data_9YC
#
_chem_comp.id 9YC
_chem_comp.name "(2~{E})-3-cyano-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylimino]propanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H14 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 2022-04-19
_chem_comp.pdbx_modified_date 2023-03-31
_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 343.229
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9YC
_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 7XET
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
9YC OAU O1 O 0 1 N N N N N N 32.109 -36.504 -37.780 -5.217 0.797 0.539 OAU 9YC 1
9YC PAT P1 P 0 1 N N N N N N 31.995 -35.035 -38.260 -3.719 1.259 0.171 PAT 9YC 2
9YC OAV O2 O 0 1 N N N N N N 32.933 -34.710 -39.469 -3.714 1.903 -1.161 OAV 9YC 3
9YC OAW O3 O 0 1 N N N N N N 30.604 -34.646 -38.629 -3.194 2.306 1.275 OAW 9YC 4
9YC OAS O4 O 0 1 N N N N N N 32.450 -34.137 -36.977 -2.751 -0.028 0.149 OAS 9YC 5
9YC CAR C1 C 0 1 N N N N N N 32.901 -32.783 -37.282 -1.379 0.037 -0.247 CAR 9YC 6
9YC CAA C2 C 0 1 Y N N N N N 33.564 -32.367 -36.120 -0.764 -1.336 -0.154 CAA 9YC 7
9YC CAB C3 C 0 1 Y N N N N N 32.925 -31.486 -35.253 -1.523 -2.415 0.260 CAB 9YC 8
9YC NAC N1 N 0 1 Y N N N N N 33.507 -31.064 -34.066 -0.995 -3.620 0.345 NAC 9YC 9
9YC CAD C4 C 0 1 Y N N N N N 34.736 -31.469 -33.683 0.268 -3.848 0.042 CAD 9YC 10
9YC CAG C5 C 0 1 N N N N N N 35.258 -30.980 -32.428 0.822 -5.245 0.156 CAG 9YC 11
9YC CAE C6 C 0 1 Y N N N N N 35.408 -32.384 -34.534 1.092 -2.816 -0.381 CAE 9YC 12
9YC OAH O5 O 0 1 N N N N N N 36.630 -32.879 -34.142 2.393 -3.055 -0.693 OAH 9YC 13
9YC CAF C7 C 0 1 Y N N N N N 34.828 -32.851 -35.766 0.566 -1.532 -0.488 CAF 9YC 14
9YC CAI C8 C 0 1 N N N N N N 35.490 -33.722 -36.659 1.423 -0.382 -0.950 CAI 9YC 15
9YC NAJ N2 N 0 1 N N N N N N 36.934 -33.327 -36.761 2.067 0.243 0.209 NAJ 9YC 16
9YC CAK C9 C 0 1 N N N N N N 37.772 -33.680 -37.745 2.912 1.190 0.038 CAK 9YC 17
9YC CAL C10 C 0 1 N N N N N N 39.238 -33.289 -37.644 3.655 1.738 1.198 CAL 9YC 18
9YC OAO O6 O 0 1 N N N N N N 40.090 -33.612 -38.493 4.456 2.635 1.036 OAO 9YC 19
9YC OAN O7 O 0 1 N N N N N N 39.587 -32.648 -36.661 3.442 1.240 2.431 OAN 9YC 20
9YC CAM C11 C 0 1 N N N N N N 37.230 -34.471 -38.916 3.151 1.747 -1.342 CAM 9YC 21
9YC CAP C12 C 0 1 N N N N N N 38.062 -34.514 -40.070 2.143 2.780 -1.635 CAP 9YC 22
9YC NAQ N3 N 0 1 N N N N N N 38.711 -34.658 -40.978 1.365 3.576 -1.861 NAQ 9YC 23
9YC H1 H1 H 0 1 N N N N N N 32.744 -36.964 -38.316 -5.855 1.523 0.570 H1 9YC 24
9YC H2 H2 H 0 1 N N N N N N 30.597 -34.290 -39.510 -3.170 1.951 2.174 H2 9YC 25
9YC H3 H3 H 0 1 N N N N N N 33.587 -32.786 -38.142 -1.314 0.396 -1.274 H3 9YC 26
9YC H4 H4 H 0 1 N N N N N N 32.045 -32.127 -37.498 -0.843 0.720 0.411 H4 9YC 27
9YC H5 H5 H 0 1 N N N N N N 31.943 -31.118 -35.513 -2.561 -2.269 0.517 H5 9YC 28
9YC H6 H6 H 0 1 N N N N N N 34.520 -30.313 -31.958 0.688 -5.768 -0.791 H6 9YC 29
9YC H7 H7 H 0 1 N N N N N N 35.462 -31.830 -31.760 1.884 -5.196 0.397 H7 9YC 30
9YC H8 H8 H 0 1 N N N N N N 36.190 -30.425 -32.610 0.295 -5.782 0.945 H8 9YC 31
9YC H9 H9 H 0 1 N N N N N N 36.883 -32.482 -33.317 2.539 -3.285 -1.621 H9 9YC 32
9YC H10 H10 H 0 1 N N N N N N 35.020 -33.656 -37.652 2.187 -0.751 -1.634 H10 9YC 33
9YC H11 H11 H 0 1 N N N N N N 35.417 -34.754 -36.286 0.801 0.353 -1.460 H11 9YC 34
9YC H12 H12 H 0 1 N N N N N N 40.522 -32.486 -36.704 3.950 1.629 3.155 H12 9YC 35
9YC H13 H13 H 0 1 N N N N N N 36.268 -34.025 -39.209 4.146 2.188 -1.388 H13 9YC 36
9YC H14 H14 H 0 1 N N N N N N 37.067 -35.505 -38.579 3.073 0.945 -2.076 H14 9YC 37
#
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
9YC NAQ CAP TRIP N N 1
9YC CAP CAM SING N N 2
9YC OAV PAT DOUB N N 3
9YC CAM CAK SING N N 4
9YC OAW PAT SING N N 5
9YC OAO CAL DOUB N N 6
9YC PAT OAU SING N N 7
9YC PAT OAS SING N N 8
9YC CAK CAL SING N N 9
9YC CAK NAJ DOUB N N 10
9YC CAL OAN SING N N 11
9YC CAR OAS SING N N 12
9YC CAR CAA SING N N 13
9YC NAJ CAI SING N N 14
9YC CAI CAF SING N N 15
9YC CAA CAF DOUB Y N 16
9YC CAA CAB SING Y N 17
9YC CAF CAE SING Y N 18
9YC CAB NAC DOUB Y N 19
9YC CAE OAH SING N N 20
9YC CAE CAD DOUB Y N 21
9YC NAC CAD SING Y N 22
9YC CAD CAG SING N N 23
9YC OAU H1 SING N N 24
9YC OAW H2 SING N N 25
9YC CAR H3 SING N N 26
9YC CAR H4 SING N N 27
9YC CAB H5 SING N N 28
9YC CAG H6 SING N N 29
9YC CAG H7 SING N N 30
9YC CAG H8 SING N N 31
9YC OAH H9 SING N N 32
9YC CAI H10 SING N N 33
9YC CAI H11 SING N N 34
9YC OAN H12 SING N N 35
9YC CAM H13 SING N N 36
9YC CAM H14 SING N N 37
#
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
9YC InChI InChI 1.03 InChI=1S/C12H14N3O7P/c1-7-11(16)9(5-15-10(2-3-13)12(17)18)8(4-14-7)6-22-23(19,20)21/h4,16H,2,5-6H2,1H3,(H,17,18)(H2,19,20,21)/b15-10+
9YC InChIKey InChI 1.03 RXBCHSOWMGDFEL-XNTDXEJSSA-N
9YC SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN=C(CC#N)C(O)=O)c1O"
9YC SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN=C(CC#N)C(O)=O)c1O"
9YC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CC#N)/C(=O)O)O"
9YC SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)CN=C(CC#N)C(=O)O)O"
#
_pdbx_chem_comp_identifier.comp_id 9YC
_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~{E})-3-cyano-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylimino]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
9YC 'Create component' 2022-04-19 PDBJ
9YC 'Initial release' 2023-04-05 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
9YC OAU O 1.877 2.485 1
9YC PAT P 1.127 3.783 2
9YC OAV O 2.425 4.535 3
9YC OAW O 0.375 5.082 4
9YC OAS O -0.172 3.033 5
9YC CAR C -0.171 1.533 6
9YC CAA C -1.469 0.782 7
9YC CAB C -2.769 1.530 8
9YC NAC N -4.067 0.780 9
9YC CAD C -4.066 -0.721 10
9YC CAG C -5.364 -1.472 11
9YC CAE C -2.766 -1.469 12
9YC OAH O -2.765 -2.970 13
9YC CAF C -1.468 -0.719 14
9YC CAI C -0.168 -1.467 15
9YC NAJ N 1.130 -0.717 16
9YC CAK C 2.430 -1.465 17
9YC CAL C 3.728 -0.714 18
9YC OAO O 3.727 0.786 19
9YC OAN O 5.028 -1.463 20
9YC CAM C 2.431 -2.965 21
9YC CAP C 1.133 -3.717 22
9YC NAQ N -0.166 -4.467 23
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
9YC NAQ CAP TRIPLE NONE 1
9YC CAP CAM SINGLE NONE 2
9YC OAV PAT DOUBLE NONE 3
9YC CAM CAK SINGLE ENDUPRIGHT 4
9YC OAW PAT SINGLE NONE 5
9YC OAO CAL DOUBLE NONE 6
9YC PAT OAU SINGLE NONE 7
9YC PAT OAS SINGLE NONE 8
9YC CAK CAL SINGLE ENDUPRIGHT 9
9YC CAK NAJ DOUBLE NONE 10
9YC CAL OAN SINGLE NONE 11
9YC CAR OAS SINGLE NONE 12
9YC CAR CAA SINGLE NONE 13
9YC NAJ CAI SINGLE ENDDOWNRIGHT 14
9YC CAI CAF SINGLE NONE 15
9YC CAA CAF DOUBLE NONE 16
9YC CAA CAB SINGLE NONE 17
9YC CAF CAE SINGLE NONE 18
9YC CAB NAC DOUBLE NONE 19
9YC CAE OAH SINGLE NONE 20
9YC CAE CAD DOUBLE NONE 21
9YC NAC CAD SINGLE NONE 22
9YC CAD CAG SINGLE NONE 23
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
9YC MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
9YC phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
9YC pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
9YC CAA S1 1
9YC CAB S1 1
9YC NAC S1 1
9YC CAD S1 1
9YC CAE S1 1
9YC CAF S1 1
9YC OAU F1 1
9YC PAT F1 1
9YC OAV F1 1
9YC OAW F1 1
9YC OAS F1 1
9YC CAB F2 1
9YC CAA F2 1
9YC CAF F2 1
9YC CAE F2 1
9YC CAD F2 1
9YC NAC F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 9YC
_pdbe_chem_comp_rdkit_properties.exactmw 343.057
_pdbe_chem_comp_rdkit_properties.amw 343.232
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 150.511
_pdbe_chem_comp_rdkit_properties.tpsa 173.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.018
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.069
_pdbe_chem_comp_rdkit_properties.chi0v 11.541
_pdbe_chem_comp_rdkit_properties.chi1v 6.625
_pdbe_chem_comp_rdkit_properties.chi2v 2.193
_pdbe_chem_comp_rdkit_properties.chi3v 2.193
_pdbe_chem_comp_rdkit_properties.chi4v 1.225
_pdbe_chem_comp_rdkit_properties.chi0n 24.647
_pdbe_chem_comp_rdkit_properties.chi1n 11.798
_pdbe_chem_comp_rdkit_properties.chi2n 1.878
_pdbe_chem_comp_rdkit_properties.chi3n 1.878
_pdbe_chem_comp_rdkit_properties.chi4n 1.022
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.310
_pdbe_chem_comp_rdkit_properties.kappa1 6.666
_pdbe_chem_comp_rdkit_properties.kappa2 7.803
_pdbe_chem_comp_rdkit_properties.kappa3 5.766
_pdbe_chem_comp_rdkit_properties.Phi 2.261
#
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
9YC OAU 3.447 1.669 3.025 ETKDGv3 1
9YC PAT 3.731 1.920 1.374 ETKDGv3 2
9YC OAV 5.221 1.998 1.135 ETKDGv3 3
9YC OAW 3.017 3.379 0.898 ETKDGv3 4
9YC OAS 3.089 0.629 0.463 ETKDGv3 5
9YC CAR 1.705 0.550 0.718 ETKDGv3 6
9YC CAA 1.074 -0.516 -0.155 ETKDGv3 7
9YC CAB 1.640 -0.748 -1.506 ETKDGv3 8
9YC NAC 1.114 -1.628 -2.302 ETKDGv3 9
9YC CAD -0.026 -2.416 -1.931 ETKDGv3 10
9YC CAG -0.538 -3.426 -2.914 ETKDGv3 11
9YC CAE -0.604 -2.227 -0.724 ETKDGv3 12
9YC OAH -1.711 -2.981 -0.320 ETKDGv3 13
9YC CAF -0.054 -1.191 0.201 ETKDGv3 14
9YC CAI -0.768 -0.934 1.517 ETKDGv3 15
9YC NAJ -1.133 0.476 1.670 ETKDGv3 16
9YC CAK -2.025 1.146 0.992 ETKDGv3 17
9YC CAL -2.189 2.582 1.286 ETKDGv3 18
9YC OAO -1.513 3.121 2.204 ETKDGv3 19
9YC OAN -3.083 3.354 0.549 ETKDGv3 20
9YC CAM -2.838 0.523 -0.118 ETKDGv3 21
9YC CAP -2.178 0.741 -1.409 ETKDGv3 22
9YC NAQ -1.657 0.912 -2.428 ETKDGv3 23
9YC H1 3.832 0.777 3.214 ETKDGv3 24
9YC H2 3.141 3.413 -0.084 ETKDGv3 25
9YC H3 1.551 0.304 1.790 ETKDGv3 26
9YC H4 1.200 1.513 0.478 ETKDGv3 27
9YC H5 2.493 -0.179 -1.849 ETKDGv3 28
9YC H6 -0.482 -4.445 -2.477 ETKDGv3 29
9YC H7 0.077 -3.409 -3.838 ETKDGv3 30
9YC H8 -1.587 -3.189 -3.191 ETKDGv3 31
9YC H9 -2.142 -3.698 -0.891 ETKDGv3 32
9YC H10 -1.673 -1.562 1.643 ETKDGv3 33
9YC H11 -0.092 -1.220 2.349 ETKDGv3 34
9YC H12 -3.200 4.342 0.742 ETKDGv3 35
9YC H13 -3.849 0.982 -0.152 ETKDGv3 36
9YC H14 -2.991 -0.562 0.040 ETKDGv3 37
#