data_LYP
#
_chem_comp.id LYP
_chem_comp.name N~6~-METHYL-N~6~-PROPYL-L-LYSINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C10 H22 N2 O2'
_chem_comp.mon_nstd_parent_comp_id LYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-03-28
_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 202.294
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LYP
_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 ?
_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
LYP N N N 0 1 N N N Y Y N 64.369 47.361 36.048 3.328 1.685 0.554 N LYP 1
LYP CA CA C 0 1 N N S Y N N 65.638 47.968 35.597 3.240 0.219 0.587 CA LYP 2
LYP CB CB C 0 1 N N N N N N 65.771 49.453 35.976 2.002 -0.235 -0.188 CB LYP 3
LYP CG CG C 0 1 N N N N N N 64.964 50.346 35.052 0.743 0.262 0.526 CG LYP 4
LYP CD CD C 0 1 N N N N N N 65.182 51.829 35.294 -0.495 -0.192 -0.249 CD LYP 5
LYP CE CE C 0 1 N N N N N N 64.596 52.623 34.119 -1.754 0.305 0.465 CE LYP 6
LYP NZ NZ N 0 1 N N N N N N 64.513 54.113 34.280 -2.944 -0.131 -0.279 NZ LYP 7
LYP CM CM C 0 1 N N N N N N 63.935 54.707 33.041 -3.009 0.517 -1.595 CM LYP 8
LYP C C C 0 1 N N N Y N Y 66.896 47.149 35.925 4.474 -0.372 -0.045 C LYP 9
LYP O O O 0 1 N N N Y N Y 67.514 46.608 35.004 5.153 0.297 -0.788 O LYP 10
LYP CCA CCA C 0 1 N N N N N N 66.589 56.739 35.862 -6.628 -0.305 0.610 CCA LYP 11
LYP CCC CCC C 0 1 N N N N N N 65.780 56.198 34.668 -5.352 -0.566 -0.193 CCC LYP 12
LYP CCD CCD C 0 1 N N N N N N 65.870 54.675 34.560 -4.168 0.119 0.492 CCD LYP 13
LYP OXT OXT O 0 1 N Y N Y N Y 67.261 47.038 37.206 4.818 -1.643 0.216 OXT LYP 14
LYP H HN1 H 0 1 N N N Y Y N 64.342 46.400 35.773 3.399 2.022 -0.395 HN1 LYP 15
LYP H2 HN2 H 0 1 N Y N Y Y N 64.305 47.425 37.044 2.544 2.105 1.029 HN2 LYP 16
LYP HA HA H 0 1 N N N Y N N 65.584 47.966 34.498 3.166 -0.117 1.621 HA LYP 17
LYP HBC1 HBC1 H 0 0 N N N N N N 65.412 49.591 37.007 2.034 0.175 -1.197 HBC1 LYP 18
LYP HBC2 HBC2 H 0 0 N N N N N N 66.830 49.742 35.915 1.985 -1.324 -0.239 HBC2 LYP 19
LYP HGC1 HGC1 H 0 0 N N N N N N 65.247 50.118 34.014 0.711 -0.148 1.535 HGC1 LYP 20
LYP HGC2 HGC2 H 0 0 N N N N N N 63.897 50.123 35.198 0.761 1.351 0.577 HGC2 LYP 21
LYP HDC1 HDC1 H 0 0 N N N N N N 64.680 52.127 36.226 -0.464 0.218 -1.258 HDC1 LYP 22
LYP HDC2 HDC2 H 0 0 N N N N N N 66.260 52.034 35.376 -0.513 -1.281 -0.300 HDC2 LYP 23
LYP HEC1 HEC1 H 0 0 N N N N N N 65.219 52.418 33.236 -1.786 -0.105 1.474 HEC1 LYP 24
LYP HEC2 HEC2 H 0 0 N N N N N N 63.576 52.251 33.942 -1.737 1.394 0.516 HEC2 LYP 25
LYP HMC1 HMC1 H 0 0 N N N N N N 63.871 55.799 33.153 -2.121 0.258 -2.173 HMC1 LYP 26
LYP HMC2 HMC2 H 0 0 N N N N N N 64.578 54.463 32.183 -3.898 0.177 -2.125 HMC2 LYP 27
LYP HMC3 HMC3 H 0 0 N N N N N N 62.928 54.297 32.873 -3.055 1.599 -1.466 HMC3 LYP 28
LYP HCD1 HCD1 H 0 0 N N N N N N 66.249 54.262 35.506 -4.051 -0.280 1.500 HCD1 LYP 29
LYP HCD2 HCD2 H 0 0 N N N N N N 66.554 54.405 33.742 -4.351 1.192 0.546 HCD2 LYP 30
LYP HXT HOT H 0 1 N Y N Y N Y 68.039 46.496 37.268 5.617 -1.979 -0.213 HOT LYP 31
LYP HCA1 HCA1 H 0 0 N N N N N N 66.497 57.834 35.902 -6.810 0.768 0.664 HCA1 LYP 32
LYP HCA2 HCA2 H 0 0 N N N N N N 66.201 56.304 36.795 -7.471 -0.794 0.122 HCA2 LYP 33
LYP HCA3 HCA3 H 0 0 N Y N N N N 67.647 56.464 35.742 -6.510 -0.704 1.618 HCA3 LYP 34
LYP HCC1 HCC1 H 0 0 N N N N N N 64.725 56.484 34.795 -5.169 -1.639 -0.247 HCC1 LYP 35
LYP HCC2 HCC2 H 0 0 N N N N N N 66.172 56.644 33.742 -5.469 -0.167 -1.201 HCC2 LYP 36
#
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
LYP N CA SING N N 1
LYP CA CB SING N N 2
LYP CB CG SING N N 3
LYP CG CD SING N N 4
LYP CD CE SING N N 5
LYP CE NZ SING N N 6
LYP NZ CM SING N N 7
LYP CA C SING N N 8
LYP C O DOUB N N 9
LYP CCA CCC SING N N 10
LYP NZ CCD SING N N 11
LYP CCC CCD SING N N 12
LYP C OXT SING N N 13
LYP N H SING N N 14
LYP N H2 SING N N 15
LYP CA HA SING N N 16
LYP CB HBC1 SING N N 17
LYP CB HBC2 SING N N 18
LYP CG HGC1 SING N N 19
LYP CG HGC2 SING N N 20
LYP CD HDC1 SING N N 21
LYP CD HDC2 SING N N 22
LYP CE HEC1 SING N N 23
LYP CE HEC2 SING N N 24
LYP CM HMC1 SING N N 25
LYP CM HMC2 SING N N 26
LYP CM HMC3 SING N N 27
LYP CCD HCD1 SING N N 28
LYP CCD HCD2 SING N N 29
LYP OXT HXT SING N N 30
LYP CCA HCA1 SING N N 31
LYP CCA HCA2 SING N N 32
LYP CCA HCA3 SING N N 33
LYP CCC HCC1 SING N N 34
LYP CCC HCC2 SING N N 35
#
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
LYP SMILES ACDLabs 12.01 'O=C(O)C(N)CCCCN(CCC)C'
LYP InChI InChI 1.03 'InChI=1S/C10H22N2O2/c1-3-7-12(2)8-5-4-6-9(11)10(13)14/h9H,3-8,11H2,1-2H3,(H,13,14)/t9-/m0/s1'
LYP InChIKey InChI 1.03 RBCPTYNDCRPSKM-VIFPVBQESA-N
LYP SMILES_CANONICAL CACTVS 3.370 'CCCN(C)CCCC[C@H](N)C(O)=O'
LYP SMILES CACTVS 3.370 'CCCN(C)CCCC[CH](N)C(O)=O'
LYP SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'CCCN(C)CCCCC(C(=O)O)N'
LYP SMILES 'OpenEye OEToolkits' 1.7.6 'CCCN(C)CCCCC(C(=O)O)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
LYP 'SYSTEMATIC NAME' ACDLabs 12.01 N~6~-methyl-N~6~-propyl-L-lysine
LYP 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '2-azanyl-6-[methyl(propyl)amino]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
LYP 'Create component' 2007-03-28 RCSB
LYP 'Modify descriptor' 2011-06-04 RCSB
LYP 'Modify parent residue' 2012-10-28 RCSB
LYP 'Modify backbone' 2023-11-03 PDBE
LYP 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id LYP
_pdbx_chem_comp_pcm.modified_residue_id LYS
_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
LYP N N 6.897 4.125 1
LYP CA C 8.196 3.375 2
LYP CB C 8.196 1.875 3
LYP CG C 6.897 1.125 4
LYP CD C 6.897 -0.375 5
LYP CE C 5.598 -1.125 6
LYP NZ N 5.598 -2.625 7
LYP CM C 6.897 -3.375 8
LYP C C 9.495 4.125 9
LYP O O 10.794 3.375 10
LYP CCA C 3.000 -5.625 11
LYP CCC C 4.299 -4.875 12
LYP CCD C 4.299 -3.375 13
LYP OXT O 9.495 5.625 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
LYP CA N SINGLE BEGINDASH 1
LYP CA CB SINGLE NONE 2
LYP CB CG SINGLE NONE 3
LYP CG CD SINGLE NONE 4
LYP CD CE SINGLE NONE 5
LYP CE NZ SINGLE NONE 6
LYP NZ CM SINGLE NONE 7
LYP CA C SINGLE NONE 8
LYP C O DOUBLE NONE 9
LYP CCA CCC SINGLE NONE 10
LYP NZ CCD SINGLE NONE 11
LYP CCC CCD SINGLE NONE 12
LYP C OXT SINGLE NONE 13
#
_pdbe_chem_comp_substructure.comp_id LYP
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys 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
LYP O F1 1
LYP C F1 1
LYP CA F1 1
LYP N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LYP
_pdbe_chem_comp_rdkit_properties.exactmw 202.168
_pdbe_chem_comp_rdkit_properties.amw 202.298
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_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 36
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.900
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_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 117.191
_pdbe_chem_comp_rdkit_properties.tpsa 66.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.910
_pdbe_chem_comp_rdkit_properties.CrippenMR 57.250
_pdbe_chem_comp_rdkit_properties.chi0v 6.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.053
_pdbe_chem_comp_rdkit_properties.chi2v 0.772
_pdbe_chem_comp_rdkit_properties.chi3v 0.772
_pdbe_chem_comp_rdkit_properties.chi4v 0.309
_pdbe_chem_comp_rdkit_properties.chi0n 28.711
_pdbe_chem_comp_rdkit_properties.chi1n 13.855
_pdbe_chem_comp_rdkit_properties.chi2n 0.772
_pdbe_chem_comp_rdkit_properties.chi3n 0.772
_pdbe_chem_comp_rdkit_properties.chi4n 0.309
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.610
_pdbe_chem_comp_rdkit_properties.kappa1 1.738
_pdbe_chem_comp_rdkit_properties.kappa2 7.762
_pdbe_chem_comp_rdkit_properties.kappa3 6.858
_pdbe_chem_comp_rdkit_properties.Phi 0.964
#
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
LYP UniChem ZINC ZINC000064436851
LYP UniChem PubChem 52945397
#
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
LYP N 3.471 1.521 0.414 ETKDGv3 1
LYP CA 3.761 0.085 0.381 ETKDGv3 2
LYP CB 2.667 -0.673 -0.394 ETKDGv3 3
LYP CG 1.301 -0.569 0.299 ETKDGv3 4
LYP CD 0.232 -1.357 -0.472 ETKDGv3 5
LYP CE -1.133 -1.295 0.222 ETKDGv3 6
LYP NZ -1.641 0.096 0.228 ETKDGv3 7
LYP CM -2.175 0.499 1.537 ETKDGv3 8
LYP C 5.114 -0.171 -0.231 ETKDGv3 9
LYP O 5.354 0.179 -1.418 ETKDGv3 10
LYP CCA -5.040 0.698 -0.340 ETKDGv3 11
LYP CCC -3.952 -0.280 -0.782 ETKDGv3 12
LYP CCD -2.560 0.393 -0.895 ETKDGv3 13
LYP OXT 6.103 -0.799 0.519 ETKDGv3 14
LYP H 3.518 1.912 -0.556 ETKDGv3 15
LYP H2 4.210 2.000 0.980 ETKDGv3 16
LYP HA 3.777 -0.295 1.426 ETKDGv3 17
LYP HBC1 2.953 -1.746 -0.464 ETKDGv3 18
LYP HBC2 2.590 -0.268 -1.427 ETKDGv3 19
LYP HGC1 1.381 -0.973 1.333 ETKDGv3 20
LYP HGC2 0.999 0.499 0.360 ETKDGv3 21
LYP HDC1 0.543 -2.422 -0.543 ETKDGv3 22
LYP HDC2 0.142 -0.957 -1.505 ETKDGv3 23
LYP HEC1 -1.019 -1.696 1.255 ETKDGv3 24
LYP HEC2 -1.825 -1.984 -0.307 ETKDGv3 25
LYP HMC1 -2.551 1.544 1.496 ETKDGv3 26
LYP HMC2 -2.990 -0.179 1.869 ETKDGv3 27
LYP HMC3 -1.363 0.474 2.295 ETKDGv3 28
LYP HCD1 -2.664 1.496 -0.996 ETKDGv3 29
LYP HCD2 -2.084 0.063 -1.845 ETKDGv3 30
LYP HXT 7.018 -0.980 0.124 ETKDGv3 31
LYP HCA1 -5.121 1.537 -1.064 ETKDGv3 32
LYP HCA2 -4.821 1.105 0.668 ETKDGv3 33
LYP HCA3 -6.017 0.173 -0.301 ETKDGv3 34
LYP HCC1 -4.239 -0.676 -1.781 ETKDGv3 35
LYP HCC2 -3.938 -1.143 -0.085 ETKDGv3 36
#