data_BGI
#
_chem_comp.id BGI
_chem_comp.name "(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H25 N5 O10"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "Nikkomycin Z"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-11-15
_chem_comp.pdbx_modified_date 2022-07-08
_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 495.440
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code BGI
_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 7STN
_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.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
BGI C13 C1 C 0 1 N N N 141.145 122.190 96.776 -1.440 -2.621 -0.162 C13 BGI 1
BGI C17 C2 C 0 1 N N R 140.459 120.053 94.092 2.148 -1.854 -0.388 C17 BGI 2
BGI C20 C3 C 0 1 N N R 139.227 119.716 92.268 3.613 -0.119 -0.729 C20 BGI 3
BGI C24 C4 C 0 1 N N N 135.380 119.736 92.427 3.937 2.946 1.299 C24 BGI 4
BGI C28 C5 C 0 1 N N N 137.556 118.690 90.637 4.551 2.072 -1.205 C28 BGI 5
BGI C01 C6 C 0 1 N N N 141.180 121.221 99.399 -3.724 -1.373 1.157 C01 BGI 6
BGI C02 C7 C 0 1 N N S 142.518 121.588 98.794 -3.344 -1.037 -0.287 C02 BGI 7
BGI C03 C8 C 0 1 N N S 143.448 122.171 99.872 -4.602 -0.664 -1.072 C03 BGI 8
BGI C04 C9 C 0 1 Y N N 143.985 121.106 100.872 -5.174 0.618 -0.525 C04 BGI 9
BGI C06 C10 C 0 1 Y N N 145.130 120.696 102.835 -6.054 1.775 1.263 C06 BGI 10
BGI C07 C11 C 0 1 Y N N 144.968 119.325 102.689 -6.212 2.919 0.494 C07 BGI 11
BGI C08 C12 C 0 1 Y N N 144.289 118.817 101.590 -5.833 2.891 -0.844 C08 BGI 12
BGI C09 C13 C 0 1 Y N N 143.792 119.740 100.670 -5.306 1.716 -1.355 C09 BGI 13
BGI C12 C14 C 0 1 N N S 142.303 122.636 97.686 -2.680 -2.253 -0.936 C12 BGI 14
BGI C16 C15 C 0 1 N N S 139.965 120.359 95.381 0.910 -2.292 0.396 C16 BGI 15
BGI C18 C16 C 0 1 N N S 140.541 121.361 93.203 3.433 -2.298 0.346 C18 BGI 16
BGI C19 C17 C 0 1 N N R 139.520 121.333 92.521 4.419 -1.130 0.116 C19 BGI 17
BGI C23 C18 C 0 1 N N N 136.775 119.971 92.766 3.627 1.685 0.929 C23 BGI 18
BGI C25 C19 C 0 1 N N N 135.041 118.997 91.225 4.577 3.799 0.368 C25 BGI 19
BGI C32 C20 C 0 1 N N N 139.306 119.093 96.001 0.891 -1.599 1.734 C32 BGI 20
BGI N05 N1 N 0 1 Y N N 144.641 121.538 101.935 -5.548 0.677 0.739 N05 BGI 21
BGI N15 N2 N 0 1 N N N 141.101 120.806 96.269 -0.296 -1.934 -0.356 N15 BGI 22
BGI N22 N3 N 0 1 N N N 137.846 119.472 91.906 3.939 1.253 -0.331 N22 BGI 23
BGI N27 N4 N 0 1 N N N 136.075 118.484 90.349 4.862 3.337 -0.866 N27 BGI 24
BGI N35 N5 N 0 1 N N N 141.974 123.915 98.262 -3.616 -3.385 -0.927 N35 BGI 25
BGI O10 O1 O 0 1 N N N 145.497 118.443 103.661 -6.734 4.049 1.039 O10 BGI 26
BGI O11 O2 O 0 1 N N N 144.527 122.772 99.248 -4.269 -0.486 -2.450 O11 BGI 27
BGI O14 O3 O 0 1 N N N 140.292 122.955 96.488 -1.472 -3.530 0.639 O14 BGI 28
BGI O21 O4 O 0 1 N N N 139.492 119.138 93.374 2.228 -0.413 -0.438 O21 BGI 29
BGI O26 O5 O 0 1 N N N 133.901 118.810 90.956 4.865 4.941 0.679 O26 BGI 30
BGI O29 O6 O 0 1 N N N 138.402 118.277 89.933 4.827 1.665 -2.317 O29 BGI 31
BGI O30 O7 O 0 1 N N N 139.756 122.010 91.229 5.570 -1.578 -0.603 O30 BGI 32
BGI O31 O8 O 0 1 N N N 141.761 121.307 92.311 3.943 -3.506 -0.223 O31 BGI 33
BGI O33 O9 O 0 1 N N N 139.903 118.456 96.909 1.902 -1.780 2.598 O33 BGI 34
BGI O34 O10 O 0 1 N N N 138.177 118.708 95.598 -0.035 -0.880 2.029 O34 BGI 35
BGI H171 H1 H 0 0 N N N 141.454 119.587 94.141 2.125 -2.268 -1.396 H171 BGI 36
BGI H201 H2 H 0 0 N N N 139.889 119.390 91.452 3.815 -0.265 -1.790 H201 BGI 37
BGI H241 H3 H 0 0 N N N 134.597 120.111 93.069 3.696 3.300 2.291 H241 BGI 38
BGI H011 H4 H 0 0 N N N 141.328 120.472 100.191 -4.518 -2.119 1.159 H011 BGI 39
BGI H013 H5 H 0 0 N N N 140.712 122.120 99.827 -2.853 -1.768 1.679 H013 BGI 40
BGI H012 H6 H 0 0 N N N 140.527 120.804 98.618 -4.072 -0.471 1.660 H012 BGI 41
BGI H021 H7 H 0 0 N N N 142.984 120.692 98.359 -2.649 -0.197 -0.293 H021 BGI 42
BGI H031 H8 H 0 0 N N N 142.879 122.916 100.447 -5.340 -1.461 -0.977 H031 BGI 43
BGI H061 H9 H 0 0 N N N 145.661 121.082 103.693 -6.349 1.785 2.302 H061 BGI 44
BGI H081 H10 H 0 0 N N N 144.152 117.755 101.453 -5.944 3.765 -1.469 H081 BGI 45
BGI H091 H11 H 0 0 N N N 143.256 119.395 99.798 -5.001 1.658 -2.389 H091 BGI 46
BGI H121 H12 H 0 0 N N N 143.221 122.713 97.085 -2.408 -2.013 -1.964 H121 BGI 47
BGI H161 H13 H 0 0 N N N 139.211 121.158 95.327 0.937 -3.371 0.546 H161 BGI 48
BGI H181 H14 H 0 0 N N N 140.614 122.233 93.870 3.239 -2.430 1.410 H181 BGI 49
BGI H191 H15 H 0 0 N N N 138.634 121.760 93.014 4.711 -0.685 1.067 H191 BGI 50
BGI H231 H16 H 0 0 N N N 137.022 120.520 93.663 3.136 1.020 1.625 H231 BGI 51
BGI H151 H17 H 0 0 N N N 141.826 120.162 96.514 -0.271 -1.204 -0.994 H151 BGI 52
BGI H271 H18 H 0 0 N N N 135.807 117.978 89.529 5.304 3.915 -1.508 H271 BGI 53
BGI H351 H19 H 0 0 N N N 142.720 124.215 98.856 -3.224 -4.181 -1.407 H351 BGI 54
BGI H352 H20 H 0 0 N N N 141.839 124.585 97.532 -3.882 -3.626 0.016 H352 BGI 55
BGI H101 H22 H 0 0 N N N 145.928 118.944 104.343 -6.074 4.642 1.424 H101 BGI 56
BGI H111 H23 H 0 0 N N N 145.110 123.137 99.904 -3.616 0.209 -2.611 H111 BGI 57
BGI H301 H24 H 0 0 N N N 139.923 122.933 91.380 6.113 -2.215 -0.119 H301 BGI 58
BGI H311 H25 H 0 0 N N N 142.546 121.329 92.846 4.750 -3.830 0.200 H311 BGI 59
BGI H2 H26 H 0 1 N N N 139.371 117.717 97.180 1.845 -1.314 3.444 H2 BGI 60
#
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
BGI O29 C28 DOUB N N 1
BGI N27 C28 SING N N 2
BGI N27 C25 SING N N 3
BGI C28 N22 SING N N 4
BGI O26 C25 DOUB N N 5
BGI C25 C24 SING N N 6
BGI O30 C19 SING N N 7
BGI N22 C20 SING N N 8
BGI N22 C23 SING N N 9
BGI C20 C19 SING N N 10
BGI C20 O21 SING N N 11
BGI O31 C18 SING N N 12
BGI C24 C23 DOUB N N 13
BGI C19 C18 SING N N 14
BGI C18 C17 SING N N 15
BGI O21 C17 SING N N 16
BGI C17 C16 SING N N 17
BGI C16 C32 SING N N 18
BGI C16 N15 SING N N 19
BGI O34 C32 DOUB N N 20
BGI C32 O33 SING N N 21
BGI N15 C13 SING N N 22
BGI O14 C13 DOUB N N 23
BGI C13 C12 SING N N 24
BGI C12 N35 SING N N 25
BGI C12 C02 SING N N 26
BGI C02 C01 SING N N 27
BGI C02 C03 SING N N 28
BGI O11 C03 SING N N 29
BGI C03 C04 SING N N 30
BGI C09 C04 DOUB Y N 31
BGI C09 C08 SING Y N 32
BGI C04 N05 SING Y N 33
BGI C08 C07 DOUB Y N 34
BGI N05 C06 DOUB Y N 35
BGI C07 C06 SING Y N 36
BGI C07 O10 SING N N 37
BGI C17 H171 SING N N 38
BGI C20 H201 SING N N 39
BGI C24 H241 SING N N 40
BGI C01 H011 SING N N 41
BGI C01 H013 SING N N 42
BGI C01 H012 SING N N 43
BGI C02 H021 SING N N 44
BGI C03 H031 SING N N 45
BGI C06 H061 SING N N 46
BGI C08 H081 SING N N 47
BGI C09 H091 SING N N 48
BGI C12 H121 SING N N 49
BGI C16 H161 SING N N 50
BGI C18 H181 SING N N 51
BGI C19 H191 SING N N 52
BGI C23 H231 SING N N 53
BGI N15 H151 SING N N 54
BGI N27 H271 SING N N 55
BGI N35 H351 SING N N 56
BGI N35 H352 SING N N 57
BGI O10 H101 SING N N 58
BGI O11 H111 SING N N 59
BGI O30 H301 SING N N 60
BGI O31 H311 SING N N 61
BGI O33 H2 SING N N 62
#
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
BGI SMILES ACDLabs 12.01 "Oc1ccc(nc1)C(O)C(C)C(N)C(=O)NC(C1OC(N2C=CC(=O)NC2=O)C(O)C1O)C(=O)O"
BGI InChI InChI 1.03 "InChI=1S/C20H25N5O10/c1-7(13(28)9-3-2-8(26)6-22-9)11(21)17(31)24-12(19(32)33)16-14(29)15(30)18(35-16)25-5-4-10(27)23-20(25)34/h2-7,11-16,18,26,28-30H,21H2,1H3,(H,24,31)(H,32,33)(H,23,27,34)/t7-,11-,12-,13-,14-,15+,16+,18+/m0/s1"
BGI InChIKey InChI 1.03 WWJFFVUVFNBJTN-VHDFTHOZSA-N
BGI SMILES_CANONICAL CACTVS 3.385 "C[C@@H]([C@H](N)C(=O)N[C@@H]([C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O)C(O)=O)[C@H](O)c3ccc(O)cn3"
BGI SMILES CACTVS 3.385 "C[CH]([CH](N)C(=O)N[CH]([CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O)C(O)=O)[CH](O)c3ccc(O)cn3"
BGI SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H]([C@@H](c1ccc(cn1)O)O)[C@@H](C(=O)N[C@@H]([C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)C(=O)O)N"
BGI SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(c1ccc(cn1)O)O)C(C(=O)NC(C2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)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
BGI "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-{[(2S,3S,4S)-2-amino-4-hydroxy-4-(5-hydroxypyridin-2-yl)-3-methylbutanoyl]amino}[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]acetic acid (non-preferred name)"
BGI "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S},3~{S},4~{S})-2-azanyl-3-methyl-4-oxidanyl-4-(5-oxidanylpyridin-2-yl)butanoyl]amino]-2-[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]ethanoic acid"
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id BGI
_pdbx_chem_comp_synonyms.name "Nikkomycin Z"
_pdbx_chem_comp_synonyms.provenance AUTHOR
_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
BGI "Create component" 2021-11-15 RCSB
BGI "Initial release" 2022-07-13 RCSB
#