data_2K8
#
_chem_comp.id 2K8
_chem_comp.name "(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H9 N5 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 6-carboxy-5,6,7,8-tetrahydropterin
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-11-14
_chem_comp.pdbx_modified_date 2021-03-13
_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 211.178
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2K8
_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 4NJH
_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
2K8 O6A O6A O 0 1 N N N N N N -11.696 83.286 23.744 -3.845 0.228 0.919 O6A 2K8 1
2K8 C6A C6A C 0 1 N N N N N N -10.835 84.025 23.212 -2.579 -0.127 0.651 C6A 2K8 2
2K8 O6B O6B O 0 1 N N N N N N -10.858 85.271 23.190 -1.800 -0.315 1.555 O6B 2K8 3
2K8 C6 C6 C 0 1 N N R N N N -9.646 83.337 22.528 -2.129 -0.291 -0.778 C6 2K8 4
2K8 N5 N5 N 0 1 N N N N N N -9.290 82.230 23.401 -0.911 -1.117 -0.825 N5 2K8 5
2K8 C4A C4A C 0 1 N N N N N N -7.947 81.950 23.609 0.315 -0.532 -0.438 C4A 2K8 6
2K8 C7 C7 C 0 1 N N N N N N -8.495 84.327 22.194 -1.794 1.083 -1.377 C7 2K8 7
2K8 N8 N8 N 0 1 N N N N N N -7.146 83.767 22.203 -0.664 1.652 -0.628 N8 2K8 8
2K8 C8A C8A C 0 1 N N N N N N -6.900 82.702 23.062 0.429 0.848 -0.345 C8A 2K8 9
2K8 N1 N1 N 0 1 N N N N N N -5.592 82.457 23.309 1.596 1.391 0.019 N1 2K8 10
2K8 C2 C2 C 0 1 N N N N N N -5.365 81.432 24.127 2.639 0.637 0.293 C2 2K8 11
2K8 N2 N2 N 0 1 N N N N N N -4.112 81.110 24.453 3.818 1.234 0.663 N2 2K8 12
2K8 N3 N3 N 0 1 N N N N N N -6.362 80.668 24.668 2.577 -0.720 0.219 N3 2K8 13
2K8 C4 C4 C 0 1 N N N N N N -7.709 80.861 24.446 1.427 -1.328 -0.145 C4 2K8 14
2K8 O4 O4 O 0 1 N N N N N N -8.546 80.104 24.943 1.360 -2.546 -0.216 O4 2K8 15
2K8 H1 H1 H 0 1 N N N N N N -12.377 83.822 24.133 -4.088 0.320 1.850 H1 2K8 16
2K8 H2 H2 H 0 1 N N N N N N -10.008 82.925 21.574 -2.918 -0.765 -1.361 H2 2K8 17
2K8 H3 H3 H 0 1 N N N N N N -9.693 82.420 24.296 -0.951 -2.042 -1.114 H3 2K8 18
2K8 H4 H4 H 0 1 N N N N N N -8.526 85.141 22.933 -1.519 0.970 -2.426 H4 2K8 19
2K8 H5 H5 H 0 1 N N N N N N -8.683 84.736 21.190 -2.659 1.741 -1.293 H5 2K8 20
2K8 H6 H6 H 0 1 N N N N N N -6.944 83.456 21.274 -0.683 2.577 -0.336 H6 2K8 21
2K8 H7 H7 H 0 1 N N N N N N -3.348 81.638 24.083 3.875 2.201 0.720 H7 2K8 22
2K8 H8 H8 H 0 1 N N N N N N -3.937 80.341 25.067 4.594 0.689 0.867 H8 2K8 23
2K8 H9 H9 H 0 1 N N N N N N -6.095 79.914 25.268 3.361 -1.253 0.428 H9 2K8 24
#
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
2K8 C7 N8 SING N N 1
2K8 C7 C6 SING N N 2
2K8 N8 C8A SING N N 3
2K8 C6 C6A SING N N 4
2K8 C6 N5 SING N N 5
2K8 C8A N1 SING N N 6
2K8 C8A C4A DOUB N N 7
2K8 O6B C6A DOUB N N 8
2K8 C6A O6A SING N N 9
2K8 N1 C2 DOUB N N 10
2K8 N5 C4A SING N N 11
2K8 C4A C4 SING N N 12
2K8 C2 N2 SING N N 13
2K8 C2 N3 SING N N 14
2K8 C4 N3 SING N N 15
2K8 C4 O4 DOUB N N 16
2K8 O6A H1 SING N N 17
2K8 C6 H2 SING N N 18
2K8 N5 H3 SING N N 19
2K8 C7 H4 SING N N 20
2K8 C7 H5 SING N N 21
2K8 N8 H6 SING N N 22
2K8 N2 H7 SING N N 23
2K8 N2 H8 SING N N 24
2K8 N3 H9 SING N N 25
#
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
2K8 SMILES ACDLabs 12.01 O=C(O)C2NC1=C(N=C(N)NC1=O)NC2
2K8 InChI InChI 1.03 InChI=1S/C7H9N5O3/c8-7-11-4-3(5(13)12-7)10-2(1-9-4)6(14)15/h2,10H,1H2,(H,14,15)(H4,8,9,11,12,13)/t2-/m1/s1
2K8 InChIKey InChI 1.03 QSIYONWVWDSRRO-UWTATZPHSA-N
2K8 SMILES_CANONICAL CACTVS 3.385 NC1=NC2=C(N[C@H](CN2)C(O)=O)C(=O)N1
2K8 SMILES CACTVS 3.385 NC1=NC2=C(N[CH](CN2)C(O)=O)C(=O)N1
2K8 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1[C@@H](NC2=C(N1)N=C(NC2=O)N)C(=O)O
2K8 SMILES "OpenEye OEToolkits" 1.7.6 C1C(NC2=C(N1)N=C(NC2=O)N)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
2K8 "SYSTEMATIC NAME" ACDLabs 12.01 "(6R)-2-amino-4-oxo-3,4,5,6,7,8-hexahydropteridine-6-carboxylic acid"
2K8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(6R)-2-azanyl-4-oxidanylidene-5,6,7,8-tetrahydro-3H-pteridine-6-carboxylic 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
2K8 'Create component' 2013-11-14 RCSB
2K8 'Modify atom id' 2013-12-13 RCSB
2K8 'Initial release' 2013-12-25 RCSB
2K8 'Modify synonyms' 2014-06-19 RCSB
2K8 'Modify synonyms' 2021-03-13 RCSB
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 2K8
_pdbx_chem_comp_synonyms.name 6-carboxy-5,6,7,8-tetrahydropterin
_pdbx_chem_comp_synonyms.provenance PDB
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 2K8
_pdbe_chem_comp_synonyms.name 6-carboxy-5,6,7,8-tetrahydropterin
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.09.6 'Core functionality.'
pdbeccdutils 0.8.6 '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
2K8 O6A O 3.805 -0.465 1
2K8 C6A C 5.104 -1.215 2
2K8 O6B O 5.104 -2.715 3
2K8 C6 C 6.404 -0.465 4
2K8 N5 N 7.702 -1.215 5
2K8 C4A C 9.002 -0.465 6
2K8 C7 C 6.404 1.035 7
2K8 N8 N 7.702 1.785 8
2K8 C8A C 9.002 1.035 9
2K8 N1 N 10.342 1.837 10
2K8 C2 C 11.701 1.066 11
2K8 N2 N 12.998 1.821 12
2K8 N3 N 11.701 -0.496 13
2K8 C4 C 10.342 -1.267 14
2K8 O4 O 10.325 -2.767 15
#
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
2K8 C7 N8 SINGLE NONE 1
2K8 C7 C6 SINGLE NONE 2
2K8 N8 C8A SINGLE NONE 3
2K8 C6 C6A SINGLE BEGINWEDGE 4
2K8 C6 N5 SINGLE NONE 5
2K8 C8A N1 SINGLE NONE 6
2K8 C8A C4A DOUBLE NONE 7
2K8 O6B C6A DOUBLE NONE 8
2K8 C6A O6A SINGLE NONE 9
2K8 N1 C2 DOUBLE NONE 10
2K8 N5 C4A SINGLE NONE 11
2K8 C4A C4 SINGLE NONE 12
2K8 C2 N2 SINGLE NONE 13
2K8 C2 N3 SINGLE NONE 14
2K8 C4 N3 SINGLE NONE 15
2K8 C4 O4 DOUBLE NONE 16
#
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
2K8 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1NCCN2' InChI=1S/C6H8N4O/c11-6-4-5(9-3-10-6)8-2-1-7-4/h3,7H,1-2H2,(H2,8,9,10,11) YMYLCENGLBCRLP-UHFFFAOYSA-N
2K8 peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
2K8 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
2K8 C6 S1 1
2K8 N5 S1 1
2K8 C4A S1 1
2K8 C7 S1 1
2K8 N8 S1 1
2K8 C8A S1 1
2K8 N1 S1 1
2K8 C2 S1 1
2K8 N3 S1 1
2K8 C4 S1 1
2K8 O4 S1 1
2K8 O6B F1 1
2K8 C6A F1 1
2K8 C6 F1 1
2K8 N5 F1 1
2K8 C4A F2 1
2K8 C8A F2 1
2K8 N1 F2 1
2K8 C2 F2 1
2K8 N3 F2 1
2K8 C4 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2K8
_pdbe_chem_comp_rdkit_properties.exactmw 211.071
_pdbe_chem_comp_rdkit_properties.amw 211.181
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.286
_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 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 96.538
_pdbe_chem_comp_rdkit_properties.tpsa 133.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.599
_pdbe_chem_comp_rdkit_properties.CrippenMR 50.442
_pdbe_chem_comp_rdkit_properties.chi0v 6.961
_pdbe_chem_comp_rdkit_properties.chi1v 3.625
_pdbe_chem_comp_rdkit_properties.chi2v 1.506
_pdbe_chem_comp_rdkit_properties.chi3v 1.506
_pdbe_chem_comp_rdkit_properties.chi4v 0.922
_pdbe_chem_comp_rdkit_properties.chi0n 15.961
_pdbe_chem_comp_rdkit_properties.chi1n 7.769
_pdbe_chem_comp_rdkit_properties.chi2n 1.506
_pdbe_chem_comp_rdkit_properties.chi3n 1.506
_pdbe_chem_comp_rdkit_properties.chi4n 0.922
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.250
_pdbe_chem_comp_rdkit_properties.kappa1 3.401
_pdbe_chem_comp_rdkit_properties.kappa2 3.154
_pdbe_chem_comp_rdkit_properties.kappa3 1.561
_pdbe_chem_comp_rdkit_properties.Phi 0.715
#
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
2K8 UniChem ZINC ZINC000062238705
2K8 UniChem PubChem 135566896
#
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
2K8 O6A 4.527 0.153 0.746 ETKDGv3 1
2K8 C6A 3.337 -0.563 0.658 ETKDGv3 2
2K8 O6B 3.326 -1.797 0.913 ETKDGv3 3
2K8 C6 2.079 0.133 0.225 ETKDGv3 4
2K8 N5 0.968 -0.202 1.123 ETKDGv3 5
2K8 C4A -0.395 -0.044 0.694 ETKDGv3 6
2K8 C7 1.725 -0.249 -1.220 ETKDGv3 7
2K8 N8 0.393 0.248 -1.556 ETKDGv3 8
2K8 C8A -0.674 0.191 -0.600 ETKDGv3 9
2K8 N1 -2.030 0.395 -1.037 ETKDGv3 10
2K8 C2 -3.048 0.345 -0.226 ETKDGv3 11
2K8 N2 -4.366 0.556 -0.728 ETKDGv3 12
2K8 N3 -2.843 0.078 1.168 ETKDGv3 13
2K8 C4 -1.512 -0.120 1.651 ETKDGv3 14
2K8 O4 -1.308 -0.351 2.872 ETKDGv3 15
2K8 H1 5.388 -0.303 1.026 ETKDGv3 16
2K8 H2 2.243 1.232 0.270 ETKDGv3 17
2K8 H3 1.166 -0.367 2.136 ETKDGv3 18
2K8 H4 2.473 0.182 -1.922 ETKDGv3 19
2K8 H5 1.729 -1.355 -1.335 ETKDGv3 20
2K8 H6 0.187 0.536 -2.539 ETKDGv3 21
2K8 H7 -4.523 0.750 -1.742 ETKDGv3 22
2K8 H8 -5.189 0.518 -0.087 ETKDGv3 23
2K8 H9 -3.654 0.032 1.824 ETKDGv3 24
#