data_DJD
#
_chem_comp.id DJD
_chem_comp.name "4-(6-methyl-1,2,4,5-tetrazin-3-yl)-L-phenylalanine"
_chem_comp.type "L-peptide linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C12 H13 N5 O2"
_chem_comp.mon_nstd_parent_comp_id PHE
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-26
_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 259.264
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DJD
_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 6BF1
_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
DJD N N1 N 0 1 N N N Y Y N -21.671 -3.904 30.252 -3.460 -1.380 0.990 N DJD 1
DJD CA C1 C 0 1 N N S Y N N -22.963 -3.414 29.793 -3.753 -0.029 0.493 CA DJD 2
DJD C C2 C 0 1 N N N Y N Y -22.874 -2.679 28.455 -5.241 0.129 0.315 C DJD 3
DJD O O1 O 0 1 N N N Y N Y -23.781 -2.759 27.686 -5.945 -0.849 0.219 O DJD 4
DJD CB C3 C 0 1 N N N N N N -23.584 -2.508 30.879 -3.053 0.182 -0.851 CB DJD 5
DJD CG C4 C 0 1 Y N N N N N -24.102 -3.421 31.996 -1.560 0.146 -0.652 CG DJD 6
DJD CD1 C5 C 0 1 Y N N N N N -23.567 -3.393 33.279 -0.881 -1.055 -0.748 CD1 DJD 7
DJD CD2 C6 C 0 1 Y N N N N N -25.115 -4.319 31.700 -0.873 1.315 -0.378 CD2 DJD 8
DJD CE1 C7 C 0 1 Y N N N N N -24.060 -4.259 34.250 0.487 -1.094 -0.566 CE1 DJD 9
DJD CE2 C8 C 0 1 Y N N N N N -25.606 -5.178 32.656 0.494 1.288 -0.194 CE2 DJD 10
DJD CZ C9 C 0 1 Y N N N N N -25.080 -5.158 33.933 1.183 0.080 -0.284 CZ DJD 11
DJD C01 C10 C 0 1 N N N N N N -25.640 -10.137 36.450 6.737 -0.056 0.471 C01 DJD 12
DJD C02 C11 C 0 1 Y N N N N N -25.619 -8.713 35.887 5.244 -0.020 0.271 C02 DJD 13
DJD C07 C12 C 0 1 Y N N N N N -25.651 -6.157 34.948 2.653 0.045 -0.087 C07 DJD 14
DJD N03 N2 N 0 1 Y N N N N N -26.406 -8.393 34.870 4.594 1.129 0.362 N03 DJD 15
DJD N04 N3 N 0 1 Y N N N N N -26.410 -7.109 34.405 3.316 1.165 0.186 N04 DJD 16
DJD N05 N4 N 0 1 Y N N N N N -24.849 -7.784 36.446 4.588 -1.136 -0.001 N05 DJD 17
DJD N06 N5 N 0 1 Y N N N N N -24.872 -6.498 35.973 3.310 -1.109 -0.174 N06 DJD 18
DJD H H1 H 0 1 N N N Y Y N -21.784 -4.375 31.127 -3.784 -2.082 0.343 H1 DJD 19
DJD H2 H2 H 0 1 N Y N Y Y N -21.297 -4.540 29.577 -2.474 -1.490 1.179 H2 DJD 20
DJD HA H4 H 0 1 N N N Y N N -23.635 -4.274 29.657 -3.392 0.708 1.210 HA DJD 21
DJD HB3 H6 H 0 1 N N N N N N -22.822 -1.822 31.277 -3.347 -0.608 -1.542 HB3 DJD 22
DJD HB2 H7 H 0 1 N N N N N N -24.415 -1.926 30.453 -3.342 1.150 -1.263 HB2 DJD 23
DJD HD1 H8 H 0 1 N N N N N N -22.773 -2.702 33.521 -1.421 -1.964 -0.967 HD11 DJD 24
DJD HD2 H9 H 0 1 N N N N N N -25.526 -4.345 30.702 -1.408 2.251 -0.308 HD21 DJD 25
DJD HE1 H10 H 0 1 N N N N N N -23.653 -4.236 35.250 1.016 -2.032 -0.641 HE11 DJD 26
DJD HE2 H11 H 0 1 N N N N N N -26.401 -5.866 32.409 1.030 2.202 0.019 HE21 DJD 27
DJD H011 H12 H 0 0 N N N N N N -26.364 -10.744 35.886 7.236 0.099 -0.486 H011 DJD 28
DJD H013 H13 H 0 0 N N N N N N -24.638 -10.582 36.359 7.030 0.732 1.165 H013 DJD 29
DJD H012 H14 H 0 0 N N N N N N -25.933 -10.108 37.510 7.026 -1.024 0.879 H012 DJD 30
DJD OXT O2 O 0 1 N Y N Y N Y -21.775 -1.971 28.202 -5.784 1.355 0.263 O1 DJD 31
DJD HXT H3 H 0 1 N Y N Y N Y -21.848 -1.567 27.345 -6.743 1.406 0.148 H3 DJD 32
#
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
DJD O C DOUB N N 1
DJD C CA SING N N 2
DJD CA N SING N N 3
DJD CA CB SING N N 4
DJD CB CG SING N N 5
DJD CD2 CG DOUB Y N 6
DJD CD2 CE2 SING Y N 7
DJD CG CD1 SING Y N 8
DJD CE2 CZ DOUB Y N 9
DJD CD1 CE1 DOUB Y N 10
DJD CZ CE1 SING Y N 11
DJD CZ C07 SING N N 12
DJD N04 N03 DOUB Y N 13
DJD N04 C07 SING Y N 14
DJD N03 C02 SING Y N 15
DJD C07 N06 DOUB Y N 16
DJD C02 N05 DOUB Y N 17
DJD C02 C01 SING N N 18
DJD N06 N05 SING Y N 19
DJD N H SING N N 20
DJD N H2 SING N N 21
DJD CA HA SING N N 22
DJD CB HB3 SING N N 23
DJD CB HB2 SING N N 24
DJD CD1 HD1 SING N N 25
DJD CD2 HD2 SING N N 26
DJD CE1 HE1 SING N N 27
DJD CE2 HE2 SING N N 28
DJD C01 H011 SING N N 29
DJD C01 H013 SING N N 30
DJD C01 H012 SING N N 31
DJD C OXT SING N N 32
DJD OXT HXT SING N N 33
#
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
DJD SMILES ACDLabs 12.01 "NC(Cc1ccc(cc1)c2nnc(C)nn2)C(O)=O"
DJD InChI InChI 1.03 "InChI=1S/C12H13N5O2/c1-7-14-16-11(17-15-7)9-4-2-8(3-5-9)6-10(13)12(18)19/h2-5,10H,6,13H2,1H3,(H,18,19)/t10-/m0/s1"
DJD InChIKey InChI 1.03 MLVVYSKCLSLPPD-JTQLQIEISA-N
DJD SMILES_CANONICAL CACTVS 3.385 "Cc1nnc(nn1)c2ccc(C[C@H](N)C(O)=O)cc2"
DJD SMILES CACTVS 3.385 "Cc1nnc(nn1)c2ccc(C[CH](N)C(O)=O)cc2"
DJD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1nnc(nn1)c2ccc(cc2)C[C@@H](C(=O)O)N"
DJD SMILES "OpenEye OEToolkits" 2.0.6 "Cc1nnc(nn1)c2ccc(cc2)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
DJD "SYSTEMATIC NAME" ACDLabs 12.01 "4-(6-methyl-1,2,4,5-tetrazin-3-yl)-L-phenylalanine"
DJD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "(2~{S})-2-azanyl-3-[4-(6-methyl-1,2,4,5-tetrazin-3-yl)phenyl]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
DJD "Create component" 2017-10-26 RCSB
DJD "Initial release" 2019-10-02 RCSB
DJD "Modify backbone" 2023-11-03 PDBE
DJD "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id DJD
_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 ?
#