data_VB4 # _chem_comp.id VB4 _chem_comp.name "(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C19 H20 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-07-22 _chem_comp.pdbx_modified_date 2021-01-29 _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 433.352 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VB4 _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 6XOY _chem_comp.pdbx_subcomponent_list "PLP TRP" _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.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 VB4 N03 N1 N 0 1 Y N N -7.178 -12.990 11.798 -2.847 2.938 1.518 N1 PLP 1 VB4 C02 C10 C 0 1 Y N N -7.407 -12.287 10.708 -1.671 3.530 1.468 C2 PLP 2 VB4 C01 C9 C 0 1 N N N -6.364 -12.267 9.595 -1.481 4.863 2.145 C2A PLP 3 VB4 C29 C19 C 0 1 Y N N -8.576 -11.565 10.527 -0.607 2.942 0.801 C3 PLP 4 VB4 O30 O7 O 0 1 N N N -8.791 -10.833 9.354 0.603 3.556 0.754 O3 PLP 5 VB4 C12 C14 C 0 1 Y N N -9.524 -11.583 11.542 -0.802 1.699 0.176 C4 PLP 6 VB4 C13 C1 C 0 1 N N N -10.847 -10.827 11.424 0.298 1.031 -0.545 C4A PLP 7 VB4 C05 C12 C 0 1 Y N N -9.255 -12.337 12.674 -2.070 1.113 0.259 C5 PLP 8 VB4 C04 C11 C 0 1 Y N N -8.065 -13.035 12.782 -3.070 1.772 0.944 C6 PLP 9 VB4 C06 C13 C 0 1 N N N -10.277 -12.379 13.803 -2.340 -0.219 -0.393 C5A PLP 10 VB4 O07 O1 O 0 1 N N N -11.466 -12.937 13.314 -3.700 -0.595 -0.164 O4P PLP 11 VB4 P08 P1 P 0 1 N N N -12.070 -14.263 14.046 -4.337 -1.965 -0.719 P PLP 12 VB4 O11 O4 O 0 1 N N N -13.441 -14.544 13.494 -3.520 -3.111 -0.258 O1P PLP 13 VB4 O09 O2 O 0 1 N N N -12.178 -13.966 15.540 -5.840 -2.121 -0.166 O2P PLP 14 VB4 O10 O3 O 0 1 N N N -11.176 -15.476 13.855 -4.357 -1.934 -2.329 O3P PLP 15 VB4 N14 N2 N 0 1 N N N -11.156 -10.167 10.398 1.463 1.589 -0.609 N TRP 16 VB4 C15 C2 C 0 1 N N R -12.454 -9.517 10.401 2.555 0.926 -1.326 CA TRP 17 VB4 C26 C8 C 0 1 N N N -12.511 -8.510 9.272 3.030 1.812 -2.448 C TRP 18 VB4 O28 O6 O 0 1 N N N -12.578 -8.919 8.087 2.510 2.887 -2.631 O TRP 19 VB4 C16 C15 C 0 1 N N N -13.516 -10.606 10.185 3.711 0.661 -0.360 CB TRP 20 VB4 C17 C3 C 0 1 Y N N -14.967 -10.208 10.492 3.271 -0.323 0.693 CG TRP 21 VB4 C18 C16 C 0 1 Y N N -15.953 -9.930 9.556 2.786 -0.026 1.909 CD1 TRP 22 VB4 C21 C5 C 0 1 Y N N -15.550 -10.086 11.775 3.285 -1.783 0.583 CD2 TRP 23 VB4 N19 N3 N 0 1 Y N N -17.082 -9.643 10.211 2.493 -1.177 2.588 NE1 TRP 24 VB4 C20 C4 C 0 1 Y N N -16.855 -9.730 11.561 2.787 -2.270 1.805 CE2 TRP 25 VB4 C22 C6 C 0 1 Y N N -15.061 -10.246 13.096 3.667 -2.677 -0.420 CE3 TRP 26 VB4 C25 C18 C 0 1 Y N N -17.729 -9.518 12.663 2.683 -3.644 1.999 CZ2 TRP 27 VB4 C23 C17 C 0 1 Y N N -15.922 -10.034 14.175 3.554 -4.022 -0.209 CZ3 TRP 28 VB4 C24 C7 C 0 1 Y N N -17.247 -9.674 13.952 3.068 -4.508 0.998 CH2 TRP 29 VB4 O27 O5 O 0 1 N N N -12.498 -7.281 9.523 4.032 1.406 -3.245 OXT TRP 30 VB4 H011 H7 H 0 0 N N N -6.027 -11.233 9.427 -2.423 5.411 2.141 H2A1 PLP 31 VB4 H012 H5 H 0 0 N N N -5.505 -12.890 9.885 -1.157 4.706 3.174 H2A2 PLP 32 VB4 H013 H6 H 0 0 N N N -6.808 -12.663 8.670 -0.724 5.437 1.610 H2A3 PLP 33 VB4 H301 H20 H 0 0 N N N -9.637 -10.403 9.399 1.192 3.322 1.484 HO3 PLP 34 VB4 H131 H1 H 0 0 N N N -11.541 -10.860 12.250 0.131 0.075 -1.020 H4A PLP 35 VB4 H041 H8 H 0 0 N N N -7.859 -13.617 13.668 -4.051 1.325 1.012 H6 PLP 36 VB4 H061 H9 H 0 0 N N N -9.891 -12.995 14.628 -2.160 -0.143 -1.465 H5A1 PLP 37 VB4 H062 H10 H 0 0 N N N -10.469 -11.359 14.166 -1.679 -0.973 0.034 H5A2 PLP 38 VB4 H1 H17 H 0 1 N N N -13.087 -14.021 15.809 -6.287 -2.927 -0.461 HOP2 PLP 39 VB4 H2 H18 H 0 1 N N N -11.666 -16.167 13.425 -4.875 -1.208 -2.701 HOP3 PLP 40 VB4 H151 H2 H 0 0 N N N -12.635 -9.012 11.361 2.199 -0.020 -1.735 HA TRP 41 VB4 H161 H12 H 0 0 N N N -13.258 -11.459 10.830 4.557 0.249 -0.911 HB2 TRP 42 VB4 H162 H11 H 0 0 N N N -13.469 -10.916 9.131 4.009 1.595 0.116 HB3 TRP 43 VB4 H181 H13 H 0 0 N N N -15.829 -9.943 8.483 2.648 0.974 2.295 HD1 TRP 44 VB4 H191 H16 H 0 0 N N N -17.954 -9.403 9.785 2.130 -1.217 3.487 HE1 TRP 45 VB4 H221 H3 H 0 0 N N N -14.033 -10.529 13.266 4.049 -2.306 -1.360 HE3 TRP 46 VB4 H251 H15 H 0 0 N N N -18.759 -9.238 12.496 2.302 -4.032 2.932 HZ2 TRP 47 VB4 H231 H14 H 0 0 N N N -15.558 -10.150 15.185 3.849 -4.713 -0.985 HZ3 TRP 48 VB4 H241 H4 H 0 0 N N N -17.906 -9.515 14.792 2.987 -5.574 1.151 HH2 TRP 49 VB4 H3 H19 H 0 1 N N N -12.545 -6.791 8.711 4.302 2.009 -3.951 HXT TRP 50 # # 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 VB4 O28 C26 DOUB N N 1 VB4 C26 O27 SING N N 2 VB4 C26 C15 SING N N 3 VB4 O30 C29 SING N N 4 VB4 C18 N19 SING Y N 5 VB4 C18 C17 DOUB Y N 6 VB4 C01 C02 SING N N 7 VB4 C16 C15 SING N N 8 VB4 C16 C17 SING N N 9 VB4 N19 C20 SING Y N 10 VB4 N14 C15 SING N N 11 VB4 N14 C13 DOUB N N 12 VB4 C17 C21 SING Y N 13 VB4 C29 C02 DOUB Y N 14 VB4 C29 C12 SING Y N 15 VB4 C02 N03 SING Y N 16 VB4 C13 C12 SING N N 17 VB4 C12 C05 DOUB Y N 18 VB4 C20 C21 DOUB Y N 19 VB4 C20 C25 SING Y N 20 VB4 C21 C22 SING Y N 21 VB4 N03 C04 DOUB Y N 22 VB4 C25 C24 DOUB Y N 23 VB4 C05 C04 SING Y N 24 VB4 C05 C06 SING N N 25 VB4 C22 C23 DOUB Y N 26 VB4 O07 C06 SING N N 27 VB4 O07 P08 SING N N 28 VB4 O11 P08 DOUB N N 29 VB4 O10 P08 SING N N 30 VB4 C24 C23 SING Y N 31 VB4 P08 O09 SING N N 32 VB4 C13 H131 SING N N 33 VB4 C15 H151 SING N N 34 VB4 C22 H221 SING N N 35 VB4 C24 H241 SING N N 36 VB4 C01 H012 SING N N 37 VB4 C01 H013 SING N N 38 VB4 C01 H011 SING N N 39 VB4 C04 H041 SING N N 40 VB4 C06 H061 SING N N 41 VB4 C06 H062 SING N N 42 VB4 C16 H162 SING N N 43 VB4 C16 H161 SING N N 44 VB4 C18 H181 SING N N 45 VB4 C23 H231 SING N N 46 VB4 C25 H251 SING N N 47 VB4 N19 H191 SING N N 48 VB4 O09 H1 SING N N 49 VB4 O10 H2 SING N N 50 VB4 O27 H3 SING N N 51 VB4 O30 H301 SING N N 52 # # 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 VB4 SMILES ACDLabs 12.01 "n1cc(c(c(c1C)O)[C@H]=NC(C(O)=O)Cc3c2ccccc2nc3)COP(O)(=O)O" VB4 InChI InChI 1.03 "InChI=1S/C19H20N3O7P/c1-11-18(23)15(13(8-20-11)10-29-30(26,27)28)9-22-17(19(24)25)6-12-7-21-16-5-3-2-4-14(12)16/h2-5,7-9,17,21,23H,6,10H2,1H3,(H,24,25)(H2,26,27,28)/b22-9+/t17-/m1/s1" VB4 InChIKey InChI 1.03 MFRRQHVPLFTBMS-KCBMDGGTSA-N VB4 SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](Cc2c[nH]c3ccccc23)C(O)=O)c1O" VB4 SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](Cc2c[nH]c3ccccc23)C(O)=O)c1O" VB4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H](Cc2c[nH]c3c2cccc3)C(=O)O)O" VB4 SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(Cc2c[nH]c3c2cccc3)C(=O)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 VB4 "SYSTEMATIC NAME" ACDLabs 12.01 "(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-tryptophan" VB4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-3-(1~{H}-indol-3-yl)-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]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 VB4 "Create component" 2020-07-22 RCSB VB4 "Modify subcomponent list" 2020-07-27 RCSB VB4 "Initial release" 2021-02-03 RCSB ##