data_YX7
#
_chem_comp.id YX7
_chem_comp.name "[(1S)-3-amino-1-(hexanoylamino)-3-oxopropyl]boronic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H19 B N2 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-04-05
_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 230.069
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YX7
_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 7MDC
_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
YX7 C01 C1 C 0 1 N N N N N N 1.546 33.962 62.613 7.022 0.266 0.092 C01 YX7 1
YX7 C02 C2 C 0 1 N N N N N N 1.355 33.025 61.429 5.663 -0.429 -0.012 C02 YX7 2
YX7 C03 C3 C 0 1 N N N N N N 1.765 33.656 60.098 4.551 0.621 0.001 C03 YX7 3
YX7 C04 C4 C 0 1 N N N N N N 1.419 32.747 58.916 3.192 -0.074 -0.103 C04 YX7 4
YX7 C05 C5 C 0 1 N N N N N N 2.381 32.935 57.754 2.079 0.976 -0.091 C05 YX7 5
YX7 C06 C6 C 0 1 N N N N N N 1.866 32.246 56.497 0.741 0.291 -0.193 C06 YX7 6
YX7 N07 N1 N 0 1 N N N N N N 2.700 31.308 55.774 -0.391 1.022 -0.201 N07 YX7 7
YX7 C08 C7 C 0 1 N N S N N N 2.220 30.666 54.567 -1.685 0.367 -0.412 C08 YX7 8
YX7 C09 C8 C 0 1 N N N N N N 2.783 29.251 54.514 -2.795 1.216 0.211 C09 YX7 9
YX7 C10 C9 C 0 1 N N N N N N 2.468 28.378 55.726 -4.134 0.605 -0.109 C10 YX7 10
YX7 N11 N2 N 0 1 N N N N N N 3.519 27.988 56.643 -5.265 1.194 0.327 N11 YX7 11
YX7 O12 O1 O 0 1 N N N N N N 1.350 28.019 55.929 -4.195 -0.416 -0.761 O12 YX7 12
YX7 O14 O2 O 0 1 N N N N N N 1.862 32.657 53.208 -1.423 -1.172 1.655 O14 YX7 13
YX7 O22 O3 O 0 1 N N N N N N 4.100 31.888 53.467 -1.903 -2.212 -0.521 O22 YX7 14
YX7 O23 O4 O 0 1 N N N N N N 0.777 32.469 56.102 0.683 -0.918 -0.268 O23 YX7 15
YX7 B13 B1 B 0 1 N N N N N N 2.708 31.489 53.313 -1.670 -1.051 0.262 B13 YX7 16
YX7 H1 H1 H 0 1 N N N N N N 1.235 33.453 63.538 7.069 0.835 1.021 H1 YX7 17
YX7 H2 H2 H 0 1 N N N N N N 2.606 34.245 62.689 7.815 -0.482 0.083 H2 YX7 18
YX7 H3 H3 H 0 1 N N N N N N 0.935 34.865 62.468 7.150 0.942 -0.754 H3 YX7 19
YX7 H4 H4 H 0 1 N N N N N N 0.293 32.744 61.372 5.616 -0.998 -0.940 H4 YX7 20
YX7 H5 H5 H 0 1 N N N N N N 1.964 32.124 61.593 5.535 -1.104 0.835 H5 YX7 21
YX7 H6 H6 H 0 1 N N N N N N 2.850 33.834 60.106 4.598 1.190 0.929 H6 YX7 22
YX7 H7 H7 H 0 1 N N N N N N 1.237 34.614 59.979 4.679 1.296 -0.846 H7 YX7 23
YX7 H8 H8 H 0 1 N N N N N N 0.400 32.980 58.575 3.145 -0.643 -1.032 H8 YX7 24
YX7 H9 H9 H 0 1 N N N N N N 1.464 31.699 59.248 3.064 -0.749 0.743 H9 YX7 25
YX7 H10 H10 H 0 1 N N N N N N 3.358 32.507 58.024 2.126 1.544 0.838 H10 YX7 26
YX7 H11 H11 H 0 1 N N N N N N 2.495 34.010 57.553 2.207 1.651 -0.937 H11 YX7 27
YX7 H12 H12 H 0 1 N N N N N N 3.618 31.101 56.112 -0.350 1.981 -0.067 H12 YX7 28
YX7 H13 H13 H 0 1 N N N N N N 1.121 30.626 54.560 -1.867 0.258 -1.481 H13 YX7 29
YX7 H14 H14 H 0 1 N N N N N N 2.373 28.755 53.622 -2.661 1.252 1.292 H14 YX7 30
YX7 H15 H15 H 0 1 N N N N N N 3.877 29.324 54.422 -2.750 2.227 -0.195 H15 YX7 31
YX7 H16 H16 H 0 1 N N N N N N 3.304 27.422 57.439 -5.217 2.011 0.848 H16 YX7 32
YX7 H17 H17 H 0 1 N N N N N N 4.460 28.285 56.480 -6.128 0.801 0.121 H17 YX7 33
YX7 H18 H18 H 0 1 N N N N N N 0.957 32.385 53.108 -1.340 -0.325 2.115 H18 YX7 34
YX7 H19 H19 H 0 1 N N N N N N 4.646 31.114 53.535 -1.986 -2.038 -1.468 H19 YX7 35
#
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
YX7 O14 B13 SING N N 1
YX7 B13 O22 SING N N 2
YX7 B13 C08 SING N N 3
YX7 C09 C08 SING N N 4
YX7 C09 C10 SING N N 5
YX7 C08 N07 SING N N 6
YX7 C10 O12 DOUB N N 7
YX7 C10 N11 SING N N 8
YX7 N07 C06 SING N N 9
YX7 O23 C06 DOUB N N 10
YX7 C06 C05 SING N N 11
YX7 C05 C04 SING N N 12
YX7 C04 C03 SING N N 13
YX7 C03 C02 SING N N 14
YX7 C02 C01 SING N N 15
YX7 C01 H1 SING N N 16
YX7 C01 H2 SING N N 17
YX7 C01 H3 SING N N 18
YX7 C02 H4 SING N N 19
YX7 C02 H5 SING N N 20
YX7 C03 H6 SING N N 21
YX7 C03 H7 SING N N 22
YX7 C04 H8 SING N N 23
YX7 C04 H9 SING N N 24
YX7 C05 H10 SING N N 25
YX7 C05 H11 SING N N 26
YX7 N07 H12 SING N N 27
YX7 C08 H13 SING N N 28
YX7 C09 H14 SING N N 29
YX7 C09 H15 SING N N 30
YX7 N11 H16 SING N N 31
YX7 N11 H17 SING N N 32
YX7 O14 H18 SING N N 33
YX7 O22 H19 SING N N 34
#
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
YX7 SMILES ACDLabs 12.01 "O=C(NC(CC(N)=O)B(O)O)CCCCC"
YX7 InChI InChI 1.03 "InChI=1S/C9H19BN2O4/c1-2-3-4-5-9(14)12-7(10(15)16)6-8(11)13/h7,15-16H,2-6H2,1H3,(H2,11,13)(H,12,14)/t7-/m1/s1"
YX7 InChIKey InChI 1.03 JFQHYAGISMLDGO-SSDOTTSWSA-N
YX7 SMILES_CANONICAL CACTVS 3.385 "CCCCCC(=O)N[C@H](CC(N)=O)B(O)O"
YX7 SMILES CACTVS 3.385 "CCCCCC(=O)N[CH](CC(N)=O)B(O)O"
YX7 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "B([C@@H](CC(=O)N)NC(=O)CCCCC)(O)O"
YX7 SMILES "OpenEye OEToolkits" 2.0.7 "B(C(CC(=O)N)NC(=O)CCCCC)(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
YX7 "SYSTEMATIC NAME" ACDLabs 12.01 "[(1S)-3-amino-1-(hexanoylamino)-3-oxopropyl]boronic acid"
YX7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(1~{S})-3-azanyl-1-(hexanoylamino)-3-oxidanylidene-propyl]boronic 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
YX7 "Create component" 2021-04-05 RCSB
YX7 "Initial release" 2022-09-28 RCSB
YX7 "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id YX7
_pdbx_chem_comp_pcm.modified_residue_id SER
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Lipid/lipid-like
_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 B13
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#