data_Q3P
#
_chem_comp.id Q3P
_chem_comp.name N~6~-glycyl-L-lysine
_chem_comp.type 'L-peptide linking'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C8 H17 N3 O3'
_chem_comp.mon_nstd_parent_comp_id LYS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-09-16
_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 203.239
_chem_comp.one_letter_code K
_chem_comp.three_letter_code Q3P
_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 6UC1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
Q3P C1 C1 C 0 1 N N N N N N -5.994 -54.304 245.576 -4.052 0.030 -0.023 C1 Q3P 1
Q3P C4 C2 C 0 1 N N N N N N -5.774 -53.002 246.318 -5.246 0.798 0.484 C4 Q3P 2
Q3P N N1 N 0 1 N N N N N N -9.937 -59.599 242.779 3.384 -1.766 0.267 N Q3P 3
Q3P CA C3 C 0 1 N N S N N N -10.807 -59.045 243.869 3.348 -0.442 -0.368 CA Q3P 4
Q3P C C4 C 0 1 N N N N N N -12.166 -58.696 243.334 4.609 0.311 -0.031 C Q3P 5
Q3P O O1 O 0 1 N N N N N N -12.378 -58.741 242.088 5.273 -0.018 0.924 O Q3P 6
Q3P CB C5 C 0 1 N N N N N N -10.207 -57.819 244.505 2.136 0.337 0.147 CB Q3P 7
Q3P CG C6 C 0 1 N N N N N N -8.854 -58.146 245.148 0.851 -0.362 -0.303 CG Q3P 8
Q3P CD C7 C 0 1 N N N N N N -8.236 -56.884 245.795 -0.361 0.417 0.211 CD Q3P 9
Q3P CE C8 C 0 1 N N N N N N -7.588 -55.951 244.769 -1.645 -0.283 -0.239 CE Q3P 10
Q3P NZ N2 N 0 1 N N N N N N -7.265 -54.627 245.291 -2.806 0.463 0.254 NZ Q3P 11
Q3P N5 N3 N 0 1 N N N N N N -6.798 -52.760 247.384 -6.479 0.126 0.052 N5 Q3P 12
Q3P O2 O2 O 0 1 N N N N N N -5.027 -55.004 245.265 -4.212 -0.980 -0.674 O2 Q3P 13
Q3P OXT O3 O 0 1 N Y N N N N -13.091 -58.330 244.216 4.995 1.348 -0.791 O1 Q3P 14
Q3P H4 H1 H 0 1 N N N N N N -4.779 -53.028 246.786 -5.216 0.839 1.573 H4 Q3P 15
Q3P H41 H2 H 0 1 N N N N N N -5.817 -52.174 245.595 -5.224 1.811 0.082 H41 Q3P 16
Q3P H2 H3 H 0 1 N N N N N N -9.037 -59.826 243.153 3.454 -1.684 1.271 H2 Q3P 17
Q3P H1 H4 H 0 1 N N N N N N -10.359 -60.424 242.403 2.579 -2.315 0.004 H1 Q3P 18
Q3P HA H6 H 0 1 N N N N N N -10.926 -59.815 244.645 3.273 -0.559 -1.449 HA Q3P 19
Q3P HB3 H7 H 0 1 N N N N N N -10.063 -57.047 243.735 2.165 0.378 1.235 HB3 Q3P 20
Q3P HB2 H8 H 0 1 N N N N N N -10.892 -57.442 245.279 2.158 1.350 -0.256 HB2 Q3P 21
Q3P HG3 H9 H 0 1 N N N N N N -8.998 -58.914 245.922 0.822 -0.403 -1.392 HG3 Q3P 22
Q3P HG2 H10 H 0 1 N N N N N N -8.170 -58.527 244.376 0.830 -1.375 0.099 HG2 Q3P 23
Q3P HD3 H11 H 0 1 N N N N N N -7.469 -57.199 246.518 -0.331 0.458 1.300 HD3 Q3P 24
Q3P HD2 H12 H 0 1 N N N N N N -9.030 -56.333 246.320 -0.339 1.430 -0.191 HD2 Q3P 25
Q3P HE3 H13 H 0 1 N N N N N N -8.282 -55.830 243.925 -1.674 -0.323 -1.328 HE3 Q3P 26
Q3P HE2 H14 H 0 1 N N N N N N -6.658 -56.419 244.415 -1.667 -1.296 0.163 HE2 Q3P 27
Q3P HZ3 H15 H 0 1 N N N N N N -7.994 -53.958 245.437 -2.677 1.269 0.778 HZ3 Q3P 28
Q3P HN5 H16 H 0 1 N N N N N N -6.606 -51.891 247.840 -6.493 -0.835 0.358 HN5 Q3P 29
Q3P HN51 H17 H 0 0 N N N N N N -7.708 -52.726 246.970 -7.294 0.622 0.379 HN51 Q3P 30
Q3P HXT H19 H 0 1 N N N N N N -13.898 -58.120 243.761 5.811 1.800 -0.536 H5 Q3P 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
Q3P O C DOUB N N 1
Q3P N CA SING N N 2
Q3P C CA SING N N 3
Q3P CA CB SING N N 4
Q3P CB CG SING N N 5
Q3P CE NZ SING N N 6
Q3P CE CD SING N N 7
Q3P CG CD SING N N 8
Q3P O2 C1 DOUB N N 9
Q3P NZ C1 SING N N 10
Q3P C1 C4 SING N N 11
Q3P C4 N5 SING N N 12
Q3P C OXT SING N N 13
Q3P C4 H4 SING N N 14
Q3P C4 H41 SING N N 15
Q3P N H2 SING N N 16
Q3P N H1 SING N N 17
Q3P CA HA SING N N 18
Q3P CB HB3 SING N N 19
Q3P CB HB2 SING N N 20
Q3P CG HG3 SING N N 21
Q3P CG HG2 SING N N 22
Q3P CD HD3 SING N N 23
Q3P CD HD2 SING N N 24
Q3P CE HE3 SING N N 25
Q3P CE HE2 SING N N 26
Q3P NZ HZ3 SING N N 27
Q3P N5 HN5 SING N N 28
Q3P N5 HN51 SING N N 29
Q3P 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
Q3P SMILES ACDLabs 12.01 'C(CN)(NCCCCC(N)C(O)=O)=O'
Q3P InChI InChI 1.03 'InChI=1S/C8H17N3O3/c9-5-7(12)11-4-2-1-3-6(10)8(13)14/h6H,1-5,9-10H2,(H,11,12)(H,13,14)/t6-/m0/s1'
Q3P InChIKey InChI 1.03 YOYBPHLYMUAKGZ-LURJTMIESA-N
Q3P SMILES_CANONICAL CACTVS 3.385 'NCC(=O)NCCCC[C@H](N)C(O)=O'
Q3P SMILES CACTVS 3.385 'NCC(=O)NCCCC[CH](N)C(O)=O'
Q3P SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C(CCNC(=O)CN)C[C@@H](C(=O)O)N'
Q3P SMILES 'OpenEye OEToolkits' 2.0.7 'C(CCNC(=O)CN)CC(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
Q3P 'SYSTEMATIC NAME' ACDLabs 12.01 N~6~-glycyl-L-lysine
Q3P 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '(2~{S})-2-azanyl-6-(2-azanylethanoylamino)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
Q3P 'Create component' 2019-09-16 RCSB
Q3P 'Initial release' 2019-10-23 RCSB
Q3P 'Modify PCM' 2024-09-27 PDBE
#
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
Q3P C1 C 5.104 -2.910 1
Q3P C4 C 5.104 -4.410 2
Q3P N N 7.702 4.590 3
Q3P CA C 9.002 3.840 4
Q3P C C 10.301 4.590 5
Q3P O O 11.600 3.840 6
Q3P CB C 9.002 2.340 7
Q3P CG C 7.702 1.590 8
Q3P CD C 7.702 0.090 9
Q3P CE C 6.404 -0.660 10
Q3P NZ N 6.404 -2.160 11
Q3P N5 N 3.805 -5.160 12
Q3P O2 O 3.805 -2.160 13
Q3P OXT O 10.301 6.090 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
Q3P O C DOUBLE NONE 1
Q3P CA N SINGLE BEGINDASH 2
Q3P C CA SINGLE NONE 3
Q3P CA CB SINGLE NONE 4
Q3P CB CG SINGLE NONE 5
Q3P CE NZ SINGLE NONE 6
Q3P CE CD SINGLE NONE 7
Q3P CG CD SINGLE NONE 8
Q3P O2 C1 DOUBLE NONE 9
Q3P NZ C1 SINGLE NONE 10
Q3P C1 C4 SINGLE NONE 11
Q3P C4 N5 SINGLE NONE 12
Q3P C OXT SINGLE NONE 13
#
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
Q3P amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
Q3P 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
Q3P NZ F1 1
Q3P C1 F1 1
Q3P O2 F1 1
Q3P C4 F1 1
Q3P O F2 1
Q3P C F2 1
Q3P CA F2 1
Q3P N F2 1
Q3P O2 F2 2
Q3P C1 F2 2
Q3P C4 F2 2
Q3P N5 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id Q3P
_pdbe_chem_comp_rdkit_properties.exactmw 203.127
_pdbe_chem_comp_rdkit_properties.amw 203.242
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 106.902
_pdbe_chem_comp_rdkit_properties.tpsa 118.440
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.356
_pdbe_chem_comp_rdkit_properties.CrippenMR 51.526
_pdbe_chem_comp_rdkit_properties.chi0v 6.566
_pdbe_chem_comp_rdkit_properties.chi1v 3.007
_pdbe_chem_comp_rdkit_properties.chi2v 0.746
_pdbe_chem_comp_rdkit_properties.chi3v 0.746
_pdbe_chem_comp_rdkit_properties.chi4v 0.273
_pdbe_chem_comp_rdkit_properties.chi0n 23.566
_pdbe_chem_comp_rdkit_properties.chi1n 11.151
_pdbe_chem_comp_rdkit_properties.chi2n 0.746
_pdbe_chem_comp_rdkit_properties.chi3n 0.746
_pdbe_chem_comp_rdkit_properties.chi4n 0.273
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.140
_pdbe_chem_comp_rdkit_properties.kappa1 2.172
_pdbe_chem_comp_rdkit_properties.kappa2 7.281
_pdbe_chem_comp_rdkit_properties.kappa3 6.384
_pdbe_chem_comp_rdkit_properties.Phi 1.130
#
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
Q3P UniChem ChEBI 21885
Q3P UniChem fdasrs O12PZI77AL
Q3P UniChem SureChEMBL SCHEMBL358166
Q3P UniChem PubChem 7000162
Q3P UniChem MetaboLights MTBLC21885
Q3P UniChem BRENDA 103240
Q3P UniChem rxnorm GLYCYL-ISOLYSINE
#
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
Q3P C1 -3.235 -0.802 -0.227 ETKDGv3 1
Q3P C4 -4.508 -1.339 -0.804 ETKDGv3 2
Q3P N 4.760 -0.144 -0.857 ETKDGv3 3
Q3P CA 3.648 0.558 -0.214 ETKDGv3 4
Q3P C 3.794 0.511 1.286 ETKDGv3 5
Q3P O 3.955 1.577 1.937 ETKDGv3 6
Q3P CB 2.311 -0.057 -0.670 ETKDGv3 7
Q3P CG 1.102 0.765 -0.198 ETKDGv3 8
Q3P CD -0.209 0.156 -0.709 ETKDGv3 9
Q3P CE -1.417 0.972 -0.236 ETKDGv3 10
Q3P NZ -2.656 0.399 -0.757 ETKDGv3 11
Q3P N5 -5.652 -0.698 -0.164 ETKDGv3 12
Q3P O2 -2.704 -1.387 0.755 ETKDGv3 13
Q3P OXT 3.755 -0.710 1.955 ETKDGv3 14
Q3P H4 -4.533 -1.158 -1.902 ETKDGv3 15
Q3P H41 -4.557 -2.437 -0.635 ETKDGv3 16
Q3P H2 4.800 -1.130 -0.509 ETKDGv3 17
Q3P H1 5.655 0.322 -0.581 ETKDGv3 18
Q3P HA 3.674 1.620 -0.548 ETKDGv3 19
Q3P HB3 2.303 -0.098 -1.781 ETKDGv3 20
Q3P HB2 2.227 -1.100 -0.292 ETKDGv3 21
Q3P HG3 1.195 1.807 -0.576 ETKDGv3 22
Q3P HG2 1.080 0.793 0.913 ETKDGv3 23
Q3P HD3 -0.297 -0.888 -0.337 ETKDGv3 24
Q3P HD2 -0.200 0.134 -1.821 ETKDGv3 25
Q3P HE3 -1.318 2.016 -0.605 ETKDGv3 26
Q3P HE2 -1.455 1.003 0.875 ETKDGv3 27
Q3P HZ3 -3.166 0.918 -1.507 ETKDGv3 28
Q3P HN5 -6.518 -1.150 -0.536 ETKDGv3 29
Q3P HN51 -5.683 0.301 -0.473 ETKDGv3 30
Q3P HXT 3.852 -0.753 2.962 ETKDGv3 31
#