data_6PY
#
_chem_comp.id 6PY
_chem_comp.name
;5-acetamido-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enon
ic acid
;
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C16 H27 N5 O9"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-
enonic acid
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-05-19
_chem_comp.pdbx_modified_date 2020-07-17
_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 433.414
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6PY
_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 5JYY
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 6PY
_pdbx_chem_comp_synonyms.name
;5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-
enonic acid
;
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
# #
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
6PY N4 N12 N 0 1 N N N 375.152 155.990 62.637 -2.848 -2.055 0.142 N4 6PY 1
6PY C17 C17 C 0 1 N N N 377.935 147.036 67.056 5.347 -3.234 2.916 C17 6PY 2
6PY C20 C20 C 0 1 N N N 375.656 149.192 65.438 4.762 -0.737 0.209 C20 6PY 3
6PY C21 C21 C 0 1 N N N 376.774 150.828 63.918 2.617 0.303 -0.295 C21 6PY 4
6PY C11 C28 C 0 1 N N N 373.871 152.139 60.494 0.127 -3.125 -2.937 C11 6PY 5
6PY C6 C01 C 0 1 N N R 378.031 153.672 62.430 -0.905 1.073 -0.667 C6 6PY 6
6PY C5 C02 C 0 1 N N R 376.560 154.113 62.413 -1.135 -0.438 -0.520 C5 6PY 7
6PY C4 C03 C 0 1 N N S 376.483 155.639 62.334 -2.633 -0.676 -0.303 C4 6PY 8
6PY C3 C04 C 0 1 N N N 377.484 156.312 63.303 -3.145 0.275 0.745 C3 6PY 9
6PY C2 C05 C 0 1 N N N 378.556 155.620 63.756 -2.478 1.363 1.100 C2 6PY 10
6PY O6 O06 O 0 1 N N N 378.681 154.293 63.472 -1.283 1.706 0.559 O6 6PY 11
6PY C7 C07 C 0 1 N N R 378.192 152.183 62.605 0.573 1.344 -0.953 C7 6PY 12
6PY C8 C08 C 0 1 N N R 379.646 151.751 62.535 0.825 2.853 -0.946 C8 6PY 13
6PY C9 C09 C 0 1 N N N 379.793 150.276 62.760 2.303 3.125 -1.232 C9 6PY 14
6PY O9 O10 O 0 1 N N N 379.204 149.468 61.777 2.562 4.525 -1.112 O9 6PY 15
6PY O7 O11 O 0 1 N N N 377.725 151.844 63.838 1.388 0.713 0.070 O7 6PY 16
6PY O8 O13 O 0 1 N N N 380.151 152.126 61.332 0.023 3.475 -1.953 O8 6PY 17
6PY C14 C14 C 0 1 N N N 374.172 156.116 61.602 -4.056 -2.671 -0.086 C14 6PY 18
6PY N15 N15 N 0 1 N N N 372.881 156.401 62.015 -5.064 -1.990 -0.727 N15 6PY 19
6PY N16 N16 N 0 1 N N N 374.462 155.948 60.351 -4.246 -3.900 0.305 N16 6PY 20
6PY O18 O18 O 0 1 N N N 377.540 148.080 66.213 4.769 -2.559 1.797 O18 6PY 21
6PY C19 C19 C 0 1 N N N 376.369 147.874 65.477 5.465 -1.372 1.411 C19 6PY 22
6PY N22 N22 N 0 1 N N N 376.587 150.262 65.214 3.424 -0.291 0.606 N22 6PY 23
6PY O23 O23 O 0 1 N N N 376.158 150.453 62.991 2.999 0.468 -1.437 O23 6PY 24
6PY N5 N25 N 0 1 N N N 375.836 153.437 61.402 -0.696 -1.124 -1.738 N5 6PY 25
6PY O10 O26 O 0 1 N N N 374.054 152.846 62.690 -0.352 -3.015 -0.629 O10 6PY 26
6PY C10 C27 C 0 1 N N N 374.578 152.828 61.641 -0.324 -2.418 -1.684 C10 6PY 27
6PY C1 C29 C 0 1 N N N 379.640 156.293 64.565 -3.061 2.241 2.129 C1 6PY 28
6PY O1B O30 O 0 1 N N N 380.633 155.651 64.886 -2.408 3.356 2.513 O1B 6PY 29
6PY O1A O31 O 0 1 N N N 379.573 157.468 64.841 -4.131 1.959 2.632 O1A 6PY 30
6PY HN41 H1 H 0 0 N N N 374.889 156.153 63.588 -2.137 -2.536 0.594 HN41 6PY 31
6PY H2 H2 H 0 1 N N N 378.863 147.316 67.577 5.351 -2.568 3.779 H2 6PY 32
6PY H1 H3 H 0 1 N N N 377.144 146.842 67.795 4.761 -4.124 3.146 H1 6PY 33
6PY H9 H4 H 0 1 N N N 378.109 146.129 66.459 6.370 -3.524 2.677 H9 6PY 34
6PY H10 H5 H 0 1 N N N 375.142 149.354 66.397 5.341 0.117 -0.140 H10 6PY 35
6PY H11 H6 H 0 1 N N N 374.917 149.179 64.624 4.677 -1.471 -0.592 H11 6PY 36
6PY H111 H7 H 0 0 N N N 372.910 151.734 60.845 1.205 -3.009 -3.051 H111 6PY 37
6PY H112 H8 H 0 0 N N N 373.690 152.864 59.686 -0.119 -4.185 -2.865 H112 6PY 38
6PY H113 H9 H 0 0 N N N 374.499 151.318 60.117 -0.379 -2.693 -3.800 H113 6PY 39
6PY H6 H10 H 0 1 N N N 378.485 153.961 61.471 -1.515 1.460 -1.484 H6 6PY 40
6PY H5 H11 H 0 1 N N N 376.135 153.826 63.386 -0.575 -0.813 0.336 H5 6PY 41
6PY H4 H12 H 0 1 N N N 376.733 155.949 61.309 -3.168 -0.508 -1.238 H4 6PY 42
6PY H3 H13 H 0 1 N N N 377.328 157.333 63.618 -4.089 0.062 1.225 H3 6PY 43
6PY H7 H14 H 0 1 N N N 377.630 151.667 61.813 0.835 0.936 -1.929 H7 6PY 44
6PY H8 H15 H 0 1 N N N 380.185 152.269 63.342 0.563 3.261 0.030 H8 6PY 45
6PY H91 H16 H 0 1 N N N 379.330 150.030 63.727 2.918 2.578 -0.517 H91 6PY 46
6PY H92 H17 H 0 1 N N N 380.867 150.041 62.797 2.544 2.797 -2.244 H92 6PY 47
6PY HO9 H18 H 0 1 N N N 379.342 148.553 61.994 3.482 4.771 -1.280 HO9 6PY 48
6PY HO8 H19 H 0 1 N N N 381.062 151.862 61.274 0.203 3.159 -2.849 HO8 6PY 49
6PY H20 H20 H 0 1 N N N 372.679 156.506 62.989 -4.923 -1.076 -1.018 H20 6PY 50
6PY H21 H21 H 0 1 N N N 372.151 156.501 61.339 -5.917 -2.424 -0.888 H21 6PY 51
6PY H22 H22 H 0 1 N N N 375.428 155.727 60.217 -3.535 -4.380 0.757 H22 6PY 52
6PY H23 H23 H 0 1 N N N 375.740 147.116 65.967 6.490 -1.624 1.140 H23 6PY 53
6PY H24 H24 H 0 1 N N N 376.614 147.544 64.457 5.471 -0.668 2.243 H24 6PY 54
6PY H25 H25 H 0 1 N N N 377.116 150.618 65.984 3.119 -0.422 1.518 H25 6PY 55
6PY HN5 H26 H 0 1 N N N 376.227 153.387 60.483 -0.674 -0.647 -2.582 HN5 6PY 56
6PY HOB1 H27 H 0 0 N N N 381.246 156.219 65.338 -2.831 3.900 3.191 HOB1 6PY 57
# #
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
6PY N16 C14 DOUB N N 1
6PY C11 C10 SING N N 2
6PY O8 C8 SING N N 3
6PY N5 C10 SING N N 4
6PY N5 C5 SING N N 5
6PY C14 N15 SING N N 6
6PY C14 N4 SING N N 7
6PY C10 O10 DOUB N N 8
6PY O9 C9 SING N N 9
6PY C4 C5 SING N N 10
6PY C4 N4 SING N N 11
6PY C4 C3 SING N N 12
6PY C5 C6 SING N N 13
6PY C6 C7 SING N N 14
6PY C6 O6 SING N N 15
6PY C8 C7 SING N N 16
6PY C8 C9 SING N N 17
6PY C7 O7 SING N N 18
6PY O23 C21 DOUB N N 19
6PY C3 C2 DOUB N N 20
6PY O6 C2 SING N N 21
6PY C2 C1 SING N N 22
6PY O7 C21 SING N N 23
6PY C21 N22 SING N N 24
6PY C1 O1A DOUB N N 25
6PY C1 O1B SING N N 26
6PY N22 C20 SING N N 27
6PY C20 C19 SING N N 28
6PY C19 O18 SING N N 29
6PY O18 C17 SING N N 30
6PY N4 HN41 SING N N 31
6PY C17 H2 SING N N 32
6PY C17 H1 SING N N 33
6PY C17 H9 SING N N 34
6PY C20 H10 SING N N 35
6PY C20 H11 SING N N 36
6PY C11 H111 SING N N 37
6PY C11 H112 SING N N 38
6PY C11 H113 SING N N 39
6PY C6 H6 SING N N 40
6PY C5 H5 SING N N 41
6PY C4 H4 SING N N 42
6PY C3 H3 SING N N 43
6PY C7 H7 SING N N 44
6PY C8 H8 SING N N 45
6PY C9 H91 SING N N 46
6PY C9 H92 SING N N 47
6PY O9 HO9 SING N N 48
6PY O8 HO8 SING N N 49
6PY N15 H20 SING N N 50
6PY N15 H21 SING N N 51
6PY N16 H22 SING N N 52
6PY C19 H23 SING N N 53
6PY C19 H24 SING N N 54
6PY N22 H25 SING N N 55
6PY N5 HN5 SING N N 56
6PY O1B HOB1 SING N N 57
# #
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
6PY SMILES ACDLabs 12.01 "N(C1C(C(C(OC(NCCOC)=O)C(CO)O)OC(=C1)C(=O)O)NC(C)=O)/C(N)=N"
6PY InChI InChI 1.03 "InChI=1S/C16H27N5O9/c1-7(23)20-11-8(21-15(17)18)5-10(14(25)26)29-13(11)12(9(24)6-22)30-16(27)19-3-4-28-2/h5,8-9,11-13,22,24H,3-4,6H2,1-2H3,(H,19,27)(H,20,23)(H,25,26)(H4,17,18,21)/t8-,9+,11+,12+,13+/m0/s1"
6PY InChIKey InChI 1.03 VAIHIAVLWLNYQQ-IINAIABHSA-N
6PY SMILES_CANONICAL CACTVS 3.385 "COCCNC(=O)O[C@H]([C@H](O)CO)[C@@H]1OC(=C[C@H](NC(N)=N)[C@H]1NC(C)=O)C(O)=O"
6PY SMILES CACTVS 3.385 "COCCNC(=O)O[CH]([CH](O)CO)[CH]1OC(=C[CH](NC(N)=N)[CH]1NC(C)=O)C(O)=O"
6PY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "[H]/N=C(\N)/N[C@H]1C=C(O[C@H]([C@@H]1NC(=O)C)[C@@H]([C@@H](CO)O)OC(=O)NCCOC)C(=O)O"
6PY SMILES "OpenEye OEToolkits" 2.0.4 "CC(=O)NC1C(C=C(OC1C(C(CO)O)OC(=O)NCCOC)C(=O)O)NC(=N)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
6PY "SYSTEMATIC NAME" ACDLabs 12.01
;5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-
enonic acid
;
6PY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4
;(2~{R},3~{R},4~{S})-3-acetamido-4-carbamimidamido-2-[(1~{R},2~{R})-1-(2-methoxyethylcarbamoyloxy)-2,3-bis(oxidanyl)prop
yl]-3,4-dihydro-2~{H}-pyran-6-carboxylic acid
;
# #
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
6PY "CARBOHYDRATE ISOMER" D PDB ?
6PY "CARBOHYDRATE RING" dihydropyran PDB ?
6PY "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose PDB ?
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
6PY "Create component" 2016-05-19 PDBJ
6PY "Initial release" 2016-06-29 RCSB
6PY "Other modification" 2020-07-03 RCSB
6PY "Modify name" 2020-07-17 RCSB
6PY "Modify synonyms" 2020-07-17 RCSB
6PY "Modify internal type" 2020-07-17 RCSB
6PY "Modify linking type" 2020-07-17 RCSB
6PY "Modify atom id" 2020-07-17 RCSB
6PY "Modify component atom id" 2020-07-17 RCSB
##