data_ARP
#
_chem_comp.id ARP
_chem_comp.name "9-HYDROXYPROPYLADENINE, R-ISOMER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H11 N5 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2000-05-24
_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 ?
_chem_comp.formula_weight 193.206
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ARP
_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 1E2I
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
ARP C7 C7 C 0 1 N N N N N N 19.657 20.465 9.523 -0.194 -0.874 2.084 C7 ARP 1
ARP C8 C8 C 0 1 N N R N N N 18.274 20.950 10.017 -0.367 0.428 2.867 C8 ARP 2
ARP O1 O1 O 0 1 N N N N N N 17.438 19.807 10.026 0.901 1.067 3.014 O1 ARP 3
ARP C9 C9 C 0 1 N N N N N N 17.656 22.006 9.109 -0.947 0.119 4.249 C9 ARP 4
ARP C4 C4 C 0 1 Y N N N N N 20.683 22.802 9.866 -0.356 -0.313 -0.378 C4 ARP 5
ARP C3 C3 C 0 1 Y N N N N N 22.009 23.252 10.070 0.593 -0.090 -1.389 C3 ARP 6
ARP C2 C2 C 0 1 Y N N N N N 22.234 24.642 10.225 0.128 0.211 -2.680 C2 ARP 7
ARP N2 N2 N 0 1 Y N N N N N 21.158 25.479 10.170 -1.183 0.277 -2.882 N2 ARP 8
ARP C1 C1 C 0 1 Y N N N N N 19.901 24.964 9.967 -2.038 0.064 -1.899 C1 ARP 9
ARP N5 N5 N 0 1 N N N N N N 23.489 25.207 10.433 1.016 0.436 -3.718 N5 ARP 10
ARP N4 N4 N 0 1 Y N N N N N 20.762 21.402 9.747 0.359 -0.579 0.761 N4 ARP 11
ARP N3 N3 N 0 1 Y N N N N N 22.874 22.138 10.074 1.816 -0.237 -0.827 N3 ARP 12
ARP C6 C6 C 0 1 Y N N N N N 22.131 21.044 9.881 1.682 -0.524 0.434 C6 ARP 13
ARP N1 N1 N 0 1 Y N N N N N 19.603 23.659 9.810 -1.648 -0.221 -0.674 N1 ARP 14
ARP H72 2H7 H 0 1 N N N N N N 19.898 19.472 9.970 0.484 -1.535 2.623 H72 ARP 15
ARP H71 1H7 H 0 1 N N N N N N 19.603 20.185 8.445 -1.163 -1.362 1.972 H71 ARP 16
ARP H8 H8 H 0 1 N N N N N N 18.386 21.422 11.020 -1.046 1.088 2.328 H8 ARP 17
ARP H1 H1 H 0 1 N N N N N N 16.588 20.104 10.329 1.470 0.451 3.495 H1 ARP 18
ARP H93 3H9 H 0 1 N N N N N N 16.658 22.355 9.465 -1.070 1.048 4.807 H93 ARP 19
ARP H92 2H9 H 0 1 N N N N N N 18.351 22.865 8.966 -1.915 -0.368 4.137 H92 ARP 20
ARP H91 1H9 H 0 1 N N N N N N 17.598 21.642 8.056 -0.268 -0.540 4.788 H91 ARP 21
ARP H1C1 1H1C H 0 0 N N N N N N 19.050 25.664 9.926 -3.096 0.127 -2.106 H1C1 ARP 22
ARP H52 2H5 H 0 1 N N N N N N 23.651 26.207 10.544 0.683 0.643 -4.605 H52 ARP 23
ARP H51 1H5 H 0 1 N N N N N N 24.090 24.888 9.673 1.972 0.385 -3.558 H51 ARP 24
ARP H6 H6 H 0 1 N N N N N N 22.567 20.031 9.839 2.497 -0.693 1.122 H6 ARP 25
#
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
ARP C7 C8 SING N N 1
ARP C7 N4 SING N N 2
ARP C7 H72 SING N N 3
ARP C7 H71 SING N N 4
ARP C8 O1 SING N N 5
ARP C8 C9 SING N N 6
ARP C8 H8 SING N N 7
ARP O1 H1 SING N N 8
ARP C9 H93 SING N N 9
ARP C9 H92 SING N N 10
ARP C9 H91 SING N N 11
ARP C4 C3 DOUB Y N 12
ARP C4 N4 SING Y N 13
ARP C4 N1 SING Y N 14
ARP C3 C2 SING Y N 15
ARP C3 N3 SING Y N 16
ARP C2 N2 DOUB Y N 17
ARP C2 N5 SING N N 18
ARP N2 C1 SING Y N 19
ARP C1 N1 DOUB Y N 20
ARP C1 H1C1 SING N N 21
ARP N5 H52 SING N N 22
ARP N5 H51 SING N N 23
ARP N4 C6 SING Y N 24
ARP N3 C6 DOUB Y N 25
ARP C6 H6 SING N N 26
#
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
ARP SMILES ACDLabs 10.04 n1c(c2ncn(c2nc1)CC(O)C)N
ARP SMILES_CANONICAL CACTVS 3.341 C[C@@H](O)Cn1cnc2c(N)ncnc12
ARP SMILES CACTVS 3.341 C[CH](O)Cn1cnc2c(N)ncnc12
ARP SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C[C@H](Cn1cnc2c1ncnc2N)O
ARP SMILES "OpenEye OEToolkits" 1.5.0 CC(Cn1cnc2c1ncnc2N)O
ARP InChI InChI 1.03 InChI=1S/C8H11N5O/c1-5(14)2-13-4-12-6-7(9)10-3-11-8(6)13/h3-5,14H,2H2,1H3,(H2,9,10,11)/t5-/m1/s1
ARP InChIKey InChI 1.03 MJZYTEBKXLVLMY-RXMQYKEDSA-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
ARP "SYSTEMATIC NAME" ACDLabs 10.04 (2R)-1-(6-amino-9H-purin-9-yl)propan-2-ol
ARP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (2R)-1-(6-aminopurin-9-yl)propan-2-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ARP 'Create component' 2000-05-24 EBI
ARP 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id ARP
_pdbe_chem_comp_drugbank_details.drugbank_id DB02765
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name R-9-(2-hydroxypropyl)adenine
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 14047-28-0
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id ARP
_pdbe_chem_comp_synonyms.name '9-Hydroxypropyladenine, R-Isomer'
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id ARP
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02765
_pdbe_chem_comp_drugbank_classification.parent 6-aminopurines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Imidazopyrimidines
_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 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.'
#
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
ARP DB02765 'Thymidine kinase' HHV-1 Q9QNF7 no 1
ARP DB02765 'Thymidine kinase' HHV-3 P09250 no 2
#
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
ARP C7 C 7.483 -2.086 1
ARP C8 C 8.951 -2.395 2
ARP O1 O 9.417 -3.821 3
ARP C9 C 9.953 -1.278 4
ARP C4 C 5.598 -0.203 5
ARP C3 C 5.598 1.297 6
ARP C2 C 4.299 2.047 7
ARP N2 N 3.000 1.297 8
ARP C1 C 3.000 -0.203 9
ARP N5 N 4.299 3.547 10
ARP N4 N 7.018 -0.660 11
ARP N3 N 7.018 1.755 12
ARP C6 C 7.893 0.547 13
ARP N1 N 4.299 -0.953 14
#
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
ARP C7 C8 SINGLE NONE 1
ARP C7 N4 SINGLE NONE 2
ARP C8 O1 SINGLE NONE 3
ARP C8 C9 SINGLE BEGINWEDGE 4
ARP C4 C3 SINGLE NONE 5
ARP C4 N4 SINGLE NONE 6
ARP C4 N1 DOUBLE NONE 7
ARP C3 C2 DOUBLE NONE 8
ARP C3 N3 SINGLE NONE 9
ARP C2 N2 SINGLE NONE 10
ARP C2 N5 SINGLE NONE 11
ARP N2 C1 DOUBLE NONE 12
ARP C1 N1 SINGLE NONE 13
ARP N4 C6 SINGLE NONE 14
ARP N3 C6 DOUBLE NONE 15
#
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
ARP MurckoScaffold S1 scaffold 'c1ncc2nc[nH]c2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
ARP adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
ARP imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
ARP purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
ARP pyrimidine F4 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
ARP C4 S1 1
ARP C3 S1 1
ARP C2 S1 1
ARP N2 S1 1
ARP C1 S1 1
ARP N4 S1 1
ARP N3 S1 1
ARP C6 S1 1
ARP N1 S1 1
ARP N2 F1 1
ARP C2 F1 1
ARP C3 F1 1
ARP C4 F1 1
ARP N1 F1 1
ARP C1 F1 1
ARP N4 F1 1
ARP C6 F1 1
ARP N3 F1 1
ARP N5 F1 1
ARP C4 F2 1
ARP C3 F2 1
ARP N3 F2 1
ARP C6 F2 1
ARP N4 F2 1
ARP N3 F3 1
ARP C6 F3 1
ARP N4 F3 1
ARP C4 F3 1
ARP C3 F3 1
ARP C2 F3 1
ARP N2 F3 1
ARP C1 F3 1
ARP N1 F3 1
ARP C3 F4 1
ARP C4 F4 1
ARP N1 F4 1
ARP C1 F4 1
ARP N2 F4 1
ARP C2 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ARP
_pdbe_chem_comp_rdkit_properties.exactmw 193.096
_pdbe_chem_comp_rdkit_properties.amw 193.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 6
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.375
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 96.078
_pdbe_chem_comp_rdkit_properties.tpsa 89.850
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.020
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.386
_pdbe_chem_comp_rdkit_properties.chi0v 6.644
_pdbe_chem_comp_rdkit_properties.chi1v 3.440
_pdbe_chem_comp_rdkit_properties.chi2v 1.422
_pdbe_chem_comp_rdkit_properties.chi3v 1.422
_pdbe_chem_comp_rdkit_properties.chi4v 0.908
_pdbe_chem_comp_rdkit_properties.chi0n 17.644
_pdbe_chem_comp_rdkit_properties.chi1n 8.743
_pdbe_chem_comp_rdkit_properties.chi2n 1.422
_pdbe_chem_comp_rdkit_properties.chi3n 1.422
_pdbe_chem_comp_rdkit_properties.chi4n 0.908
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.690
_pdbe_chem_comp_rdkit_properties.kappa1 2.664
_pdbe_chem_comp_rdkit_properties.kappa2 3.224
_pdbe_chem_comp_rdkit_properties.kappa3 1.395
_pdbe_chem_comp_rdkit_properties.Phi 0.614
#
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
ARP UniChem DrugBank DB02765
ARP UniChem PDBe ARP
ARP UniChem ZINC ZINC000002046906
ARP UniChem fdasrs 43H6SBP55W
ARP UniChem SureChEMBL SCHEMBL1393316
ARP UniChem 'EPA CompTox Dashboard' DTXSID20332178
ARP UniChem ChemicalBook CB5946929
ARP UniChem 'Probes And Drugs' PD007467
ARP UniChem Nikkaji J3.287.859H
ARP UniChem eMolecules 31588704
ARP UniChem 'PubChem TPHARMA' 14867711
ARP UniChem PubChem 445211
#
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
ARP C7 -1.620 0.280 -1.408 ETKDGv3 1
ARP C8 -2.524 0.368 -0.166 ETKDGv3 2
ARP O1 -1.972 1.265 0.762 ETKDGv3 3
ARP C9 -2.737 -1.002 0.489 ETKDGv3 4
ARP C4 0.784 0.533 -0.488 ETKDGv3 5
ARP C3 1.797 -0.388 -0.129 ETKDGv3 6
ARP C2 2.903 0.033 0.482 ETKDGv3 7
ARP N2 3.017 1.452 0.740 ETKDGv3 8
ARP C1 2.063 2.288 0.397 ETKDGv3 9
ARP N5 3.937 -0.867 0.878 ETKDGv3 10
ARP N4 -0.276 -0.189 -1.078 ETKDGv3 11
ARP N3 1.377 -1.701 -0.479 ETKDGv3 12
ARP C6 0.192 -1.552 -1.013 ETKDGv3 13
ARP N1 0.862 1.807 -0.252 ETKDGv3 14
ARP H72 -2.076 -0.404 -2.157 ETKDGv3 15
ARP H71 -1.550 1.284 -1.878 ETKDGv3 16
ARP H8 -3.515 0.747 -0.506 ETKDGv3 17
ARP H1 -2.700 1.512 1.391 ETKDGv3 18
ARP H93 -1.795 -1.368 0.949 ETKDGv3 19
ARP H92 -3.091 -1.740 -0.261 ETKDGv3 20
ARP H91 -3.504 -0.919 1.288 ETKDGv3 21
ARP H1C1 2.174 3.344 0.605 ETKDGv3 22
ARP H52 4.789 -0.502 1.358 ETKDGv3 23
ARP H51 3.860 -1.893 0.697 ETKDGv3 24
ARP H6 -0.393 -2.391 -1.364 ETKDGv3 25
#