data_YND
#
_chem_comp.id YND
_chem_comp.name N-(3-chloropyridin-4-yl)-2-(3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H12 Cl N5 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-03-12
_chem_comp.pdbx_modified_date 2022-03-04
_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 317.730
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YND
_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 7LWE
_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.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
YND C1 C1 C 0 1 N N N N N N -19.354 -4.212 17.713 5.369 -2.232 1.156 C1 YND 1
YND N N1 N 0 1 Y N N N N N -18.790 -2.864 12.470 1.495 1.014 -1.102 N YND 2
YND CA C2 C 0 1 N N N N N N -19.196 -1.785 11.655 0.177 0.756 -1.688 CA YND 3
YND C C3 C 0 1 N N N N N N -20.585 -1.865 11.159 -0.859 0.717 -0.595 C YND 4
YND O O1 O 0 1 N N N N N N -21.324 -2.757 11.543 -0.530 0.887 0.560 O YND 5
YND CAD C4 C 0 1 Y N N N N N -24.561 -1.007 9.528 -3.939 0.956 2.278 CAD YND 6
YND CAE C5 C 0 1 Y N N N N N -23.359 -1.271 10.168 -2.983 1.106 1.296 CAE YND 7
YND CAF C6 C 0 1 Y N N N N N -17.725 -4.799 12.996 3.279 2.131 -0.401 CAF YND 8
YND CAG C7 C 0 1 Y N N N N N -17.988 -3.921 11.961 2.075 2.250 -0.988 CAG YND 9
YND CAH C8 C 0 1 N N N N N N -19.788 -2.701 15.826 3.186 -1.969 0.092 CAH YND 10
YND CAI C9 C 0 1 Y N N N N N -23.521 0.263 7.932 -5.095 -0.593 1.018 CAI YND 11
YND CAP C10 C 0 1 Y N N N N N -22.267 0.027 8.519 -4.187 -0.493 -0.016 CAP YND 12
YND CAQ C11 C 0 1 Y N N N N N -22.148 -0.748 9.640 -3.099 0.369 0.118 CAQ YND 13
YND CAR C12 C 0 1 N N N N N N -18.447 -4.709 15.493 4.509 -0.060 0.452 CAR YND 14
YND CAS C13 C 0 1 Y N N N N N -18.389 -4.256 14.136 3.474 0.710 -0.129 CAS YND 15
YND CAT C14 C 0 1 Y N N N N N -19.011 -3.081 13.759 2.321 0.059 -0.586 CAT YND 16
YND NAK N2 N 0 1 Y N N N N N -24.658 -0.240 8.418 -4.952 0.125 2.116 NAK YND 17
YND NAL N3 N 0 1 N N N N N N -19.733 -2.284 14.597 2.227 -1.274 -0.452 NAL YND 18
YND NAM N4 N 0 1 N N N N N N -20.937 -0.936 10.251 -2.152 0.493 -0.900 NAM YND 19
YND NAN N5 N 0 1 N N N N N N -19.212 -3.842 16.309 4.327 -1.397 0.553 NAN YND 20
YND OAB O2 O 0 1 N N N N N N -17.950 -5.715 15.988 5.528 0.467 0.863 OAB YND 21
YND CLAC CL1 CL 0 0 N N N N N N -20.940 0.783 7.788 -4.384 -1.444 -1.456 CLAC YND 22
YND H1 H1 H 0 1 N N N N N N -19.967 -3.460 18.231 5.051 -3.274 1.145 H1 YND 23
YND H2 H2 H 0 1 N N N N N N -19.842 -5.195 17.785 6.293 -2.128 0.587 H2 YND 24
YND H3 H3 H 0 1 N N N N N N -18.360 -4.261 18.182 5.539 -1.914 2.185 H3 YND 25
YND HA2 H4 H 0 1 N N N N N N -18.525 -1.744 10.785 -0.068 1.551 -2.393 HA2 YND 26
YND HA1 H5 H 0 1 N N N N N N -19.095 -0.859 12.240 0.192 -0.201 -2.209 HA1 YND 27
YND HAD H6 H 0 1 N N N N N N -25.465 -1.435 9.936 -3.856 1.523 3.194 HAD YND 28
YND HAE H7 H 0 1 N N N N N N -23.344 -1.872 11.065 -2.155 1.785 1.437 HAE YND 29
YND HAF H8 H 0 1 N N N N N N -17.140 -5.706 12.951 3.970 2.931 -0.179 HAF YND 30
YND HAG H9 H 0 1 N N N N N N -17.644 -4.021 10.942 1.633 3.178 -1.319 HAG YND 31
YND HAH H10 H 0 1 N N N N N N -20.338 -2.092 16.528 3.068 -3.039 0.179 HAH YND 32
YND HAI H11 H 0 1 N N N N N N -23.567 0.880 7.047 -5.938 -1.262 0.925 HAI YND 33
YND HNA H12 H 0 1 N N N N N N -20.216 -0.296 9.986 -2.425 0.417 -1.828 HNA YND 34
#
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
YND CLAC CAP SING N N 1
YND CAI NAK DOUB Y N 2
YND CAI CAP SING Y N 3
YND NAK CAD SING Y N 4
YND CAP CAQ DOUB Y N 5
YND CAD CAE DOUB Y N 6
YND CAQ CAE SING Y N 7
YND CAQ NAM SING N N 8
YND NAM C SING N N 9
YND C O DOUB N N 10
YND C CA SING N N 11
YND CA N SING N N 12
YND CAG N SING Y N 13
YND CAG CAF DOUB Y N 14
YND N CAT SING Y N 15
YND CAF CAS SING Y N 16
YND CAT CAS DOUB Y N 17
YND CAT NAL SING N N 18
YND CAS CAR SING N N 19
YND NAL CAH DOUB N N 20
YND CAR OAB DOUB N N 21
YND CAR NAN SING N N 22
YND CAH NAN SING N N 23
YND NAN C1 SING N N 24
YND C1 H1 SING N N 25
YND C1 H2 SING N N 26
YND C1 H3 SING N N 27
YND CA HA2 SING N N 28
YND CA HA1 SING N N 29
YND CAD HAD SING N N 30
YND CAE HAE SING N N 31
YND CAF HAF SING N N 32
YND CAG HAG SING N N 33
YND CAH HAH SING N N 34
YND CAI HAI SING N N 35
YND NAM HNA SING N N 36
#
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
YND SMILES ACDLabs 12.01 Clc1cnccc1NC(=O)Cn1ccc2c1N=CN(C)C2=O
YND InChI InChI 1.03 InChI=1S/C14H12ClN5O2/c1-19-8-17-13-9(14(19)22)3-5-20(13)7-12(21)18-11-2-4-16-6-10(11)15/h2-6,8H,7H2,1H3,(H,16,18,21)
YND InChIKey InChI 1.03 KGIZMIOMJSGVEF-UHFFFAOYSA-N
YND SMILES_CANONICAL CACTVS 3.385 CN1C=Nc2n(CC(=O)Nc3ccncc3Cl)ccc2C1=O
YND SMILES CACTVS 3.385 CN1C=Nc2n(CC(=O)Nc3ccncc3Cl)ccc2C1=O
YND SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CN1C=Nc2c(ccn2CC(=O)Nc3ccncc3Cl)C1=O
YND SMILES "OpenEye OEToolkits" 2.0.7 CN1C=Nc2c(ccn2CC(=O)Nc3ccncc3Cl)C1=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
YND "SYSTEMATIC NAME" ACDLabs 12.01 N-(3-chloropyridin-4-yl)-2-(3-methyl-4-oxo-3,4-dihydro-7H-pyrrolo[2,3-d]pyrimidin-7-yl)acetamide
YND "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(3-chloranylpyridin-4-yl)-2-(3-methyl-4-oxidanylidene-pyrrolo[2,3-d]pyrimidin-7-yl)ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YND 'Create component' 2021-03-12 RCSB
YND 'Initial release' 2022-03-09 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
YND C1 C 3.000 3.610 1
YND N N 8.316 0.903 2
YND CA C 8.783 -0.523 3
YND C C 10.250 -0.833 4
YND O O 11.252 0.284 5
YND CAD C 14.653 -1.760 6
YND CAE C 13.186 -1.451 7
YND CAF C 8.316 3.317 8
YND CAG C 9.192 2.110 9
YND CAH C 4.299 1.360 10
YND CAI C 14.118 -4.303 11
YND CAP C 12.650 -3.993 12
YND CAQ C 12.184 -2.567 13
YND CAR C 5.598 3.610 14
YND CAS C 6.897 2.860 15
YND CAT C 6.897 1.360 16
YND NAK N 15.119 -3.186 17
YND NAL N 5.598 0.610 18
YND NAM N 10.716 -2.258 19
YND NAN N 4.299 2.860 20
YND OAB O 5.598 5.110 21
YND CLAC Cl 11.648 -5.110 22
#
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
YND CLAC CAP SINGLE NONE 1
YND CAI NAK SINGLE NONE 2
YND CAI CAP DOUBLE NONE 3
YND NAK CAD DOUBLE NONE 4
YND CAP CAQ SINGLE NONE 5
YND CAD CAE SINGLE NONE 6
YND CAQ CAE DOUBLE NONE 7
YND CAQ NAM SINGLE NONE 8
YND NAM C SINGLE NONE 9
YND C O DOUBLE NONE 10
YND C CA SINGLE NONE 11
YND CA N SINGLE NONE 12
YND CAG N SINGLE NONE 13
YND CAG CAF DOUBLE NONE 14
YND N CAT SINGLE NONE 15
YND CAF CAS SINGLE NONE 16
YND CAT CAS DOUBLE NONE 17
YND CAT NAL SINGLE NONE 18
YND CAS CAR SINGLE NONE 19
YND NAL CAH DOUBLE NONE 20
YND CAR OAB DOUBLE NONE 21
YND CAR NAN SINGLE NONE 22
YND CAH NAN SINGLE NONE 23
YND NAN C1 SINGLE NONE 24
#
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
YND MurckoScaffold S1 scaffold 'O=C(Cn1ccc2c(=O)[nH]cnc21)Nc1ccncc1' InChI=1S/C13H11N5O2/c19-11(17-9-1-4-14-5-2-9)7-18-6-3-10-12(18)15-8-16-13(10)20/h1-6,8H,7H2,(H,14,17,19)(H,15,16,20) PNKYDCRCKVFSFG-UHFFFAOYSA-N
YND amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YND peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
YND pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
YND pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
YND pyrrole F5 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
YND N S1 1
YND CA S1 1
YND C S1 1
YND O S1 1
YND CAD S1 1
YND CAE S1 1
YND CAF S1 1
YND CAG S1 1
YND CAH S1 1
YND CAI S1 1
YND CAP S1 1
YND CAQ S1 1
YND CAR S1 1
YND CAS S1 1
YND CAT S1 1
YND NAK S1 1
YND NAL S1 1
YND NAM S1 1
YND NAN S1 1
YND OAB S1 1
YND NAM F1 1
YND C F1 1
YND O F1 1
YND CA F1 1
YND O F2 1
YND C F2 1
YND CA F2 1
YND N F2 1
YND CAD F3 1
YND CAE F3 1
YND CAQ F3 1
YND CAP F3 1
YND CAI F3 1
YND NAK F3 1
YND CAS F4 1
YND CAT F4 1
YND NAL F4 1
YND CAH F4 1
YND NAN F4 1
YND CAR F4 1
YND CAG F5 1
YND CAF F5 1
YND CAS F5 1
YND CAT F5 1
YND N F5 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YND
_pdbe_chem_comp_rdkit_properties.exactmw 317.068
_pdbe_chem_comp_rdkit_properties.amw 317.736
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.143
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_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 146.647
_pdbe_chem_comp_rdkit_properties.tpsa 81.810
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.513
_pdbe_chem_comp_rdkit_properties.CrippenMR 79.929
_pdbe_chem_comp_rdkit_properties.chi0v 11.186
_pdbe_chem_comp_rdkit_properties.chi1v 5.908
_pdbe_chem_comp_rdkit_properties.chi2v 2.677
_pdbe_chem_comp_rdkit_properties.chi3v 2.677
_pdbe_chem_comp_rdkit_properties.chi4v 1.620
_pdbe_chem_comp_rdkit_properties.chi0n 22.431
_pdbe_chem_comp_rdkit_properties.chi1n 11.478
_pdbe_chem_comp_rdkit_properties.chi2n 2.414
_pdbe_chem_comp_rdkit_properties.chi3n 2.414
_pdbe_chem_comp_rdkit_properties.chi4n 1.488
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.670
_pdbe_chem_comp_rdkit_properties.kappa1 5.846
_pdbe_chem_comp_rdkit_properties.kappa2 5.608
_pdbe_chem_comp_rdkit_properties.kappa3 2.579
_pdbe_chem_comp_rdkit_properties.Phi 1.490
#
_pdbe_chem_comp_external_mappings.comp_id YND
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id YND
#
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
YND C1 -3.658 2.737 0.814 ETKDGv3 1
YND N -1.057 -1.550 -1.800 ETKDGv3 2
YND CA 0.214 -1.559 -2.516 ETKDGv3 3
YND C 1.350 -1.468 -1.542 ETKDGv3 4
YND O 1.855 -2.528 -1.084 ETKDGv3 5
YND CAD 4.991 -0.453 0.905 ETKDGv3 6
YND CAE 3.957 -0.688 -0.121 ETKDGv3 7
YND CAF -2.471 -2.205 -0.135 ETKDGv3 8
YND CAG -1.586 -2.637 -1.033 ETKDGv3 9
YND CAH -2.039 1.927 -0.945 ETKDGv3 10
YND CAI 3.565 1.168 1.933 ETKDGv3 11
YND CAP 2.598 0.984 1.024 ETKDGv3 12
YND CAQ 2.798 -0.009 -0.063 ETKDGv3 13
YND CAR -3.226 0.270 0.483 ETKDGv3 14
YND CAS -2.526 -0.755 -0.282 ETKDGv3 15
YND CAT -1.694 -0.411 -1.236 ETKDGv3 16
YND NAK 4.787 0.417 1.851 ETKDGv3 17
YND NAL -1.442 0.957 -1.586 ETKDGv3 18
YND NAM 1.788 -0.184 -1.069 ETKDGv3 19
YND NAN -2.954 1.646 0.143 ETKDGv3 20
YND OAB -4.031 -0.037 1.403 ETKDGv3 21
YND CLAC 1.095 1.887 1.161 ETKDGv3 22
YND H1 -3.699 2.551 1.909 ETKDGv3 23
YND H2 -4.692 2.813 0.416 ETKDGv3 24
YND H3 -3.136 3.704 0.651 ETKDGv3 25
YND HA2 0.252 -0.704 -3.224 ETKDGv3 26
YND HA1 0.299 -2.495 -3.109 ETKDGv3 27
YND HAD 5.924 -1.000 0.868 ETKDGv3 28
YND HAE 4.159 -1.385 -0.924 ETKDGv3 29
YND HAF -2.999 -2.813 0.587 ETKDGv3 30
YND HAG -1.274 -3.668 -1.144 ETKDGv3 31
YND HAH -1.834 2.950 -1.232 ETKDGv3 32
YND HAI 3.432 1.879 2.738 ETKDGv3 33
YND HNA 1.255 0.659 -1.377 ETKDGv3 34
#