data_HCX
#
_chem_comp.id HCX
_chem_comp.name "(SOUTH) BICYCLO[3.1.0]HEXANE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H13 O4 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-03-15
_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 192.149
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HCX
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1SKM
_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
HCX P P P 0 1 N N R N N N -29.983 72.876 190.347 1.444 -4.458 4.597 P HCX 1
HCX O1P O1P O 0 1 N N N N N N -30.498 74.124 190.960 0.880 -3.875 5.866 O1P HCX 2
HCX O2P O2P O 0 1 N N N N N N -30.588 72.370 189.089 0.669 -5.823 4.172 O2P HCX 3
HCX "O5'" O5* O 0 1 N N N N N N -28.425 73.040 190.088 1.157 -3.506 3.309 "O5'" HCX 4
HCX C4 C4 C 0 1 N N R N N N -26.635 71.887 191.765 0.681 -1.862 1.011 C4 HCX 5
HCX C7 C7 C 0 1 N N N N N N -25.915 71.099 192.828 0.885 -0.537 0.323 C7 HCX 6
HCX "C2'" C2* C 0 1 N N N N N N -24.683 73.303 192.053 2.466 -0.951 2.391 "C2'" HCX 7
HCX "C5'" C5* C 0 1 N N N N N N -27.657 73.968 190.842 1.359 -4.045 2.016 "C5'" HCX 8
HCX "C4'" C4* C 0 1 N N R N N N -27.096 73.291 192.068 1.768 -2.912 1.078 "C4'" HCX 9
HCX "C1'" C1* C 0 1 N N R N N N -25.143 71.877 191.792 1.110 -0.675 1.805 "C1'" HCX 10
HCX "C3'" C3* C 0 1 N N S N N N -25.888 73.991 192.688 3.009 -2.164 1.618 "C3'" HCX 11
HCX "O3'" O3* O 0 1 N N N N N N -25.900 73.791 194.099 3.807 -1.697 0.533 "O3'" HCX 12
HCX H2P H2P H 0 1 N N N N N N -30.258 71.570 188.696 -0.312 -5.834 4.200 H2P HCX 13
HCX H4 H4 H 0 1 N N N N N N -27.480 71.597 191.098 -0.327 -2.239 1.100 H4 HCX 14
HCX H71 1H7 H 0 1 N N N N N N -25.936 71.065 193.942 0.000 0.000 0.000 H71 HCX 15
HCX H72 2H7 H 0 1 N N N N N N -25.929 70.040 193.177 1.736 -0.407 -0.332 H72 HCX 16
HCX "H2'1" 1H2* H 0 0 N N N N N N -23.749 73.374 192.658 3.116 -0.075 2.309 "H2'1" HCX 17
HCX "H2'2" 2H2* H 0 0 N N N N N N -24.287 73.824 191.149 2.343 -1.209 3.449 "H2'2" HCX 18
HCX "H5'1" 1H5* H 0 0 N N N N N N -26.860 74.449 190.227 2.149 -4.796 2.057 "H5'1" HCX 19
HCX "H5'2" 2H5* H 0 0 N N N N N N -28.239 74.883 191.098 0.434 -4.502 1.666 "H5'2" HCX 20
HCX "H4'" H4* H 0 1 N N N N N N -27.950 73.319 192.784 1.952 -3.321 0.078 "H4'" HCX 21
HCX "H1'" H1* H 0 1 N N N N N N -24.263 71.565 191.181 0.415 -0.205 2.485 "H1'" HCX 22
HCX H1 H1 H 0 1 N N N N N N -25.878 75.091 192.511 3.654 -2.793 2.240 H1 HCX 23
HCX "H3'" H3* H 0 1 N N N N N N -26.650 74.219 194.494 4.317 -2.459 0.218 "H3'" HCX 24
HCX HP1 HP1 H 0 1 N Y N N N N -30.349 71.900 191.311 2.808 -4.796 4.464 HP1 HCX 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
HCX P O1P DOUB N N 1
HCX P O2P SING N N 2
HCX P "O5'" SING N N 3
HCX O2P H2P SING N N 4
HCX "O5'" "C5'" SING N N 5
HCX C4 C7 SING N N 6
HCX C4 "C4'" SING N N 7
HCX C4 "C1'" SING N N 8
HCX C4 H4 SING N N 9
HCX C7 "C1'" SING N N 10
HCX C7 H71 SING N N 11
HCX C7 H72 SING N N 12
HCX "C2'" "C1'" SING N N 13
HCX "C2'" "C3'" SING N N 14
HCX "C2'" "H2'1" SING N N 15
HCX "C2'" "H2'2" SING N N 16
HCX "C5'" "C4'" SING N N 17
HCX "C5'" "H5'1" SING N N 18
HCX "C5'" "H5'2" SING N N 19
HCX "C4'" "C3'" SING N N 20
HCX "C4'" "H4'" SING N N 21
HCX "C1'" "H1'" SING N N 22
HCX "C3'" "O3'" SING N N 23
HCX "C3'" H1 SING N N 24
HCX "O3'" "H3'" SING N N 25
HCX HP1 P 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
HCX SMILES ACDLabs 10.04 O=P(OCC1C2CC2CC1O)O
HCX SMILES_CANONICAL CACTVS 3.341 O[C@H]1C[C@H]2C[C@H]2[C@@H]1CO[P@H](O)=O
HCX SMILES CACTVS 3.341 O[CH]1C[CH]2C[CH]2[CH]1CO[PH](O)=O
HCX SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1[C@H]2[C@@H]1[C@@H]([C@H](C2)O)CO[P@@H](=O)O
HCX SMILES "OpenEye OEToolkits" 1.5.0 C1C2C1C(C(C2)O)COP(=O)O
HCX InChI InChI 1.03 InChI=1S/C7H13O4P/c8-7-2-4-1-5(4)6(7)3-11-12(9)10/h4-8,12H,1-3H2,(H,9,10)/t4-,5-,6+,7+/m1/s1
HCX InChIKey InChI 1.03 MHTBERPCQUPUKA-JWXFUTCRSA-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
HCX "SYSTEMATIC NAME" ACDLabs 10.04 "[(1R,2R,3S,5R)-3-hydroxybicyclo[3.1.0]hex-2-yl]methyl hydrogen (S)-phosphonate"
HCX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2R,3S,5R)-3-hydroxy-2-bicyclo[3.1.0]hexanyl]methoxyphosphinic 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
HCX 'Create component' 2004-03-15 RCSB
HCX '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
HCX P P 4.427 1.986 1
HCX O1P O 3.963 3.413 2
HCX O2P O 3.000 1.522 3
HCX "O5'" O 4.890 0.559 4
HCX C4 C 8.248 -1.643 5
HCX C7 C 9.547 -2.393 6
HCX "C2'" C 6.821 -3.606 7
HCX "C5'" C 6.357 0.248 8
HCX "C4'" C 6.821 -1.179 9
HCX "C1'" C 8.248 -3.143 10
HCX "C3'" C 5.939 -2.393 11
HCX "O3'" O 4.439 -2.393 12
#
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
HCX P O1P DOUBLE NONE 1
HCX P O2P SINGLE BEGINWEDGE 2
HCX P "O5'" SINGLE NONE 3
HCX "O5'" "C5'" SINGLE NONE 4
HCX C4 C7 SINGLE NONE 5
HCX C4 "C4'" SINGLE NONE 6
HCX C4 "C1'" SINGLE NONE 7
HCX C7 "C1'" SINGLE NONE 8
HCX "C2'" "C1'" SINGLE NONE 9
HCX "C2'" "C3'" SINGLE NONE 10
HCX "C4'" "C5'" SINGLE BEGINWEDGE 11
HCX "C4'" "C3'" SINGLE NONE 12
HCX "C3'" "O3'" SINGLE BEGINDASH 13
#
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
HCX MurckoScaffold S1 scaffold 'C1C[C@@H]2C[C@@H]2C1' InChI=1S/C6H10/c1-2-5-4-6(5)3-1/h5-6H,1-4H2/t5-,6+ JAPMJSVZDUYFKL-OLQVQODUSA-N
HCX cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
HCX cyclopentane F2 fragment C1CCCC1 InChI=1S/C5H10/c1-2-4-5-3-1/h1-5H2 RGSFGYAAUTVSQA-UHFFFAOYSA-N
HCX cyclopropane F3 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-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
HCX C4 S1 1
HCX C7 S1 1
HCX "C2'" S1 1
HCX "C4'" S1 1
HCX "C1'" S1 1
HCX "C3'" S1 1
HCX C4 F1 1
HCX C7 F1 1
HCX "C1'" F1 1
HCX "C2'" F1 1
HCX "C3'" F1 1
HCX "C4'" F1 1
HCX C4 F2 1
HCX "C4'" F2 1
HCX "C3'" F2 1
HCX "C2'" F2 1
HCX "C1'" F2 1
HCX C4 F3 1
HCX C7 F3 1
HCX "C1'" F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HCX
_pdbe_chem_comp_rdkit_properties.exactmw 192.055
_pdbe_chem_comp_rdkit_properties.amw 192.151
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 25
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 89.812
_pdbe_chem_comp_rdkit_properties.tpsa 66.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.402
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.883
_pdbe_chem_comp_rdkit_properties.chi0v 6.475
_pdbe_chem_comp_rdkit_properties.chi1v 4.051
_pdbe_chem_comp_rdkit_properties.chi2v 1.616
_pdbe_chem_comp_rdkit_properties.chi3v 1.616
_pdbe_chem_comp_rdkit_properties.chi4v 1.011
_pdbe_chem_comp_rdkit_properties.chi0n 18.580
_pdbe_chem_comp_rdkit_properties.chi1n 9.220
_pdbe_chem_comp_rdkit_properties.chi2n 1.375
_pdbe_chem_comp_rdkit_properties.chi3n 1.375
_pdbe_chem_comp_rdkit_properties.chi4n 0.845
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.110
_pdbe_chem_comp_rdkit_properties.kappa1 2.193
_pdbe_chem_comp_rdkit_properties.kappa2 3.110
_pdbe_chem_comp_rdkit_properties.kappa3 1.571
_pdbe_chem_comp_rdkit_properties.Phi 0.568
#
_pdbe_chem_comp_external_mappings.comp_id HCX
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource ZINC
_pdbe_chem_comp_external_mappings.resource_id ZINC000058633229
#
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
HCX P 3.285 -0.794 -0.260 ETKDGv3 1
HCX O1P 3.944 -0.075 0.895 ETKDGv3 2
HCX O2P 3.817 -2.400 -0.295 ETKDGv3 3
HCX "O5'" 1.594 -0.774 -0.056 ETKDGv3 4
HCX C4 -1.138 -0.471 -1.007 ETKDGv3 5
HCX C7 -2.599 -0.189 -1.327 ETKDGv3 6
HCX "C2'" -2.157 -0.301 1.223 ETKDGv3 7
HCX "C5'" 1.128 0.507 -0.412 ETKDGv3 8
HCX "C4'" -0.392 0.599 -0.205 ETKDGv3 9
HCX "C1'" -2.231 -1.029 -0.114 ETKDGv3 10
HCX "C3'" -0.804 0.400 1.262 ETKDGv3 11
HCX "O3'" -0.911 1.629 1.930 ETKDGv3 12
HCX H2P 4.774 -2.342 -0.541 ETKDGv3 13
HCX H4 -0.609 -1.252 -1.595 ETKDGv3 14
HCX H71 -2.951 0.842 -1.110 ETKDGv3 15
HCX H72 -2.995 -0.780 -2.180 ETKDGv3 16
HCX "H2'1" -2.992 0.430 1.302 ETKDGv3 17
HCX "H2'2" -2.244 -1.028 2.058 ETKDGv3 18
HCX "H5'1" 1.612 1.295 0.210 ETKDGv3 19
HCX "H5'2" 1.342 0.714 -1.486 ETKDGv3 20
HCX "H4'" -0.725 1.603 -0.554 ETKDGv3 21
HCX "H1'" -2.328 -2.135 -0.173 ETKDGv3 22
HCX H1 -0.084 -0.266 1.795 ETKDGv3 23
HCX "H3'" 0.016 1.933 2.112 ETKDGv3 24
HCX HP1 3.647 -0.169 -1.470 ETKDGv3 25
#