data_5J9
#
_chem_comp.id 5J9
_chem_comp.name "3'-{4-[(4-amino-2-oxopyrimidin-1(2H)-yl)methyl]-1H-1,2,3-triazol-1-yl}-3'-deoxyadenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H19 N11 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-09-30
_chem_comp.pdbx_modified_date 2015-11-13
_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 441.404
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5J9
_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 5E13
_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
5J9 C4 C1 C 0 1 Y N N N N N -8.961 -9.890 21.140 -3.627 1.072 -0.149 C4 5J9 1
5J9 C14 C2 C 0 1 Y N N N N N -8.235 -16.364 19.073 1.812 -1.651 -0.268 C14 5J9 2
5J9 C5 C3 C 0 1 Y N N N N N -9.844 -9.068 21.754 -5.003 1.145 0.125 C5 5J9 3
5J9 C6 C4 C 0 1 Y N N N N N -9.395 -7.904 22.300 -5.600 2.416 0.193 C6 5J9 4
5J9 C8 C5 C 0 1 Y N N N N N -10.891 -10.833 21.031 -4.462 -0.955 0.093 C8 5J9 5
5J9 C13 C6 C 0 1 Y N N N N N -7.207 -16.831 19.775 3.077 -1.496 0.189 C13 5J9 6
5J9 N1 N1 N 0 1 Y N N N N N -8.104 -7.557 22.234 -4.836 3.485 -0.005 N1 5J9 7
5J9 N3 N2 N 0 1 Y N N N N N -7.657 -9.571 21.038 -2.945 2.197 -0.333 N3 5J9 8
5J9 O2T O1 O 0 1 N N N N N N -6.924 -18.890 17.298 5.800 0.092 1.213 O2T 5J9 9
5J9 C2T C7 C 0 1 N N N N N N -5.819 -18.941 17.849 5.291 0.827 0.383 C2T 5J9 10
5J9 N3T N3 N 0 1 N N N N N N -4.747 -19.297 17.106 5.515 2.138 0.445 N3T 5J9 11
5J9 C4T C8 C 0 1 N N N N N N -3.509 -19.385 17.637 4.973 2.961 -0.444 C4T 5J9 12
5J9 N4T N4 N 0 1 N N N N N N -2.497 -19.736 16.858 5.212 4.313 -0.371 N4T 5J9 13
5J9 C5T C9 C 0 1 N N N N N N -3.303 -19.114 18.996 4.153 2.440 -1.466 C5T 5J9 14
5J9 C6T C10 C 0 1 N N N N N N -4.404 -18.754 19.773 3.935 1.104 -1.515 C6T 5J9 15
5J9 N1T N5 N 0 1 N N N N N N -5.684 -18.667 19.169 4.517 0.299 -0.583 N1T 5J9 16
5J9 C15 C11 C 0 1 N N N N N N -6.856 -18.308 19.991 4.295 -1.148 -0.629 C15 5J9 17
5J9 N12 N6 N 0 1 Y N N N N N -6.514 -15.837 20.306 3.034 -1.712 1.508 N12 5J9 18
5J9 N11 N7 N 0 1 Y N N N N N -7.106 -14.710 19.909 1.823 -1.982 1.847 N11 5J9 19
5J9 N10 N8 N 0 1 Y N N N N N -8.168 -15.029 19.151 1.057 -1.956 0.812 N10 5J9 20
5J9 "C3'" C12 C 0 1 N N S N N N -9.076 -14.022 18.547 -0.386 -2.213 0.806 "C3'" 5J9 21
5J9 "C2'" C13 C 0 1 N N R N N N -9.891 -13.280 19.607 -1.172 -0.887 0.900 "C2'" 5J9 22
5J9 "O2'" O2 O 0 1 N N N N N N -10.138 -14.088 20.779 -0.275 0.224 0.968 "O2'" 5J9 23
5J9 "C4'" C14 C 0 1 N N S N N N -8.276 -12.866 17.888 -0.822 -2.813 -0.549 "C4'" 5J9 24
5J9 "C5'" C15 C 0 1 N N N N N N -8.751 -12.352 16.548 -0.944 -4.334 -0.443 "C5'" 5J9 25
5J9 "O5'" O3 O 0 1 N N N N N N -10.142 -12.634 16.320 -1.235 -4.880 -1.732 "O5'" 5J9 26
5J9 "O4'" O4 O 0 1 N N N N N N -8.485 -11.674 18.720 -2.113 -2.223 -0.815 "O4'" 5J9 27
5J9 "C1'" C16 C 0 1 N N R N N N -8.968 -12.120 19.966 -1.991 -0.842 -0.409 "C1'" 5J9 28
5J9 N9 N9 N 0 1 Y N N N N N -9.616 -10.968 20.690 -3.315 -0.264 -0.163 N9 5J9 29
5J9 N7 N10 N 0 1 Y N N N N N -11.029 -9.683 21.671 -5.450 -0.126 0.267 N7 5J9 30
5J9 C2 C17 C 0 1 Y N N N N N -7.192 -8.396 21.595 -3.546 3.366 -0.260 C2 5J9 31
5J9 N6 N11 N 0 1 N N N N N N -10.220 -7.046 22.943 -6.951 2.550 0.459 N6 5J9 32
5J9 H1 H1 H 0 1 N N N N N N -8.976 -16.946 18.545 1.474 -1.546 -1.288 H1 5J9 33
5J9 H2 H2 H 0 1 N N N N N N -11.680 -11.540 20.822 -4.537 -2.030 0.151 H2 5J9 34
5J9 H3 H3 H 0 1 N N N N N N -2.655 -19.932 15.890 5.777 4.669 0.333 H3 5J9 35
5J9 H4 H4 H 0 1 N N N N N N -1.574 -19.805 17.238 4.814 4.912 -1.023 H4 5J9 36
5J9 H5 H5 H 0 1 N N N N N N -2.317 -19.182 19.431 3.704 3.096 -2.197 H5 5J9 37
5J9 H6 H6 H 0 1 N N N N N N -4.283 -18.543 20.825 3.309 0.681 -2.288 H6 5J9 38
5J9 H7 H7 H 0 1 N N N N N N -7.712 -18.934 19.699 5.165 -1.663 -0.221 H7 5J9 39
5J9 H8 H8 H 0 1 N N N N N N -6.623 -18.477 21.053 4.140 -1.460 -1.662 H8 5J9 40
5J9 H9 H9 H 0 1 N N N N N N -9.744 -14.487 17.807 -0.658 -2.878 1.626 H9 5J9 41
5J9 H10 H10 H 0 1 N N N N N N -10.828 -12.902 19.172 -1.835 -0.896 1.765 H10 5J9 42
5J9 H11 H11 H 0 1 N N N N N N -10.645 -13.588 21.408 -0.716 1.082 1.028 H11 5J9 43
5J9 H12 H12 H 0 1 N N N N N N -7.209 -13.131 17.840 -0.113 -2.542 -1.331 H12 5J9 44
5J9 H13 H13 H 0 1 N N N N N N -8.158 -12.830 15.755 -0.005 -4.749 -0.076 H13 5J9 45
5J9 H14 H14 H 0 1 N N N N N N -8.600 -11.263 16.513 -1.748 -4.588 0.248 H14 5J9 46
5J9 H15 H15 H 0 1 N N N N N N -10.399 -12.296 15.470 -1.326 -5.843 -1.740 H15 5J9 47
5J9 H16 H16 H 0 1 N N N N N N -8.140 -12.506 20.579 -1.461 -0.268 -1.169 H16 5J9 48
5J9 H17 H17 H 0 1 N N N N N N -6.146 -8.133 21.537 -2.962 4.262 -0.415 H17 5J9 49
5J9 H18 H18 H 0 1 N N N N N N -9.694 -6.262 23.274 -7.498 1.762 0.602 H18 5J9 50
5J9 H19 H19 H 0 1 N N N N N N -10.929 -6.730 22.313 -7.351 3.433 0.504 H19 5J9 51
#
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
5J9 "O5'" "C5'" SING N N 1
5J9 "C5'" "C4'" SING N N 2
5J9 N4T C4T SING N N 3
5J9 N3T C4T DOUB N N 4
5J9 N3T C2T SING N N 5
5J9 O2T C2T DOUB N N 6
5J9 C4T C5T SING N N 7
5J9 C2T N1T SING N N 8
5J9 "C4'" "C3'" SING N N 9
5J9 "C4'" "O4'" SING N N 10
5J9 "C3'" N10 SING N N 11
5J9 "C3'" "C2'" SING N N 12
5J9 "O4'" "C1'" SING N N 13
5J9 C5T C6T DOUB N N 14
5J9 C14 N10 SING Y N 15
5J9 C14 C13 DOUB Y N 16
5J9 N10 N11 SING Y N 17
5J9 N1T C6T SING N N 18
5J9 N1T C15 SING N N 19
5J9 "C2'" "C1'" SING N N 20
5J9 "C2'" "O2'" SING N N 21
5J9 C13 C15 SING N N 22
5J9 C13 N12 SING Y N 23
5J9 N11 N12 DOUB Y N 24
5J9 "C1'" N9 SING N N 25
5J9 N9 C8 SING Y N 26
5J9 N9 C4 SING Y N 27
5J9 C8 N7 DOUB Y N 28
5J9 N3 C4 DOUB Y N 29
5J9 N3 C2 SING Y N 30
5J9 C4 C5 SING Y N 31
5J9 C2 N1 DOUB Y N 32
5J9 N7 C5 SING Y N 33
5J9 C5 C6 DOUB Y N 34
5J9 N1 C6 SING Y N 35
5J9 C6 N6 SING N N 36
5J9 C14 H1 SING N N 37
5J9 C8 H2 SING N N 38
5J9 N4T H3 SING N N 39
5J9 N4T H4 SING N N 40
5J9 C5T H5 SING N N 41
5J9 C6T H6 SING N N 42
5J9 C15 H7 SING N N 43
5J9 C15 H8 SING N N 44
5J9 "C3'" H9 SING N N 45
5J9 "C2'" H10 SING N N 46
5J9 "O2'" H11 SING N N 47
5J9 "C4'" H12 SING N N 48
5J9 "C5'" H13 SING N N 49
5J9 "C5'" H14 SING N N 50
5J9 "O5'" H15 SING N N 51
5J9 "C1'" H16 SING N N 52
5J9 C2 H17 SING N N 53
5J9 N6 H18 SING N N 54
5J9 N6 H19 SING N N 55
#
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
5J9 SMILES ACDLabs 12.01 c12c(c(N)ncn1)ncn2C5C(C(n4cc(CN3C(=O)N=C(C=C3)N)nn4)C(O5)CO)O
5J9 InChI InChI 1.03 InChI=1S/C17H19N11O4/c18-10-1-2-26(17(31)23-10)3-8-4-28(25-24-8)12-9(5-29)32-16(13(12)30)27-7-22-11-14(19)20-6-21-15(11)27/h1-2,4,6-7,9,12-13,16,29-30H,3,5H2,(H2,18,23,31)(H2,19,20,21)/t9-,12-,13-,16-/m1/s1
5J9 InChIKey InChI 1.03 RYUXRYKLIYXCJZ-RVXWVPLUSA-N
5J9 SMILES_CANONICAL CACTVS 3.385 NC1=NC(=O)N(Cc2cn(nn2)[C@H]3[C@@H](O)[C@@H](O[C@@H]3CO)n4cnc5c(N)ncnc45)C=C1
5J9 SMILES CACTVS 3.385 NC1=NC(=O)N(Cc2cn(nn2)[CH]3[CH](O)[CH](O[CH]3CO)n4cnc5c(N)ncnc45)C=C1
5J9 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1c(nnn1[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)CO)CN5C=CC(=NC5=O)N
5J9 SMILES "OpenEye OEToolkits" 1.9.2 c1c(nnn1C2C(OC(C2O)n3cnc4c3ncnc4N)CO)CN5C=CC(=NC5=O)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
5J9 "SYSTEMATIC NAME" ACDLabs 12.01 "3'-{4-[(4-amino-2-oxopyrimidin-1(2H)-yl)methyl]-1H-1,2,3-triazol-1-yl}-3'-deoxyadenosine"
5J9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 1-[[1-[(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]-1,2,3-triazol-4-yl]methyl]-4-azanyl-pyrimidin-2-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
5J9 'Create component' 2015-09-30 EBI
5J9 'Initial release' 2015-11-18 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
5J9 C4 C 5.598 -3.008 1
5J9 C14 C 10.131 3.215 2
5J9 C5 C 5.598 -4.508 3
5J9 C6 C 4.299 -5.258 4
5J9 C8 C 7.893 -3.758 5
5J9 C13 C 11.558 3.676 6
5J9 N1 N 3.000 -4.508 7
5J9 N3 N 4.299 -2.258 8
5J9 O2T O 14.028 2.869 9
5J9 C2T C 14.494 4.295 10
5J9 N3T N 15.962 4.604 11
5J9 C4T C 16.428 6.030 12
5J9 N4T N 17.895 6.339 13
5J9 C5T C 15.426 7.146 14
5J9 C6T C 13.958 6.837 15
5J9 N1T N 13.492 5.411 16
5J9 C15 C 12.024 5.102 17
5J9 N12 N 12.438 2.461 18
5J9 N11 N 11.554 1.249 19
5J9 N10 N 10.129 1.715 20
5J9 "C3'" C 8.913 0.836 21
5J9 "C2'" C 8.911 -0.664 22
5J9 "O2'" O 10.123 -1.548 23
5J9 "C4'" C 7.487 1.302 24
5J9 "C5'" C 7.027 2.729 25
5J9 "O5'" O 5.560 3.043 26
5J9 "O4'" O 6.604 0.090 27
5J9 "C1'" C 7.483 -1.125 28
5J9 N9 N 7.018 -2.551 29
5J9 N7 N 7.018 -4.965 30
5J9 C2 C 3.000 -3.008 31
5J9 N6 N 4.299 -6.758 32
#
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
5J9 "O5'" "C5'" SINGLE NONE 1
5J9 "C4'" "C5'" SINGLE BEGINDASH 2
5J9 N4T C4T SINGLE NONE 3
5J9 N3T C4T DOUBLE NONE 4
5J9 N3T C2T SINGLE NONE 5
5J9 O2T C2T DOUBLE NONE 6
5J9 C4T C5T SINGLE NONE 7
5J9 C2T N1T SINGLE NONE 8
5J9 "C4'" "C3'" SINGLE NONE 9
5J9 "C4'" "O4'" SINGLE NONE 10
5J9 "C3'" N10 SINGLE BEGINWEDGE 11
5J9 "C3'" "C2'" SINGLE NONE 12
5J9 "O4'" "C1'" SINGLE NONE 13
5J9 C5T C6T DOUBLE NONE 14
5J9 C14 N10 SINGLE NONE 15
5J9 C14 C13 DOUBLE NONE 16
5J9 N10 N11 SINGLE NONE 17
5J9 N1T C6T SINGLE NONE 18
5J9 N1T C15 SINGLE NONE 19
5J9 "C2'" "C1'" SINGLE NONE 20
5J9 "C2'" "O2'" SINGLE BEGINWEDGE 21
5J9 C13 C15 SINGLE NONE 22
5J9 C13 N12 SINGLE NONE 23
5J9 N11 N12 DOUBLE NONE 24
5J9 "C1'" N9 SINGLE BEGINDASH 25
5J9 N9 C8 SINGLE NONE 26
5J9 N9 C4 SINGLE NONE 27
5J9 C8 N7 DOUBLE NONE 28
5J9 N3 C4 DOUBLE NONE 29
5J9 N3 C2 SINGLE NONE 30
5J9 C4 C5 SINGLE NONE 31
5J9 C2 N1 DOUBLE NONE 32
5J9 N7 C5 SINGLE NONE 33
5J9 C5 C6 DOUBLE NONE 34
5J9 N1 C6 SINGLE NONE 35
5J9 C6 N6 SINGLE NONE 36
#
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
5J9 MurckoScaffold S1 scaffold 'O=c1ncccn1Cc1cn([C@@H]2CO[C@@H](n3cnc4cncnc43)C2)nn1' InChI=1S/C16H15N9O2/c26-16-18-2-1-3-23(16)6-11-7-25(22-21-11)12-4-14(27-8-12)24-10-20-13-5-17-9-19-15(13)24/h1-3,5,7,9-10,12,14H,4,6,8H2/t12-,14+/m0/s1 DUNUXTGWUPODHC-GXTWGEPZSA-N
5J9 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
5J9 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
5J9 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
5J9 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
5J9 C4 S1 1
5J9 C14 S1 1
5J9 C5 S1 1
5J9 C6 S1 1
5J9 C8 S1 1
5J9 C13 S1 1
5J9 N1 S1 1
5J9 N3 S1 1
5J9 O2T S1 1
5J9 C2T S1 1
5J9 N3T S1 1
5J9 C4T S1 1
5J9 C5T S1 1
5J9 C6T S1 1
5J9 N1T S1 1
5J9 C15 S1 1
5J9 N12 S1 1
5J9 N11 S1 1
5J9 N10 S1 1
5J9 "C3'" S1 1
5J9 "C2'" S1 1
5J9 "C4'" S1 1
5J9 "O4'" S1 1
5J9 "C1'" S1 1
5J9 N9 S1 1
5J9 N7 S1 1
5J9 C2 S1 1
5J9 N1 F1 1
5J9 C6 F1 1
5J9 C5 F1 1
5J9 C4 F1 1
5J9 N3 F1 1
5J9 C2 F1 1
5J9 N9 F1 1
5J9 C8 F1 1
5J9 N7 F1 1
5J9 N6 F1 1
5J9 C4 F2 1
5J9 C5 F2 1
5J9 N7 F2 1
5J9 C8 F2 1
5J9 N9 F2 1
5J9 N7 F3 1
5J9 C8 F3 1
5J9 N9 F3 1
5J9 C4 F3 1
5J9 C5 F3 1
5J9 C6 F3 1
5J9 N1 F3 1
5J9 C2 F3 1
5J9 N3 F3 1
5J9 C5 F4 1
5J9 C4 F4 1
5J9 N3 F4 1
5J9 C2 F4 1
5J9 N1 F4 1
5J9 C6 F4 1
5J9 C5T F4 2
5J9 C4T F4 2
5J9 N3T F4 2
5J9 C2T F4 2
5J9 N1T F4 2
5J9 C6T F4 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 5J9
_pdbe_chem_comp_rdkit_properties.exactmw 441.162
_pdbe_chem_comp_rdkit_properties.amw 441.412
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 15
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 15
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 32
_pdbe_chem_comp_rdkit_properties.NumAtoms 51
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 15
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.353
_pdbe_chem_comp_rdkit_properties.NumRings 5
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 5
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 205.577
_pdbe_chem_comp_rdkit_properties.tpsa 210.930
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.665
_pdbe_chem_comp_rdkit_properties.CrippenMR 103.796
_pdbe_chem_comp_rdkit_properties.chi0v 15.052
_pdbe_chem_comp_rdkit_properties.chi1v 8.169
_pdbe_chem_comp_rdkit_properties.chi2v 3.876
_pdbe_chem_comp_rdkit_properties.chi3v 3.876
_pdbe_chem_comp_rdkit_properties.chi4v 2.561
_pdbe_chem_comp_rdkit_properties.chi0n 34.052
_pdbe_chem_comp_rdkit_properties.chi1n 17.275
_pdbe_chem_comp_rdkit_properties.chi2n 3.876
_pdbe_chem_comp_rdkit_properties.chi3n 3.876
_pdbe_chem_comp_rdkit_properties.chi4n 2.561
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.950
_pdbe_chem_comp_rdkit_properties.kappa1 7.875
_pdbe_chem_comp_rdkit_properties.kappa2 7.630
_pdbe_chem_comp_rdkit_properties.kappa3 3.238
_pdbe_chem_comp_rdkit_properties.Phi 1.878
#
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
5J9 UniChem ZINC ZINC000263621013
5J9 UniChem PubChem 92045007
#
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
5J9 C4 4.047 -1.178 -1.282 ETKDGv3 1
5J9 C14 -2.030 1.471 0.498 ETKDGv3 2
5J9 C5 5.329 -1.381 -0.717 ETKDGv3 3
5J9 C6 5.942 -2.557 -0.846 ETKDGv3 4
5J9 C8 4.675 0.584 -0.073 ETKDGv3 5
5J9 C13 -2.873 1.419 -0.521 ETKDGv3 6
5J9 N1 5.257 -3.582 -1.603 ETKDGv3 7
5J9 N3 3.401 -2.100 -1.927 ETKDGv3 8
5J9 O2T -4.989 0.874 2.173 ETKDGv3 9
5J9 C2T -5.360 0.149 1.212 ETKDGv3 10
5J9 N3T -6.050 -1.077 1.471 ETKDGv3 11
5J9 C4T -6.430 -1.857 0.502 ETKDGv3 12
5J9 N4T -7.115 -3.072 0.802 ETKDGv3 13
5J9 C5T -6.152 -1.496 -0.906 ETKDGv3 14
5J9 C6T -5.515 -0.358 -1.199 ETKDGv3 15
5J9 N1T -5.099 0.535 -0.150 ETKDGv3 16
5J9 C15 -4.333 1.740 -0.475 ETKDGv3 17
5J9 N12 -2.190 0.933 -1.675 ETKDGv3 18
5J9 N11 -0.981 0.718 -1.344 ETKDGv3 19
5J9 N10 -0.783 1.003 0.013 ETKDGv3 20
5J9 "C3'" 0.520 1.217 0.650 ETKDGv3 21
5J9 "C2'" 1.483 0.089 0.369 ETKDGv3 22
5J9 "O2'" 0.819 -1.130 0.155 ETKDGv3 23
5J9 "C4'" 1.228 2.428 0.032 ETKDGv3 24
5J9 "C5'" 1.936 3.273 1.102 ETKDGv3 25
5J9 "O5'" 2.618 4.345 0.509 ETKDGv3 26
5J9 "O4'" 2.179 1.982 -0.915 ETKDGv3 27
5J9 "C1'" 2.207 0.571 -0.883 ETKDGv3 28
5J9 N9 3.592 0.105 -0.901 ETKDGv3 29
5J9 N7 5.686 -0.237 0.047 ETKDGv3 30
5J9 C2 4.065 -3.372 -2.113 ETKDGv3 31
5J9 N6 7.210 -2.818 -0.245 ETKDGv3 32
5J9 H1 -2.239 1.800 1.507 ETKDGv3 33
5J9 H2 4.650 1.541 0.431 ETKDGv3 34
5J9 H3 -7.314 -3.337 1.793 ETKDGv3 35
5J9 H4 -7.426 -3.712 0.037 ETKDGv3 36
5J9 H5 -6.461 -2.158 -1.705 ETKDGv3 37
5J9 H6 -5.311 -0.114 -2.234 ETKDGv3 38
5J9 H7 -4.527 2.539 0.273 ETKDGv3 39
5J9 H8 -4.650 2.139 -1.463 ETKDGv3 40
5J9 H9 0.372 1.324 1.749 ETKDGv3 41
5J9 H10 2.191 0.003 1.228 ETKDGv3 42
5J9 H11 1.509 -1.840 0.214 ETKDGv3 43
5J9 H12 0.490 3.081 -0.486 ETKDGv3 44
5J9 H13 2.672 2.645 1.648 ETKDGv3 45
5J9 H14 1.196 3.653 1.843 ETKDGv3 46
5J9 H15 1.930 5.016 0.259 ETKDGv3 47
5J9 H16 1.688 0.196 -1.792 ETKDGv3 48
5J9 H17 3.573 -4.158 -2.669 ETKDGv3 49
5J9 H18 7.708 -2.085 0.308 ETKDGv3 50
5J9 H19 7.657 -3.755 -0.357 ETKDGv3 51
#