data_64A
#
_chem_comp.id 64A
_chem_comp.name "{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H16 N2 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-01-24
_chem_comp.pdbx_modified_date 2016-02-05
_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 312.275
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 64A
_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 5HLF
_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
64A C2 C1 C 0 1 N N N N N N -1.556 22.323 159.057 -4.792 -0.552 0.669 C2 64A 1
64A C3 C2 C 0 1 N N N N N N -0.432 22.810 159.703 -4.730 0.695 0.003 C3 64A 2
64A C4 C3 C 0 1 N N N N N N -0.572 23.813 160.817 -5.963 1.553 -0.128 C4 64A 3
64A C5 C4 C 0 1 N N N N N N 0.814 22.340 159.288 -3.553 1.107 -0.514 C5 64A 4
64A C12 C5 C 0 1 N N N N N N 4.970 23.936 158.459 3.552 0.126 -0.211 C12 64A 5
64A C10 C6 C 0 1 N N S N N N 4.516 21.651 157.736 1.254 0.638 -0.661 C10 64A 6
64A C13 C7 C 0 1 N N N N N N 5.249 24.495 159.780 4.386 -1.122 -0.075 C13 64A 7
64A N21 N1 N 0 1 N N N N N N -1.413 21.427 158.069 -3.675 -1.299 0.779 N21 64A 8
64A N6 N2 N 0 1 N N N N N N 0.892 21.439 158.292 -2.443 0.316 -0.386 N6 64A 9
64A C22 C8 C 0 1 N N N N N N -0.213 20.997 157.693 -2.514 -0.865 0.255 C22 64A 10
64A C7 C9 C 0 1 N N R N N N 2.211 20.933 157.830 -1.166 0.761 -0.947 C7 64A 11
64A C20 C10 C 0 1 N N N N N N 3.104 22.078 157.471 -0.060 0.762 0.138 C20 64A 12
64A C9 C11 C 0 1 N N N N N N 4.456 20.353 158.502 0.890 -0.014 -2.007 C9 64A 13
64A C8 C12 C 0 1 N N N N N N 3.017 20.075 158.819 -0.632 -0.263 -1.979 C8 64A 14
64A O1 O1 O 0 1 N N N N N N -2.775 22.743 159.418 -5.843 -0.944 1.144 O1 64A 15
64A O11 O2 O 0 1 N N N N N N 5.191 22.569 158.433 2.181 -0.186 0.048 O11 64A 16
64A O18 O3 O 0 1 N N N N N N 5.310 24.760 156.328 3.299 1.515 1.676 O18 64A 17
64A O17 O4 O 0 1 N N N N N N 6.777 25.196 157.741 5.259 1.679 0.667 O17 64A 18
64A O14 O5 O 0 1 N N N N N N 4.339 24.804 160.493 5.712 -1.068 -0.275 O14 64A 19
64A O15 O6 O 0 1 N N N N N N 6.385 24.652 160.154 3.861 -2.171 0.213 O15 64A 20
64A O23 O7 O 0 1 N N N N N N -0.132 20.210 156.820 -1.515 -1.549 0.363 O23 64A 21
64A C16 C13 C 0 1 N N N N N N 5.733 24.670 157.450 4.027 1.158 0.780 C16 64A 22
64A H1 H1 H 0 1 N N N N N N 0.424 24.077 161.201 -6.805 1.053 0.349 H1 64A 23
64A H2 H2 H 0 1 N N N N N N -1.069 24.717 160.436 -5.789 2.514 0.355 H2 64A 24
64A H3 H3 H 0 1 N N N N N N -1.174 23.378 161.628 -6.184 1.712 -1.183 H3 64A 25
64A H4 H4 H 0 1 N N N N N N 1.714 22.699 159.765 -3.486 2.055 -1.026 H4 64A 26
64A H5 H5 H 0 1 N N N N N N 3.905 24.114 158.251 3.650 0.521 -1.222 H5 64A 27
64A H6 H6 H 0 1 N N N N N N 5.006 21.458 156.770 1.684 1.625 -0.828 H6 64A 28
64A H7 H7 H 0 1 N N N N N N -2.226 21.075 157.606 -3.708 -2.153 1.238 H7 64A 29
64A H8 H8 H 0 1 N N N N N N 2.049 20.330 156.924 -1.267 1.748 -1.399 H8 64A 30
64A H9 H9 H 0 1 N N N N N N 2.855 22.955 158.087 -0.182 -0.090 0.807 H9 64A 31
64A H10 H10 H 0 1 N N N N N N 2.982 22.330 156.407 -0.078 1.695 0.700 H10 64A 32
64A H11 H11 H 0 1 N N N N N N 4.869 19.538 157.890 1.144 0.657 -2.827 H11 64A 33
64A H12 H12 H 0 1 N N N N N N 5.034 20.441 159.434 1.422 -0.959 -2.119 H12 64A 34
64A H13 H13 H 0 1 N N N N N N 2.788 20.364 159.855 -0.846 -1.281 -1.651 H13 64A 35
64A H14 H14 H 0 1 N N N N N N 2.790 19.008 158.677 -1.067 -0.078 -2.961 H14 64A 36
64A H15 H15 H 0 1 N N N N N N 7.134 25.636 156.978 5.519 2.338 1.325 H15 64A 37
64A H16 H16 H 0 1 N N N N N N 4.679 25.153 161.308 6.205 -1.894 -0.177 H16 64A 38
#
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
64A O18 C16 DOUB N N 1
64A O23 C22 DOUB N N 2
64A C16 O17 SING N N 3
64A C16 C12 SING N N 4
64A C20 C10 SING N N 5
64A C20 C7 SING N N 6
64A C22 N21 SING N N 7
64A C22 N6 SING N N 8
64A C10 O11 SING N N 9
64A C10 C9 SING N N 10
64A C7 N6 SING N N 11
64A C7 C8 SING N N 12
64A N21 C2 SING N N 13
64A N6 C5 SING N N 14
64A O11 C12 SING N N 15
64A C12 C13 SING N N 16
64A C9 C8 SING N N 17
64A C2 O1 DOUB N N 18
64A C2 C3 SING N N 19
64A C5 C3 DOUB N N 20
64A C3 C4 SING N N 21
64A C13 O15 DOUB N N 22
64A C13 O14 SING N N 23
64A C4 H1 SING N N 24
64A C4 H2 SING N N 25
64A C4 H3 SING N N 26
64A C5 H4 SING N N 27
64A C12 H5 SING N N 28
64A C10 H6 SING N N 29
64A N21 H7 SING N N 30
64A C7 H8 SING N N 31
64A C20 H9 SING N N 32
64A C20 H10 SING N N 33
64A C9 H11 SING N N 34
64A C9 H12 SING N N 35
64A C8 H13 SING N N 36
64A C8 H14 SING N N 37
64A O17 H15 SING N N 38
64A O14 H16 SING N N 39
#
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
64A SMILES ACDLabs 12.01 C1(=O)C(C)=CN(C(N1)=O)C2CCC(OC(C(=O)O)C(=O)O)C2
64A InChI InChI 1.03 InChI=1S/C13H16N2O7/c1-6-5-15(13(21)14-10(6)16)7-2-3-8(4-7)22-9(11(17)18)12(19)20/h5,7-9H,2-4H2,1H3,(H,17,18)(H,19,20)(H,14,16,21)/t7-,8+/m1/s1
64A InChIKey InChI 1.03 LBUPGXBDONMGHG-SFYZADRCSA-N
64A SMILES_CANONICAL CACTVS 3.385 CC1=CN([C@@H]2CC[C@@H](C2)OC(C(O)=O)C(O)=O)C(=O)NC1=O
64A SMILES CACTVS 3.385 CC1=CN([CH]2CC[CH](C2)OC(C(O)=O)C(O)=O)C(=O)NC1=O
64A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CC1=CN(C(=O)NC1=O)[C@@H]2CC[C@@H](C2)OC(C(=O)O)C(=O)O
64A SMILES "OpenEye OEToolkits" 2.0.4 CC1=CN(C(=O)NC1=O)C2CCC(C2)OC(C(=O)O)C(=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
64A "SYSTEMATIC NAME" ACDLabs 12.01 "{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}propanedioic acid"
64A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "2-[(1~{S},3~{R})-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]cyclopentyl]oxypropanedioic 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
64A 'Create component' 2016-01-24 RCSB
64A 'Initial release' 2016-02-10 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
64A C2 C 6.395 5.614 1
64A C3 C 5.096 4.864 2
64A C4 C 3.797 5.614 3
64A C5 C 5.096 3.364 4
64A C12 C 5.373 -3.778 5
64A C10 C 5.645 -1.194 6
64A C13 C 6.865 -3.935 7
64A N21 N 7.694 4.864 8
64A N6 N 6.395 2.614 9
64A C22 C 7.694 3.364 10
64A C7 C 6.395 1.114 11
64A C20 C 5.181 0.233 12
64A C9 C 7.145 -1.194 13
64A C8 C 7.609 0.233 14
64A O1 O 6.395 7.114 15
64A O11 O 4.763 -2.408 16
64A O18 O 5.102 -6.362 17
64A O17 O 3.000 -4.835 18
64A O14 O 7.747 -2.721 19
64A O15 O 7.475 -5.305 20
64A O23 O 8.993 2.614 21
64A C16 C 4.492 -4.991 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
64A O18 C16 DOUBLE NONE 1
64A O23 C22 DOUBLE NONE 2
64A C16 O17 SINGLE NONE 3
64A C16 C12 SINGLE NONE 4
64A C20 C10 SINGLE NONE 5
64A C20 C7 SINGLE NONE 6
64A C22 N21 SINGLE NONE 7
64A C22 N6 SINGLE NONE 8
64A C10 O11 SINGLE BEGINDASH 9
64A C10 C9 SINGLE NONE 10
64A C7 N6 SINGLE BEGINDASH 11
64A C7 C8 SINGLE NONE 12
64A N21 C2 SINGLE NONE 13
64A N6 C5 SINGLE NONE 14
64A O11 C12 SINGLE NONE 15
64A C12 C13 SINGLE NONE 16
64A C9 C8 SINGLE NONE 17
64A C2 O1 DOUBLE NONE 18
64A C2 C3 SINGLE NONE 19
64A C5 C3 DOUBLE NONE 20
64A C3 C4 SINGLE NONE 21
64A C13 O15 DOUBLE NONE 22
64A C13 O14 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
64A MurckoScaffold S1 scaffold 'O=c1ccn(C2CCCC2)c(=O)[nH]1' InChI=1S/C9H12N2O2/c12-8-5-6-11(9(13)10-8)7-3-1-2-4-7/h5-7H,1-4H2,(H,10,12,13) OZKLJGHFJCKYKI-UHFFFAOYSA-N
64A cyclopentane F1 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
64A pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
64A C2 S1 1
64A C3 S1 1
64A C5 S1 1
64A C10 S1 1
64A N21 S1 1
64A N6 S1 1
64A C22 S1 1
64A C7 S1 1
64A C20 S1 1
64A C9 S1 1
64A C8 S1 1
64A O1 S1 1
64A O23 S1 1
64A C10 F1 1
64A C20 F1 1
64A C7 F1 1
64A C8 F1 1
64A C9 F1 1
64A C3 F2 1
64A C2 F2 1
64A N21 F2 1
64A C22 F2 1
64A N6 F2 1
64A C5 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 64A
_pdbe_chem_comp_rdkit_properties.exactmw 312.096
_pdbe_chem_comp_rdkit_properties.amw 312.278
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.538
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 146.418
_pdbe_chem_comp_rdkit_properties.tpsa 138.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.238
_pdbe_chem_comp_rdkit_properties.CrippenMR 72.830
_pdbe_chem_comp_rdkit_properties.chi0v 10.252
_pdbe_chem_comp_rdkit_properties.chi1v 5.251
_pdbe_chem_comp_rdkit_properties.chi2v 2.151
_pdbe_chem_comp_rdkit_properties.chi3v 2.151
_pdbe_chem_comp_rdkit_properties.chi4v 1.269
_pdbe_chem_comp_rdkit_properties.chi0n 26.252
_pdbe_chem_comp_rdkit_properties.chi1n 13.015
_pdbe_chem_comp_rdkit_properties.chi2n 2.151
_pdbe_chem_comp_rdkit_properties.chi3n 2.151
_pdbe_chem_comp_rdkit_properties.chi4n 1.269
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.420
_pdbe_chem_comp_rdkit_properties.kappa1 5.051
_pdbe_chem_comp_rdkit_properties.kappa2 6.141
_pdbe_chem_comp_rdkit_properties.kappa3 3.247
_pdbe_chem_comp_rdkit_properties.Phi 1.410
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
64A UniChem PDBe 64A
64A UniChem ZINC ZINC000263620688
64A UniChem PubChem 117094742
#
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
64A C2 4.214 1.422 0.579 ETKDGv3 1
64A C3 4.035 0.053 0.057 ETKDGv3 2
64A C4 5.168 -0.635 -0.654 ETKDGv3 3
64A C5 2.891 -0.610 0.303 ETKDGv3 4
64A C12 -3.305 0.600 -0.839 ETKDGv3 5
64A C10 -1.837 -0.772 0.363 ETKDGv3 6
64A C13 -4.647 -0.055 -0.694 ETKDGv3 7
64A N21 3.191 2.010 1.379 ETKDGv3 8
64A N6 1.772 0.007 0.989 ETKDGv3 9
64A C22 1.994 1.279 1.641 ETKDGv3 10
64A C7 0.487 -0.708 1.193 ETKDGv3 11
64A C20 -0.727 0.168 0.860 ETKDGv3 12
64A C9 -1.207 -2.161 0.276 ETKDGv3 13
64A C8 0.292 -1.938 0.306 ETKDGv3 14
64A O1 5.270 2.067 0.342 ETKDGv3 15
64A O11 -2.283 -0.379 -0.925 ETKDGv3 16
64A O18 -3.142 0.876 -3.213 ETKDGv3 17
64A O17 -3.503 2.800 -2.011 ETKDGv3 18
64A O14 -5.601 0.503 0.151 ETKDGv3 19
64A O15 -4.925 -1.091 -1.357 ETKDGv3 20
64A O23 1.151 1.746 2.453 ETKDGv3 21
64A C16 -3.298 1.426 -2.088 ETKDGv3 22
64A H1 5.727 0.089 -1.285 ETKDGv3 23
64A H2 4.796 -1.442 -1.321 ETKDGv3 24
64A H3 5.861 -1.074 0.093 ETKDGv3 25
64A H4 2.822 -1.637 -0.027 ETKDGv3 26
64A H5 -3.142 1.297 0.018 ETKDGv3 27
64A H6 -2.673 -0.818 1.104 ETKDGv3 28
64A H7 3.331 2.957 1.799 ETKDGv3 29
64A H8 0.420 -1.031 2.257 ETKDGv3 30
64A H9 -0.459 0.902 0.067 ETKDGv3 31
64A H10 -1.075 0.723 1.758 ETKDGv3 32
64A H11 -1.505 -2.765 1.162 ETKDGv3 33
64A H12 -1.513 -2.706 -0.644 ETKDGv3 34
64A H13 0.632 -1.731 -0.733 ETKDGv3 35
64A H14 0.822 -2.827 0.713 ETKDGv3 36
64A H15 -3.515 3.371 -2.848 ETKDGv3 37
64A H16 -6.516 0.081 0.253 ETKDGv3 38
#