data_E9V
#
_chem_comp.id E9V
_chem_comp.name N-methyl-L-histidine
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C7 H11 N3 O2"
_chem_comp.mon_nstd_parent_comp_id HIS
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-12-14
_chem_comp.pdbx_modified_date 2023-11-08
_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 169.181
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code E9V
_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 6BVY
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
E9V N N1 N 0 1 N N N Y Y N 2.807 -2.121 2.533 -0.832 1.408 0.144 N E9V 1
E9V CA C1 C 0 1 N N S N Y N 3.824 -2.660 3.429 -0.954 -0.016 -0.196 CA E9V 2
E9V CB C2 C 0 1 N N N N N N 4.690 -3.682 2.693 0.010 -0.831 0.667 CB E9V 3
E9V CG C3 C 0 1 Y N N N N N 3.900 -4.684 1.910 1.430 -0.459 0.323 CG E9V 4
E9V ND1 N2 N 0 1 Y N N N N N 4.353 -5.248 0.735 2.249 -1.102 -0.566 ND1 E9V 5
E9V CD2 C4 C 0 1 Y N N N N N 2.680 -5.223 2.139 2.134 0.572 0.826 CD2 E9V 6
E9V CE1 C5 C 0 1 Y N N N N N 3.445 -6.090 0.276 3.426 -0.440 -0.575 CE1 E9V 7
E9V NE2 N3 N 0 1 Y N N N N N 2.420 -6.094 1.109 3.352 0.557 0.264 NE2 E9V 8
E9V C C6 C 0 1 N N N N Y Y 4.700 -1.544 3.992 -2.367 -0.474 0.059 C E9V 9
E9V O O1 O 0 1 N N N N Y Y 5.786 -1.795 4.511 -3.044 0.089 0.887 O E9V 10
E9V CN2 C7 C 0 1 N N N N N N 3.222 -1.485 1.276 -1.290 2.255 -0.965 CN2 E9V 11
E9V H H1 H 0 1 N Y N Y Y N 2.295 -1.436 3.051 0.115 1.637 0.407 H E9V 12
E9V HA H3 H 0 1 N N N N Y N 3.331 -3.169 4.270 -0.710 -0.160 -1.249 HA E9V 13
E9V HB2 H4 H 0 1 N N N N N N 5.298 -4.221 3.435 -0.176 -0.618 1.720 HB2 E9V 14
E9V HB3 H5 H 0 1 N N N N N N 5.352 -3.142 2.000 -0.143 -1.894 0.479 HB3 E9V 15
E9V HD1 H6 H 0 1 N N N N N N 5.231 -5.050 0.299 2.026 -1.886 -1.091 HD1 E9V 16
E9V HD2 H7 H 0 1 N N N N N N 2.032 -5.008 2.976 1.780 1.287 1.554 HD2 E9V 17
E9V HE1 H8 H 0 1 N N N N N N 3.527 -6.676 -0.627 4.287 -0.696 -1.174 HE1 E9V 18
E9V HN3 H11 H 0 1 N N N N N N 2.333 -1.138 0.729 -0.740 1.998 -1.870 HN3 E9V 19
E9V HN1 H12 H 0 1 N N N N N N 3.874 -0.627 1.497 -2.356 2.094 -1.129 HN1 E9V 20
E9V HN2 H13 H 0 1 N N N N N N 3.770 -2.213 0.660 -1.115 3.302 -0.719 HN2 E9V 21
E9V OXT O2 O 0 1 N Y N N Y Y 4.272 -0.364 3.868 -2.873 -1.508 -0.632 OXT E9V 22
E9V HXT H2 H 0 1 N Y N N Y Y 4.908 0.243 4.228 -3.783 -1.765 -0.433 HXT E9V 23
#
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
E9V CE1 ND1 SING Y N 1
E9V CE1 NE2 DOUB Y N 2
E9V ND1 CG SING Y N 3
E9V NE2 CD2 SING Y N 4
E9V CN2 N SING N N 5
E9V CG CD2 DOUB Y N 6
E9V CG CB SING N N 7
E9V N CA SING N N 8
E9V CB CA SING N N 9
E9V CA C SING N N 10
E9V C O DOUB N N 11
E9V N H SING N N 12
E9V CA HA SING N N 13
E9V CB HB2 SING N N 14
E9V CB HB3 SING N N 15
E9V ND1 HD1 SING N N 16
E9V CD2 HD2 SING N N 17
E9V CE1 HE1 SING N N 18
E9V CN2 HN3 SING N N 19
E9V CN2 HN1 SING N N 20
E9V CN2 HN2 SING N N 21
E9V C OXT SING N N 22
E9V OXT HXT SING N N 23
#
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
E9V SMILES ACDLabs 12.01 "CNC(Cc1cnc[NH]1)C(=O)O"
E9V InChI InChI 1.06 "InChI=1S/C7H11N3O2/c1-8-6(7(11)12)2-5-3-9-4-10-5/h3-4,6,8H,2H2,1H3,(H,9,10)(H,11,12)/t6-/m0/s1"
E9V InChIKey InChI 1.06 CYZKJBZEIFWZSR-LURJTMIESA-N
E9V SMILES_CANONICAL CACTVS 3.385 "CN[C@@H](Cc1[nH]cnc1)C(O)=O"
E9V SMILES CACTVS 3.385 "CN[CH](Cc1[nH]cnc1)C(O)=O"
E9V SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN[C@@H](Cc1cnc[nH]1)C(=O)O"
E9V SMILES "OpenEye OEToolkits" 2.0.7 "CNC(Cc1cnc[nH]1)C(=O)O"
#
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
E9V "SYSTEMATIC NAME" ACDLabs 12.01 N-methyl-L-histidine
E9V "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-3-(1~{H}-imidazol-5-yl)-2-(methylamino)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
E9V 'Create component' 2017-12-14 RCSB
E9V 'Initial release' 2018-04-18 RCSB
E9V 'Modify backbone' 2023-11-03 PDBE
E9V 'Modify atom id' 2023-11-08 RCSB
#
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
E9V N N 6.738 1.408 1
E9V CA C 6.426 -0.059 2
E9V CB C 7.540 -1.063 3
E9V CG C 8.967 -0.600 4
E9V ND1 N 10.181 -1.481 5
E9V CD2 C 9.431 0.827 6
E9V CE1 C 11.394 -0.600 7
E9V NE2 N 10.931 0.827 8
E9V C C 4.999 -0.523 9
E9V O O 3.884 0.481 10
E9V CN2 C 5.623 2.411 11
E9V OXT O 4.687 -1.990 12
#
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
E9V CE1 ND1 SINGLE NONE 1
E9V CE1 NE2 DOUBLE NONE 2
E9V ND1 CG SINGLE NONE 3
E9V NE2 CD2 SINGLE NONE 4
E9V CN2 N SINGLE NONE 5
E9V CG CD2 DOUBLE NONE 6
E9V CG CB SINGLE NONE 7
E9V N CA SINGLE NONE 8
E9V CA CB SINGLE BEGINWEDGE 9
E9V CA C SINGLE NONE 10
E9V C O DOUBLE NONE 11
E9V C OXT SINGLE NONE 12
#
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
E9V MurckoScaffold S1 scaffold 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
E9V imidazole F1 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
E9V 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
E9V CG S1 1
E9V ND1 S1 1
E9V CD2 S1 1
E9V CE1 S1 1
E9V NE2 S1 1
E9V CG F1 1
E9V CD2 F1 1
E9V NE2 F1 1
E9V CE1 F1 1
E9V ND1 F1 1
E9V O F2 1
E9V C F2 1
E9V CA F2 1
E9V N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id E9V
_pdbe_chem_comp_rdkit_properties.exactmw 169.085
_pdbe_chem_comp_rdkit_properties.amw 169.184
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.429
_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 85.483
_pdbe_chem_comp_rdkit_properties.tpsa 78.010
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.430
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.509
_pdbe_chem_comp_rdkit_properties.chi0v 5.658
_pdbe_chem_comp_rdkit_properties.chi1v 2.750
_pdbe_chem_comp_rdkit_properties.chi2v 0.916
_pdbe_chem_comp_rdkit_properties.chi3v 0.916
_pdbe_chem_comp_rdkit_properties.chi4v 0.471
_pdbe_chem_comp_rdkit_properties.chi0n 16.658
_pdbe_chem_comp_rdkit_properties.chi1n 8.053
_pdbe_chem_comp_rdkit_properties.chi2n 0.916
_pdbe_chem_comp_rdkit_properties.chi3n 0.916
_pdbe_chem_comp_rdkit_properties.chi4n 0.471
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.360
_pdbe_chem_comp_rdkit_properties.kappa1 2.111
_pdbe_chem_comp_rdkit_properties.kappa2 3.868
_pdbe_chem_comp_rdkit_properties.kappa3 2.062
_pdbe_chem_comp_rdkit_properties.Phi 0.681
#
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
E9V UniChem ChEMBL CHEMBL1229144
E9V UniChem PDBe E9V
E9V UniChem 'KEGG LIGAND' C03298
E9V UniChem ChEBI 50601
E9V UniChem ChEBI 75895
E9V UniChem ZINC ZINC000000901700
E9V UniChem SureChEMBL SCHEMBL151335
E9V UniChem NMRShiftDB 60058721
E9V UniChem ACTor 24886-03-1
E9V UniChem 'EPA CompTox Dashboard' DTXSID20179585
E9V UniChem MetaboLights MTBLC50601
E9V UniChem MetaboLights MTBLC75895
E9V UniChem BRENDA 108678
E9V UniChem BRENDA 129520
E9V UniChem BRENDA 132278
E9V UniChem BRENDA 31049
E9V UniChem BRENDA 45760
E9V UniChem BRENDA 89415
E9V UniChem Rhea 75895
E9V UniChem Nikkaji J286.413D
E9V UniChem PubChem 6971273
E9V UniChem PubChem 90638
#
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
E9V N -2.330 -0.153 0.016 ETKDGv3 1
E9V CA -0.915 0.106 0.337 ETKDGv3 2
E9V CB 0.032 -0.486 -0.732 ETKDGv3 3
E9V CG 1.473 -0.329 -0.341 ETKDGv3 4
E9V ND1 2.292 0.765 -0.713 ETKDGv3 5
E9V CD2 2.149 -1.119 0.477 ETKDGv3 6
E9V CE1 3.507 0.494 -0.024 ETKDGv3 7
E9V NE2 3.461 -0.594 0.677 ETKDGv3 8
E9V C -0.717 1.593 0.445 ETKDGv3 9
E9V O -0.208 2.089 1.485 ETKDGv3 10
E9V CN2 -2.769 -1.474 0.474 ETKDGv3 11
E9V H -2.485 -0.091 -1.019 ETKDGv3 12
E9V HA -0.661 -0.344 1.326 ETKDGv3 13
E9V HB2 -0.135 0.012 -1.712 ETKDGv3 14
E9V HB3 -0.177 -1.567 -0.872 ETKDGv3 15
E9V HD1 2.054 1.586 -1.312 ETKDGv3 16
E9V HD2 1.768 -2.014 0.950 ETKDGv3 17
E9V HE1 4.381 1.129 -0.073 ETKDGv3 18
E9V HN3 -2.192 -2.284 -0.019 ETKDGv3 19
E9V HN1 -2.664 -1.556 1.578 ETKDGv3 20
E9V HN2 -3.842 -1.610 0.225 ETKDGv3 21
E9V OXT -1.079 2.422 -0.613 ETKDGv3 22
E9V HXT -0.942 3.424 -0.558 ETKDGv3 23
#