data_HBI
#
_chem_comp.id HBI
_chem_comp.name 7,8-DIHYDROBIOPTERIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H13 N5 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces HBL
_chem_comp.formula_weight 239.231
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HBI
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1DCP
_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
HBI N1 N1 N 0 1 Y N N N N N 14.495 28.670 66.885 -1.052 0.259 -2.800 N1 HBI 1
HBI N2 N2 N 0 1 N N N N N N 12.449 28.892 65.907 -0.086 0.004 -4.891 N2 HBI 2
HBI C2 C2 C 0 1 Y N N N N N 13.495 28.068 66.301 0.018 0.001 -3.526 C2 HBI 3
HBI N3 N3 N 0 1 Y N N N N N 13.386 26.794 66.006 1.223 -0.266 -2.955 N3 HBI 4
HBI C4 C4 C 0 1 Y N N N N N 14.393 25.997 66.353 1.357 -0.282 -1.611 C4 HBI 5
HBI O4 O4 O 0 1 N N N N N N 14.292 24.653 66.077 2.434 -0.522 -1.092 O4 HBI 6
HBI C4A C4A C 0 1 Y N N N N N 15.551 26.512 66.988 0.220 -0.012 -0.823 C4A HBI 7
HBI C8A C8A C 0 1 Y N N N N N 15.540 27.927 67.237 -0.990 0.266 -1.471 C8A HBI 8
HBI N8 N8 N 0 1 N N N N N N 16.683 28.550 67.894 -2.099 0.547 -0.694 N8 HBI 9
HBI C7 C7 C 0 1 N N N N N N 17.699 27.620 68.500 -2.157 -0.066 0.644 C7 HBI 10
HBI C6 C6 C 0 1 N N N N N N 17.681 26.137 68.019 -0.783 -0.025 1.263 C6 HBI 11
HBI N5 N5 N 0 1 N N N N N N 16.654 25.684 67.388 0.280 -0.021 0.538 N5 HBI 12
HBI C9 C9 C 0 1 N N R N N N 18.832 25.168 68.377 -0.652 0.005 2.764 C9 HBI 13
HBI O9 O9 O 0 1 N N N N N N 18.328 24.057 69.140 -1.262 -1.161 3.319 O9 HBI 14
HBI C10 C10 C 0 1 N N S N N N 19.609 24.606 67.141 0.828 0.037 3.145 C10 HBI 15
HBI O10 O10 O 0 1 N N N N N N 20.236 25.670 66.438 1.438 1.204 2.590 O10 HBI 16
HBI C11 C11 C 0 1 N N N N N N 20.623 23.511 67.535 0.962 0.069 4.669 C11 HBI 17
HBI HN21 1HN2 H 0 0 N N N N N N 11.667 28.421 65.450 -0.939 0.194 -5.312 HN21 HBI 18
HBI HN22 2HN2 H 0 0 N N N N N N 12.800 29.642 65.312 0.692 -0.183 -5.438 HN22 HBI 19
HBI H3 H3 H 0 1 N N N N N N 12.556 26.439 65.529 1.992 -0.449 -3.518 H3 HBI 20
HBI H8 H8 H 0 1 N N N N N N 16.355 29.208 68.601 -2.810 1.122 -1.018 H8 HBI 21
HBI H71 1H7 H 0 1 N N N N N N 18.720 28.043 68.358 -2.494 -1.099 0.557 H71 HBI 22
HBI H72 2H7 H 0 1 N N N N N N 17.614 27.650 69.611 -2.851 0.492 1.272 H72 HBI 23
HBI H9 H9 H 0 1 N N N N N N 19.553 25.777 68.969 -1.147 0.894 3.154 H9 HBI 24
HBI HO9 HO9 H 0 1 N N N N N N 19.035 23.461 69.359 -0.795 -1.923 2.949 HO9 HBI 25
HBI H10 H10 H 0 1 N N N N N N 18.870 24.116 66.464 1.324 -0.851 2.755 H10 HBI 26
HBI HO1 HO1 H 0 1 N N N N N N 20.707 25.328 65.687 0.972 1.966 2.960 HO1 HBI 27
HBI H111 1H11 H 0 0 N N N N N N 21.176 23.110 66.654 2.017 0.092 4.941 H111 HBI 28
HBI H112 2H11 H 0 0 N N N N N N 21.325 23.876 68.320 0.467 0.958 5.059 H112 HBI 29
HBI H113 3H11 H 0 0 N N N N N N 20.128 22.691 68.106 0.497 -0.821 5.093 H113 HBI 30
#
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
HBI N1 C2 DOUB Y N 1
HBI N1 C8A SING Y N 2
HBI N2 C2 SING N N 3
HBI N2 HN21 SING N N 4
HBI N2 HN22 SING N N 5
HBI C2 N3 SING Y N 6
HBI N3 C4 SING Y N 7
HBI N3 H3 SING N N 8
HBI C4 O4 DOUB N N 9
HBI C4 C4A SING Y N 10
HBI C4A C8A DOUB Y N 11
HBI C4A N5 SING N N 12
HBI C8A N8 SING N N 13
HBI N8 C7 SING N N 14
HBI N8 H8 SING N N 15
HBI C7 C6 SING N N 16
HBI C7 H71 SING N N 17
HBI C7 H72 SING N N 18
HBI C6 N5 DOUB N N 19
HBI C6 C9 SING N N 20
HBI C9 O9 SING N N 21
HBI C9 C10 SING N N 22
HBI C9 H9 SING N N 23
HBI O9 HO9 SING N N 24
HBI C10 O10 SING N N 25
HBI C10 C11 SING N N 26
HBI C10 H10 SING N N 27
HBI O10 HO1 SING N N 28
HBI C11 H111 SING N N 29
HBI C11 H112 SING N N 30
HBI C11 H113 SING N N 31
#
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
HBI SMILES ACDLabs 10.04 O=C1NC(=NC=2NCC(=NC1=2)C(O)C(O)C)N
HBI SMILES_CANONICAL CACTVS 3.341 C[C@H](O)[C@H](O)C1=NC2=C(NC1)N=C(N)NC2=O
HBI SMILES CACTVS 3.341 C[CH](O)[CH](O)C1=NC2=C(NC1)N=C(N)NC2=O
HBI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@@H]([C@@H](C1=NC2=C(NC1)N=C(NC2=O)N)O)O
HBI SMILES "OpenEye OEToolkits" 1.5.0 CC(C(C1=NC2=C(NC1)N=C(NC2=O)N)O)O
HBI InChI InChI 1.03 InChI=1S/C9H13N5O3/c1-3(15)6(16)4-2-11-7-5(12-4)8(17)14-9(10)13-7/h3,6,15-16H,2H2,1H3,(H4,10,11,13,14,17)/t3-,6-/m0/s1
HBI InChIKey InChI 1.03 FEMXZDUTFRTWPE-DZSWIPIPSA-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
HBI "SYSTEMATIC NAME" ACDLabs 10.04 2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydropteridin-4(3H)-one
HBI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-amino-6-[(1R,2S)-1,2-dihydroxypropyl]-7,8-dihydro-3H-pteridin-4-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HBI 'Create component' 1999-07-08 RCSB
HBI 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id HBI
_pdbe_chem_comp_drugbank_details.drugbank_id DB04400
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name L-erythro-7,8-dihydrobiopterin
_pdbe_chem_comp_drugbank_details.description
'7,8-Dihydrobiopterin is an inhibitor of the enzyme dihydroneopterin aldolase (DHNA), which catalyzes the conversion of 7,8-Dihydrobiopterin to 6-hydroxymethyl-7,8-dihydropterin and glycolaldehyde.'
_pdbe_chem_comp_drugbank_details.cas_number 6779-87-9
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
HBI Dihydrobiopterin DrugBank ?
HBI L-erythro-q-Dihydrobiopterin DrugBank ?
HBI q-BH2 DrugBank ?
HBI 'Quinonoid dihydrobiopterin' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HBI
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04400
_pdbe_chem_comp_drugbank_classification.parent 'Biopterins and derivatives'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pteridines and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as biopterins and derivatives. These are coenzymes containing a 2-amino-pteridine-4-one derivative. They are mainly synthesized in several parts of the body, including the pineal gland.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
HBI DB04400 Phenylalanine-4-hydroxylase Humans P00439 unknown 1
HBI DB04400 'Pteridine reductase 1' 'Leishmania major' Q01782 unknown 2
HBI DB04400 'Nitric oxide synthase, inducible' Humans P35228 unknown 3
HBI DB04400 'Tyrosine 3-monooxygenase' Humans P07101 unknown 4
HBI DB04400 'Pterin-4-alpha-carbinolamine dehydratase' Humans P61457 unknown 5
HBI DB04400 'Dihydroneopterin aldolase' 'Staphylococcus aureus' P56740 unknown 6
#
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
HBI N1 N 6.404 -2.011 1
HBI N2 N 3.805 -2.011 2
HBI C2 C 5.104 -1.261 3
HBI N3 N 5.104 0.239 4
HBI C4 C 6.404 0.989 5
HBI O4 O 6.404 2.489 6
HBI C4A C 7.702 0.239 7
HBI C8A C 7.702 -1.261 8
HBI N8 N 9.043 -2.063 9
HBI C7 C 10.402 -1.292 10
HBI C6 C 10.402 0.270 11
HBI N5 N 9.043 1.041 12
HBI C9 C 11.699 1.025 13
HBI O9 O 11.693 2.525 14
HBI C10 C 13.001 0.280 15
HBI O10 O 14.297 1.035 16
HBI C11 C 13.006 -1.220 17
#
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
HBI N1 C2 DOUBLE NONE 1
HBI N1 C8A SINGLE NONE 2
HBI N2 C2 SINGLE NONE 3
HBI C2 N3 SINGLE NONE 4
HBI N3 C4 SINGLE NONE 5
HBI C4 O4 DOUBLE NONE 6
HBI C4 C4A SINGLE NONE 7
HBI C4A C8A DOUBLE NONE 8
HBI C4A N5 SINGLE NONE 9
HBI C8A N8 SINGLE NONE 10
HBI N8 C7 SINGLE NONE 11
HBI C7 C6 SINGLE NONE 12
HBI C6 N5 DOUBLE NONE 13
HBI C6 C9 SINGLE NONE 14
HBI C9 O9 SINGLE BEGINWEDGE 15
HBI C9 C10 SINGLE NONE 16
HBI C10 O10 SINGLE NONE 17
HBI C10 C11 SINGLE BEGINWEDGE 18
#
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
HBI MurckoScaffold S1 scaffold 'O=c1[nH]cnc2c1N=CCN2' InChI=1S/C6H6N4O/c11-6-4-5(9-3-10-6)8-2-1-7-4/h1,3H,2H2,(H2,8,9,10,11) RSPZIHWNURGJFC-UHFFFAOYSA-N
HBI pyrimidine F1 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
HBI N1 S1 1
HBI C2 S1 1
HBI N3 S1 1
HBI C4 S1 1
HBI O4 S1 1
HBI C4A S1 1
HBI C8A S1 1
HBI N8 S1 1
HBI C7 S1 1
HBI C6 S1 1
HBI N5 S1 1
HBI C4A F1 1
HBI C4 F1 1
HBI N3 F1 1
HBI C2 F1 1
HBI N1 F1 1
HBI C8A F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HBI
_pdbe_chem_comp_rdkit_properties.exactmw 239.102
_pdbe_chem_comp_rdkit_properties.amw 239.235
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.444
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 114.895
_pdbe_chem_comp_rdkit_properties.tpsa 136.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.650
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.178
_pdbe_chem_comp_rdkit_properties.chi0v 7.961
_pdbe_chem_comp_rdkit_properties.chi1v 4.125
_pdbe_chem_comp_rdkit_properties.chi2v 1.734
_pdbe_chem_comp_rdkit_properties.chi3v 1.734
_pdbe_chem_comp_rdkit_properties.chi4v 1.040
_pdbe_chem_comp_rdkit_properties.chi0n 20.961
_pdbe_chem_comp_rdkit_properties.chi1n 10.230
_pdbe_chem_comp_rdkit_properties.chi2n 1.734
_pdbe_chem_comp_rdkit_properties.chi3n 1.734
_pdbe_chem_comp_rdkit_properties.chi4n 1.040
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.930
_pdbe_chem_comp_rdkit_properties.kappa1 3.530
_pdbe_chem_comp_rdkit_properties.kappa2 4.149
_pdbe_chem_comp_rdkit_properties.kappa3 2.123
_pdbe_chem_comp_rdkit_properties.Phi 0.862
#
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
HBI UniChem DrugBank DB04400
HBI UniChem PDBe HBI
HBI UniChem ChEBI 43029
HBI UniChem ZINC ZINC000018181336
HBI UniChem eMolecules 5747833
HBI UniChem HMDB HMDB0000038
HBI UniChem PubChem 135398687
HBI UniChem Nikkaji J959.455H
HBI UniChem BRENDA 105191
HBI UniChem BRENDA 106396
HBI UniChem BRENDA 12803
HBI UniChem BRENDA 1378
HBI UniChem BRENDA 15595
HBI UniChem BRENDA 158000
HBI UniChem BRENDA 163890
HBI UniChem BRENDA 195363
HBI UniChem BRENDA 92793
HBI UniChem Rhea 43029
HBI UniChem MedChemExpress HY-W008646
HBI UniChem 'Probes And Drugs' PD020658
#
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
HBI N1 3.129 0.420 -0.813 ETKDGv3 1
HBI N2 5.247 1.014 0.051 ETKDGv3 2
HBI C2 3.889 0.613 0.228 ETKDGv3 3
HBI N3 3.361 0.423 1.549 ETKDGv3 4
HBI C4 1.997 0.023 1.700 ETKDGv3 5
HBI O4 1.505 -0.149 2.847 ETKDGv3 6
HBI C4A 1.187 -0.182 0.493 ETKDGv3 7
HBI C8A 1.752 0.014 -0.705 ETKDGv3 8
HBI N8 0.972 -0.174 -1.889 ETKDGv3 9
HBI C7 -0.410 -0.658 -1.853 ETKDGv3 10
HBI C6 -0.949 -0.784 -0.443 ETKDGv3 11
HBI N5 -0.187 -0.573 0.592 ETKDGv3 12
HBI C9 -2.391 -1.196 -0.237 ETKDGv3 13
HBI O9 -2.460 -2.399 0.488 ETKDGv3 14
HBI C10 -3.244 -0.094 0.436 ETKDGv3 15
HBI O10 -2.717 0.234 1.697 ETKDGv3 16
HBI C11 -3.331 1.166 -0.435 ETKDGv3 17
HBI HN21 5.864 1.171 0.878 ETKDGv3 18
HBI HN22 5.638 1.154 -0.907 ETKDGv3 19
HBI H3 3.963 0.575 2.389 ETKDGv3 20
HBI H8 1.418 -0.010 -2.819 ETKDGv3 21
HBI H71 -1.051 0.046 -2.424 ETKDGv3 22
HBI H72 -0.456 -1.652 -2.346 ETKDGv3 23
HBI H9 -2.843 -1.400 -1.233 ETKDGv3 24
HBI HO9 -2.096 -2.232 1.396 ETKDGv3 25
HBI H10 -4.276 -0.499 0.559 ETKDGv3 26
HBI HO1 -3.437 0.699 2.198 ETKDGv3 27
HBI H111 -3.724 0.912 -1.442 ETKDGv3 28
HBI H112 -4.020 1.900 0.034 ETKDGv3 29
HBI H113 -2.332 1.639 -0.541 ETKDGv3 30
#