data_VYT
#
_chem_comp.id VYT
_chem_comp.name "Azo-Combretastatin A4 (trans)"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H18 N2 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "2-methoxy-5-[(E)-(3,4,5-trimethoxyphenyl)diazenyl]phenol"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-09-20
_chem_comp.pdbx_modified_date 2023-09-22
_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 318.325
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VYT
_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 7YZ1
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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.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
VYT N1 N1 N 0 1 N N N 14.289 -17.202 17.300 -0.130 0.566 -0.056 N1 VYT 1
VYT C7 C1 C 0 1 Y N N 13.688 -19.940 14.946 3.465 1.209 -0.133 C7 VYT 2
VYT C8 C2 C 0 1 N N N 15.709 -21.005 14.360 3.750 3.571 -0.136 C8 VYT 3
VYT C9 C3 C 0 1 Y N N 12.308 -19.860 14.708 3.959 -0.092 -0.152 C9 VYT 4
VYT O1 O1 O 0 1 N N N 14.308 -20.937 14.260 4.326 2.263 -0.151 O1 VYT 5
VYT C1 C4 C 0 1 Y N N 15.741 -13.769 20.530 -5.030 0.229 0.064 C1 VYT 6
VYT C5 C5 C 0 1 Y N N 13.518 -18.088 16.456 1.217 0.349 -0.088 C5 VYT 7
VYT C6 C6 C 0 1 Y N N 14.305 -19.064 15.835 2.101 1.433 -0.101 C6 VYT 8
VYT C4 C7 C 0 1 Y N N 14.435 -15.592 18.906 -2.292 -0.217 -0.011 C4 VYT 9
VYT O4 O2 O 0 1 N N N 13.610 -13.456 21.688 -5.402 -2.126 0.036 O4 VYT 10
VYT C3 C8 C 0 1 Y N N 15.794 -15.336 18.713 -2.791 1.088 0.019 C3 VYT 11
VYT O3 O3 O 0 1 N N N 10.235 -18.843 14.988 3.568 -2.443 -0.159 O3 VYT 12
VYT C2 C9 C 0 1 Y N N 16.448 -14.423 19.527 -4.152 1.305 0.057 C2 VYT 13
VYT N N2 N 0 1 N N N 13.640 -16.486 18.096 -0.945 -0.434 -0.044 N VYT 14
VYT C C10 C 0 1 N N N 17.432 -12.196 20.959 -6.804 1.810 0.125 C VYT 15
VYT O O4 O 0 1 N N N 16.295 -12.888 21.413 -6.370 0.449 0.095 O VYT 16
VYT C10 C11 C 0 1 N N N 11.581 -20.342 12.583 5.970 -0.419 1.074 C10 VYT 17
VYT C11 C12 C 0 1 Y N N 11.549 -18.872 15.346 3.082 -1.173 -0.139 C11 VYT 18
VYT C12 C13 C 0 1 N N N 9.350 -18.255 15.912 2.611 -3.504 -0.144 C12 VYT 19
VYT C13 C14 C 0 1 Y N N 12.149 -17.970 16.224 1.717 -0.957 -0.107 C13 VYT 20
VYT C14 C15 C 0 1 Y N N 13.710 -14.950 19.915 -3.177 -1.301 0.002 C14 VYT 21
VYT C15 C16 C 0 1 Y N N 14.371 -14.028 20.724 -4.539 -1.075 0.034 C15 VYT 22
VYT O2 O5 O 0 1 N N N 11.712 -20.796 13.913 5.301 -0.308 -0.184 O2 VYT 23
VYT H6 H1 H 0 1 N N N 16.079 -21.850 13.762 4.544 4.317 -0.153 H6 VYT 24
VYT H7 H2 H 0 1 N N N 16.149 -20.069 13.984 3.113 3.698 -1.011 H7 VYT 25
VYT H8 H3 H 0 1 N N N 15.995 -21.148 15.413 3.154 3.695 0.768 H8 VYT 26
VYT H5 H4 H 0 1 N N N 15.363 -19.136 16.040 1.719 2.442 -0.086 H5 VYT 27
VYT H17 H5 H 0 1 N N N 14.138 -12.845 22.188 -5.670 -2.417 -0.846 H17 VYT 28
VYT H4 H6 H 0 1 N N N 16.335 -15.848 17.931 -2.111 1.927 0.009 H4 VYT 29
VYT H3 H7 H 0 1 N N N 17.499 -14.221 19.383 -4.537 2.314 0.080 H3 VYT 30
VYT H2 H8 H 0 1 N N N 17.790 -11.519 21.749 -7.893 1.844 0.148 H2 VYT 31
VYT H1 H9 H 0 1 N N N 18.224 -12.917 20.708 -6.407 2.299 1.014 H1 VYT 32
VYT H H10 H 0 1 N N N 17.172 -11.611 20.065 -6.444 2.326 -0.765 H VYT 33
VYT H9 H11 H 0 1 N N N 11.098 -21.121 11.975 7.034 -0.590 0.906 H9 VYT 34
VYT H10 H12 H 0 1 N N N 10.966 -19.430 12.566 5.835 0.502 1.640 H10 VYT 35
VYT H11 H13 H 0 1 N N N 12.577 -20.121 12.171 5.552 -1.255 1.635 H11 VYT 36
VYT H12 H14 H 0 1 N N N 8.326 -18.291 15.513 2.007 -3.436 0.761 H12 VYT 37
VYT H14 H15 H 0 1 N N N 9.393 -18.807 16.863 1.966 -3.424 -1.019 H14 VYT 38
VYT H13 H16 H 0 1 N N N 9.641 -17.208 16.082 3.131 -4.462 -0.162 H13 VYT 39
VYT H15 H17 H 0 1 N N N 11.568 -17.201 16.711 1.036 -1.796 -0.097 H15 VYT 40
VYT H16 H18 H 0 1 N N N 12.662 -15.164 20.064 -2.796 -2.311 -0.022 H16 VYT 41
#
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
VYT C10 O2 SING N N 1
VYT O2 C9 SING N N 2
VYT O1 C8 SING N N 3
VYT O1 C7 SING N N 4
VYT C9 C7 DOUB Y N 5
VYT C9 C11 SING Y N 6
VYT C7 C6 SING Y N 7
VYT O3 C11 SING N N 8
VYT O3 C12 SING N N 9
VYT C11 C13 DOUB Y N 10
VYT C6 C5 DOUB Y N 11
VYT C13 C5 SING Y N 12
VYT C5 N1 SING N N 13
VYT N1 N DOUB N N 14
VYT N C4 SING N N 15
VYT C3 C4 DOUB Y N 16
VYT C3 C2 SING Y N 17
VYT C4 C14 SING Y N 18
VYT C2 C1 DOUB Y N 19
VYT C14 C15 DOUB Y N 20
VYT C1 C15 SING Y N 21
VYT C1 O SING N N 22
VYT C15 O4 SING N N 23
VYT C O SING N N 24
VYT C8 H6 SING N N 25
VYT C8 H7 SING N N 26
VYT C8 H8 SING N N 27
VYT C6 H5 SING N N 28
VYT O4 H17 SING N N 29
VYT C3 H4 SING N N 30
VYT C2 H3 SING N N 31
VYT C H2 SING N N 32
VYT C H1 SING N N 33
VYT C H SING N N 34
VYT C10 H9 SING N N 35
VYT C10 H10 SING N N 36
VYT C10 H11 SING N N 37
VYT C12 H12 SING N N 38
VYT C12 H14 SING N N 39
VYT C12 H13 SING N N 40
VYT C13 H15 SING N N 41
VYT C14 H16 SING N N 42
#
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
VYT InChI InChI 1.06 "InChI=1S/C16H18N2O5/c1-20-13-6-5-10(7-12(13)19)17-18-11-8-14(21-2)16(23-4)15(9-11)22-3/h5-9,19H,1-4H3/b18-17+"
VYT InChIKey InChI 1.06 AIRZFEKQGRSBNX-ISLYRVAYSA-N
VYT SMILES_CANONICAL CACTVS 3.385 "COc1ccc(cc1O)N=Nc2cc(OC)c(OC)c(OC)c2"
VYT SMILES CACTVS 3.385 "COc1ccc(cc1O)N=Nc2cc(OC)c(OC)c(OC)c2"
VYT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1O)/N=N/c2cc(c(c(c2)OC)OC)OC"
VYT SMILES "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1O)N=Nc2cc(c(c(c2)OC)OC)OC"
#
_pdbx_chem_comp_identifier.comp_id VYT
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier "2-methoxy-5-[(~{E})-(3,4,5-trimethoxyphenyl)diazenyl]phenol"
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id VYT
_pdbx_chem_comp_synonyms.name "2-methoxy-5-[(E)-(3,4,5-trimethoxyphenyl)diazenyl]phenol"
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VYT "Create component" 2023-09-20 PDBE
VYT "Initial release" 2023-09-27 RCSB
#