 1.594 -0.458 O1 P1V 30
P1V HXT H15 H 0 1 N Y N Y N Y -16.844 9.527 0.095 -5.641 1.845 -1.063 H15 P1V 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
P1V C3 C1 SING N N 1
P1V C1 N1 SING Y N 2
P1V C1 N3 DOUB Y N 3
P1V N1 N2 SING Y N 4
P1V N3 C2 SING Y N 5
P1V N2 C2 DOUB Y N 6
P1V C2 C4 SING N N 7
P1V C4 C5 SING N N 8
P1V C5 C6 SING N N 9
P1V C6 C7 SING N N 10
P1V C7 CA SING N N 11
P1V CA N SING N N 12
P1V CA C SING N N 13
P1V O C DOUB N N 14
P1V C4 H1 SING N N 15
P1V C4 H17 SING N N 16
P1V C5 H3 SING N N 17
P1V C5 H4 SING N N 18
P1V C6 H5 SING N N 19
P1V C6 H6 SING N N 20
P1V C7 H7 SING N N 21
P1V C7 H8 SING N N 22
P1V N1 H9 SING N N 23
P1V C3 H10 SING N N 24
P1V C3 H11 SING N N 25
P1V C3 H12 SING N N 26
P1V N H SING N N 27
P1V N H2 SING N N 28
P1V CA HA SING N N 29
P1V C OXT SING N N 30
P1V OXT HXT SING N N 31
#
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
P1V InChI InChI 1.06 'InChI=1S/C9H16N4O2/c1-6-11-8(13-12-6)5-3-2-4-7(10)9(14)15/h7H,2-5,10H2,1H3,(H,14,15)(H,11,12,13)/t7-/m0/s1'
P1V InChIKey InChI 1.06 BIBVPKMXAKDABB-ZETCQYMHSA-N
P1V SMILES_CANONICAL CACTVS 3.385 'Cc1[nH]nc(CCCC[C@H](N)C(O)=O)n1'
P1V SMILES CACTVS 3.385 'Cc1[nH]nc(CCCC[CH](N)C(O)=O)n1'
P1V SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'Cc1[nH]nc(n1)CCCC[C@@H](C(=O)O)N'
P1V SMILES 'OpenEye OEToolkits' 2.0.7 'Cc1[nH]nc(n1)CCCCC(C(=O)O)N'
#
_pdbx_chem_comp_identifier.comp_id P1V
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier '(2~{S})-2-azanyl-6-(5-methyl-1~{H}-1,2,4-triazol-3-yl)hexanoic 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
P1V 'Create component' 2022-09-29 PDBE
P1V 'Initial release' 2023-01-11 RCSB
P1V 'Modify formula' 2023-05-15 PDBE
P1V 'Modify backbone' 2023-11-03 PDBE
P1V 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id P1V
_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 ?
#
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
P1V C4 C 5.582 -2.075 1
P1V C5 C 6.192 -0.704 2
P1V C6 C 5.310 0.509 3
P1V C7 C 5.920 1.879 4
P1V N1 N 7.213 -5.596 5
P1V N2 N 6.000 -4.715 6
P1V C3 C 9.853 -5.178 7
P1V N3 N 7.963 -3.288 8
P1V N N 3.547 2.936 9
P1V CA C 5.038 3.093 10
P1V C C 5.649 4.463 11
P1V O O 4.767 5.677 12
P1V C1 C 8.427 -4.715 13
P1V C2 C 6.463 -3.288 14
P1V OXT O 7.140 4.620 15
#
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
P1V C3 C1 SINGLE NONE 1
P1V C1 N1 SINGLE NONE 2
P1V C1 N3 DOUBLE NONE 3
P1V N1 N2 SINGLE NONE 4
P1V N3 C2 SINGLE NONE 5
P1V N2 C2 DOUBLE NONE 6
P1V C2 C4 SINGLE NONE 7
P1V C4 C5 SINGLE NONE 8
P1V C5 C6 SINGLE NONE 9
P1V C6 C7 SINGLE NONE 10
P1V C7 CA SINGLE NONE 11
P1V CA N SINGLE BEGINDASH 12
P1V CA C SINGLE NONE 13
P1V O C DOUBLE NONE 14
P1V C OXT SINGLE NONE 15
#
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
P1V MurckoScaffold S1 scaffold 'c1nc[nH]n1' InChI=1S/C2H3N3/c1-3-2-5-4-1/h1-2H,(H,3,4,5) NSPMIYGKQJPBQR-UHFFFAOYSA-N
P1V peptide F1 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
P1V N1 S1 1
P1V N2 S1 1
P1V N3 S1 1
P1V C1 S1 1
P1V C2 S1 1
P1V O F1 1
P1V C F1 1
P1V CA F1 1
P1V N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id P1V
_pdbe_chem_comp_rdkit_properties.exactmw 212.127
_pdbe_chem_comp_rdkit_properties.amw 212.253
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 110.639
_pdbe_chem_comp_rdkit_properties.tpsa 104.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.128
_pdbe_chem_comp_rdkit_properties.CrippenMR 53.754
_pdbe_chem_comp_rdkit_properties.chi0v 7.105
_pdbe_chem_comp_rdkit_properties.chi1v 3.476
_pdbe_chem_comp_rdkit_properties.chi2v 1.062
_pdbe_chem_comp_rdkit_properties.chi3v 1.062
_pdbe_chem_comp_rdkit_properties.chi4v 0.521
_pdbe_chem_comp_rdkit_properties.chi0n 23.105
_pdbe_chem_comp_rdkit_properties.chi1n 11.226
_pdbe_chem_comp_rdkit_properties.chi2n 1.062
_pdbe_chem_comp_rdkit_properties.chi3n 1.062
_pdbe_chem_comp_rdkit_properties.chi4n 0.521
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.430
_pdbe_chem_comp_rdkit_properties.kappa1 2.452
_pdbe_chem_comp_rdkit_properties.kappa2 5.451
_pdbe_chem_comp_rdkit_properties.kappa3 4.073
_pdbe_chem_comp_rdkit_properties.Phi 0.891
#
_pdbe_chem_comp_external_mappings.comp_id P1V
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 166449938
#
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
P1V C4 -0.533 0.589 1.049 ETKDGv3 1
P1V C5 -0.251 -0.906 0.850 ETKDGv3 2
P1V C6 1.085 -1.352 1.471 ETKDGv3 3
P1V C7 2.337 -0.652 0.903 ETKDGv3 4
P1V N1 -4.035 1.204 0.497 ETKDGv3 5
P1V N2 -2.955 0.893 1.320 ETKDGv3 6
P1V C3 -4.292 1.674 -2.017 ETKDGv3 7
P1V N3 -2.204 1.231 -0.804 ETKDGv3 8
P1V N 2.646 -2.222 -1.021 ETKDGv3 9
P1V CA 2.533 -0.816 -0.623 ETKDGv3 10
P1V C 3.762 -0.074 -1.061 ETKDGv3 11
P1V O 4.909 -0.514 -0.774 ETKDGv3 12
P1V C1 -3.484 1.406 -0.792 ETKDGv3 13
P1V C2 -1.906 0.929 0.563 ETKDGv3 14
P1V H1 -0.447 0.852 2.126 ETKDGv3 15
P1V H17 0.199 1.197 0.478 ETKDGv3 16
P1V H3 -1.061 -1.491 1.338 ETKDGv3 17
P1V H4 -0.278 -1.158 -0.232 ETKDGv3 18
P1V H5 1.189 -2.450 1.345 ETKDGv3 19
P1V H6 1.047 -1.164 2.566 ETKDGv3 20
P1V H7 2.297 0.429 1.156 ETKDGv3 21
P1V H8 3.225 -1.065 1.431 ETKDGv3 22
P1V H9 -5.037 1.235 0.789 ETKDGv3 23
P1V H10 -4.574 0.711 -2.491 ETKDGv3 24
P1V H11 -5.212 2.232 -1.746 ETKDGv3 25
P1V H12 -3.703 2.279 -2.738 ETKDGv3 26
P1V H 3.279 -2.729 -0.359 ETKDGv3 27
P1V H2 1.703 -2.670 -0.966 ETKDGv3 28
P1V HA 1.669 -0.362 -1.155 ETKDGv3 29
P1V OXT 3.636 1.122 -1.760 ETKDGv3 30
P1V HXT 4.454 1.642 -2.053 ETKDGv3 31
#