data_DX6
#
_chem_comp.id DX6
_chem_comp.name 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H14 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2007-12-17
_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 254.287
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DX6
_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 3BMH
_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
DX6 CAF CAF C 0 1 Y N N N N N 20.937 15.793 8.731 -3.387 -1.278 0.154 CAF DX6 1
DX6 CAD CAD C 0 1 Y N N N N N 20.871 16.119 10.083 -4.695 -1.647 -0.100 CAD DX6 2
DX6 CAC CAC C 0 1 Y N N N N N 20.346 17.354 10.466 -5.690 -0.688 -0.131 CAC DX6 3
DX6 CAE CAE C 0 1 Y N N N N N 19.889 18.265 9.513 -5.378 0.640 0.093 CAE DX6 4
DX6 CAG CAG C 0 1 Y N N N N N 19.956 17.936 8.162 -4.070 1.009 0.348 CAG DX6 5
DX6 CAN CAN C 0 1 Y N N N N N 20.478 16.700 7.773 -3.075 0.050 0.378 CAN DX6 6
DX6 CAI CAI C 0 1 N N N N N N 20.554 16.330 6.291 -1.649 0.452 0.655 CAI DX6 7
DX6 CAJ CAJ C 0 1 N N N N N N 19.158 16.108 5.694 -0.944 0.773 -0.664 CAJ DX6 8
DX6 CAP CAP C 0 1 Y N N N N N 18.605 14.685 5.890 0.482 1.175 -0.386 CAP DX6 9
DX6 CAH CAH C 0 1 Y N N N N N 18.949 13.805 6.831 0.949 2.426 -0.244 CAH DX6 10
DX6 NAL NAL N 0 1 Y N N N N N 18.250 12.678 6.678 2.299 2.390 0.000 NAL DX6 11
DX6 CAR CAR C 0 1 Y N N N N N 17.428 12.807 5.641 2.737 1.098 0.021 CAR DX6 12
DX6 NAK NAK N 0 1 N N N N N N 16.528 11.968 5.095 3.937 0.531 0.214 NAK DX6 13
DX6 CAS CAS C 0 1 Y N N N N N 17.627 14.079 5.111 1.624 0.278 -0.213 CAS DX6 14
DX6 CAQ CAQ C 0 1 N N N N N N 16.886 14.487 4.002 1.796 -1.123 -0.238 CAQ DX6 15
DX6 OAB OAB O 0 1 N N N N N N 17.033 15.603 3.506 0.852 -1.867 -0.442 OAB DX6 16
DX6 NAM NAM N 0 1 N N N N N N 15.960 13.598 3.449 3.038 -1.618 -0.031 NAM DX6 17
DX6 CAO CAO C 0 1 N N N N N N 15.802 12.328 4.020 4.086 -0.773 0.181 CAO DX6 18
DX6 NAA NAA N 0 1 N N N N N N 14.921 11.484 3.499 5.336 -1.303 0.385 NAA DX6 19
DX6 HAF HAF H 0 1 N N N N N N 21.342 14.840 8.423 -2.611 -2.028 0.183 HAF DX6 20
DX6 HAD HAD H 0 1 N N N N N N 21.223 15.422 10.829 -4.939 -2.684 -0.275 HAD DX6 21
DX6 HAC HAC H 0 1 N N N N N N 20.293 17.608 11.514 -6.712 -0.976 -0.330 HAC DX6 22
DX6 HAE HAE H 0 1 N N N N N N 19.486 19.218 9.821 -6.155 1.389 0.068 HAE DX6 23
DX6 HAG HAG H 0 1 N N N N N N 19.605 18.634 7.417 -3.826 2.046 0.523 HAG DX6 24
DX6 HAI HAI H 0 1 N N N N N N 21.046 17.149 5.746 -1.638 1.333 1.297 HAI DX6 25
DX6 HAIA HAIA H 0 0 N N N N N N 21.123 15.394 6.197 -1.131 -0.367 1.154 HAIA DX6 26
DX6 HAJ HAJ H 0 1 N N N N N N 18.466 16.810 6.182 -0.954 -0.108 -1.305 HAJ DX6 27
DX6 HAJA HAJA H 0 0 N N N N N N 19.247 16.268 4.609 -1.462 1.592 -1.163 HAJA DX6 28
DX6 HAH HAH H 0 1 N N N N N N 19.684 13.978 7.603 0.353 3.324 -0.312 HAH DX6 29
DX6 HNAL HNAL H 0 0 N N N N N N 18.332 11.864 7.253 2.860 3.169 0.138 HNAL DX6 30
DX6 HNAM HNAM H 0 0 N N N N N N 15.416 13.866 2.654 3.184 -2.577 -0.043 HNAM DX6 31
DX6 HNAA HNAA H 0 0 N N N N N N 14.927 10.630 4.020 6.091 -0.717 0.549 HNAA DX6 32
DX6 HNAB HNAB H 0 0 N N N N N N 14.340 11.672 2.707 5.464 -2.264 0.364 HNAB DX6 33
#
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
DX6 CAF CAD DOUB Y N 1
DX6 CAF CAN SING Y N 2
DX6 CAD CAC SING Y N 3
DX6 CAC CAE DOUB Y N 4
DX6 CAE CAG SING Y N 5
DX6 CAG CAN DOUB Y N 6
DX6 CAN CAI SING N N 7
DX6 CAI CAJ SING N N 8
DX6 CAJ CAP SING N N 9
DX6 CAP CAH DOUB Y N 10
DX6 CAP CAS SING Y N 11
DX6 CAH NAL SING Y N 12
DX6 NAL CAR SING Y N 13
DX6 CAR NAK SING N N 14
DX6 CAR CAS DOUB Y N 15
DX6 NAK CAO DOUB N N 16
DX6 CAS CAQ SING N N 17
DX6 CAQ OAB DOUB N N 18
DX6 CAQ NAM SING N N 19
DX6 NAM CAO SING N N 20
DX6 CAO NAA SING N N 21
DX6 CAF HAF SING N N 22
DX6 CAD HAD SING N N 23
DX6 CAC HAC SING N N 24
DX6 CAE HAE SING N N 25
DX6 CAG HAG SING N N 26
DX6 CAI HAI SING N N 27
DX6 CAI HAIA SING N N 28
DX6 CAJ HAJ SING N N 29
DX6 CAJ HAJA SING N N 30
DX6 CAH HAH SING N N 31
DX6 NAL HNAL SING N N 32
DX6 NAM HNAM SING N N 33
DX6 NAA HNAA SING N N 34
DX6 NAA HNAB SING N N 35
#
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
DX6 SMILES ACDLabs 10.04 O=C1c2c(cnc2N=C(N1)N)CCc3ccccc3
DX6 SMILES_CANONICAL CACTVS 3.341 NC1=Nc2[nH]cc(CCc3ccccc3)c2C(=O)N1
DX6 SMILES CACTVS 3.341 NC1=Nc2[nH]cc(CCc3ccccc3)c2C(=O)N1
DX6 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CCc2c[nH]c3c2C(=O)NC(=N3)N
DX6 SMILES "OpenEye OEToolkits" 1.5.0 c1ccc(cc1)CCc2c[nH]c3c2C(=O)NC(=N3)N
DX6 InChI InChI 1.03 InChI=1S/C14H14N4O/c15-14-17-12-11(13(19)18-14)10(8-16-12)7-6-9-4-2-1-3-5-9/h1-5,8H,6-7H2,(H4,15,16,17,18,19)
DX6 InChIKey InChI 1.03 GPZHVIFHNQJWLA-UHFFFAOYSA-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
DX6 "SYSTEMATIC NAME" ACDLabs 10.04 2-amino-5-(2-phenylethyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
DX6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-amino-5-phenethyl-3,7-dihydropyrrolo[3,2-e]pyrimidin-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
DX6 'Create component' 2007-12-17 RCSB
DX6 'Modify aromatic_flag' 2011-06-04 RCSB
DX6 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
DX6 CAF C 12.989 2.283 1
DX6 CAD C 13.455 3.708 2
DX6 CAC C 12.454 4.825 3
DX6 CAE C 10.986 4.515 4
DX6 CAG C 10.520 3.090 5
DX6 CAN C 11.522 1.973 6
DX6 CAI C 11.056 0.547 7
DX6 CAJ C 9.588 0.238 8
DX6 CAP C 9.122 -1.188 9
DX6 CAH C 9.997 -2.395 10
DX6 NAL N 9.122 -3.602 11
DX6 CAR C 7.702 -3.145 12
DX6 NAK N 6.404 -3.895 13
DX6 CAS C 7.702 -1.645 14
DX6 CAQ C 6.404 -0.895 15
DX6 OAB O 6.404 0.605 16
DX6 NAM N 5.104 -1.645 17
DX6 CAO C 5.104 -3.145 18
DX6 NAA N 3.805 -3.895 19
#
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
DX6 CAF CAD DOUBLE NONE 1
DX6 CAF CAN SINGLE NONE 2
DX6 CAD CAC SINGLE NONE 3
DX6 CAC CAE DOUBLE NONE 4
DX6 CAE CAG SINGLE NONE 5
DX6 CAG CAN DOUBLE NONE 6
DX6 CAN CAI SINGLE NONE 7
DX6 CAI CAJ SINGLE NONE 8
DX6 CAJ CAP SINGLE NONE 9
DX6 CAP CAH DOUBLE NONE 10
DX6 CAP CAS SINGLE NONE 11
DX6 CAH NAL SINGLE NONE 12
DX6 NAL CAR SINGLE NONE 13
DX6 CAR NAK SINGLE NONE 14
DX6 CAR CAS DOUBLE NONE 15
DX6 NAK CAO DOUBLE NONE 16
DX6 CAS CAQ SINGLE NONE 17
DX6 CAQ OAB DOUBLE NONE 18
DX6 CAQ NAM SINGLE NONE 19
DX6 NAM CAO SINGLE NONE 20
DX6 CAO NAA SINGLE NONE 21
#
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
DX6 MurckoScaffold S1 scaffold 'O=c1[nH]cnc2[nH]cc(CCc3ccccc3)c12' InChI=1S/C14H13N3O/c18-14-12-11(8-15-13(12)16-9-17-14)7-6-10-4-2-1-3-5-10/h1-5,8-9H,6-7H2,(H2,15,16,17,18) GYMUFHDRARXLAZ-UHFFFAOYSA-N
DX6 phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
DX6 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
DX6 pyrrole F3 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
DX6 CAF S1 1
DX6 CAD S1 1
DX6 CAC S1 1
DX6 CAE S1 1
DX6 CAG S1 1
DX6 CAN S1 1
DX6 CAI S1 1
DX6 CAJ S1 1
DX6 CAP S1 1
DX6 CAH S1 1
DX6 NAL S1 1
DX6 CAR S1 1
DX6 NAK S1 1
DX6 CAS S1 1
DX6 CAQ S1 1
DX6 OAB S1 1
DX6 NAM S1 1
DX6 CAO S1 1
DX6 CAF F1 1
DX6 CAD F1 1
DX6 CAC F1 1
DX6 CAE F1 1
DX6 CAG F1 1
DX6 CAN F1 1
DX6 CAS F2 1
DX6 CAR F2 1
DX6 NAK F2 1
DX6 CAO F2 1
DX6 NAM F2 1
DX6 CAQ F2 1
DX6 CAH F3 1
DX6 CAP F3 1
DX6 CAS F3 1
DX6 CAR F3 1
DX6 NAL F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DX6
_pdbe_chem_comp_rdkit_properties.exactmw 254.117
_pdbe_chem_comp_rdkit_properties.amw 254.293
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_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 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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.952
_pdbe_chem_comp_rdkit_properties.tpsa 87.560
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.600
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.523
_pdbe_chem_comp_rdkit_properties.chi0v 9.197
_pdbe_chem_comp_rdkit_properties.chi1v 5.019
_pdbe_chem_comp_rdkit_properties.chi2v 2.181
_pdbe_chem_comp_rdkit_properties.chi3v 2.181
_pdbe_chem_comp_rdkit_properties.chi4v 1.410
_pdbe_chem_comp_rdkit_properties.chi0n 23.197
_pdbe_chem_comp_rdkit_properties.chi1n 11.808
_pdbe_chem_comp_rdkit_properties.chi2n 2.181
_pdbe_chem_comp_rdkit_properties.chi3n 2.181
_pdbe_chem_comp_rdkit_properties.chi4n 1.410
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.560
_pdbe_chem_comp_rdkit_properties.kappa1 3.724
_pdbe_chem_comp_rdkit_properties.kappa2 4.605
_pdbe_chem_comp_rdkit_properties.kappa3 2.221
_pdbe_chem_comp_rdkit_properties.Phi 0.903
#
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
DX6 UniChem ZINC ZINC000036374070
DX6 UniChem 'PubChem TPHARMA' 16843050
DX6 UniChem BindingDb 50303508
DX6 UniChem BRENDA 27753
DX6 UniChem PubChem 135531129
DX6 UniChem 'PubChem TPHARMA' 87553941
#
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
DX6 CAF -3.386 -1.456 1.278 ETKDGv3 1
DX6 CAD -4.558 -1.181 1.865 ETKDGv3 2
DX6 CAC -4.713 0.048 2.669 ETKDGv3 3
DX6 CAE -3.683 0.892 2.807 ETKDGv3 4
DX6 CAG -2.390 0.595 2.157 ETKDGv3 5
DX6 CAN -2.236 -0.531 1.437 ETKDGv3 6
DX6 CAI -0.936 -0.826 0.740 ETKDGv3 7
DX6 CAJ -0.927 -0.213 -0.662 ETKDGv3 8
DX6 CAP 0.380 -0.481 -1.345 ETKDGv3 9
DX6 CAH 0.645 -1.511 -2.152 ETKDGv3 10
DX6 NAL 2.018 -1.504 -2.544 ETKDGv3 11
DX6 CAR 2.555 -0.377 -1.871 ETKDGv3 12
DX6 NAK 3.928 0.040 -1.897 ETKDGv3 13
DX6 CAS 1.637 0.242 -1.162 ETKDGv3 14
DX6 CAQ 2.004 1.405 -0.357 ETKDGv3 15
DX6 OAB 1.160 2.022 0.345 ETKDGv3 16
DX6 NAM 3.378 1.818 -0.397 ETKDGv3 17
DX6 CAO 4.321 1.077 -1.205 ETKDGv3 18
DX6 NAA 5.691 1.476 -1.246 ETKDGv3 19
DX6 HAF -3.282 -2.356 0.685 ETKDGv3 20
DX6 HAD -5.395 -1.857 1.749 ETKDGv3 21
DX6 HAC -5.662 0.266 3.143 ETKDGv3 22
DX6 HAE -3.796 1.796 3.392 ETKDGv3 23
DX6 HAG -1.572 1.297 2.267 ETKDGv3 24
DX6 HAI -0.086 -0.424 1.335 ETKDGv3 25
DX6 HAIA -0.796 -1.927 0.666 ETKDGv3 26
DX6 HAJ -1.086 0.885 -0.598 ETKDGv3 27
DX6 HAJA -1.758 -0.642 -1.265 ETKDGv3 28
DX6 HAH -0.067 -2.269 -2.451 ETKDGv3 29
DX6 HNAL 2.521 -2.198 -3.140 ETKDGv3 30
DX6 HNAM 3.693 2.645 0.158 ETKDGv3 31
DX6 HNAA 6.380 0.947 -1.826 ETKDGv3 32
DX6 HNAB 6.018 2.302 -0.697 ETKDGv3 33
#