data_K38
#
_chem_comp.id K38
_chem_comp.name
(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynylamino]methyl]oxolane-3,4-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H27 N11 O7"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-04-16
_chem_comp.pdbx_modified_date 2020-02-14
_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 569.530
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K38
_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 6RGB
_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
K38 N1 N1 N 0 1 Y N N N N N 19.493 4.158 7.723 -8.177 2.325 1.786 N1 K38 1
K38 C2 C1 C 0 1 Y N N N N N 19.864 5.287 8.329 -7.713 1.176 2.243 C2 K38 2
K38 C4 C2 C 0 1 Y N N N N N 17.824 6.161 8.198 -6.115 1.045 0.596 C4 K38 3
K38 C5 C3 C 0 1 Y N N N N N 17.386 5.042 7.564 -6.572 2.265 0.070 C5 K38 4
K38 C6 C4 C 0 1 Y N N N N N 18.264 4.008 7.315 -7.646 2.904 0.714 C6 K38 5
K38 "C1'" C5 C 0 1 N N R N N N 19.310 9.247 13.874 4.554 -0.842 0.920 "C1'" K38 6
K38 "C2'" C6 C 0 1 N N R N N N 18.314 9.099 14.970 3.333 -0.562 1.833 "C2'" K38 7
K38 "C3'" C7 C 0 1 N N S N N N 18.341 7.608 14.973 2.798 -1.989 2.106 "C3'" K38 8
K38 "C4'" C8 C 0 1 N N R N N N 18.573 7.317 13.494 3.376 -2.836 0.956 "C4'" K38 9
K38 "C5'" C9 C 0 1 N N N N N N 17.364 6.703 12.864 2.238 -3.491 0.170 "C5'" K38 10
K38 C8 C10 C 0 1 Y N N N N N 15.797 6.405 7.768 -4.928 1.601 -1.177 C8 K38 11
K38 CAF C11 C 0 1 N N R N N N 16.859 8.258 8.949 -4.279 -0.569 -0.062 CAF K38 12
K38 CAG C12 C 0 1 N N R N N N 16.726 9.343 7.942 -4.941 -1.743 -0.817 CAG K38 13
K38 CAH C13 C 0 1 N N S N N N 15.455 9.987 8.398 -3.749 -2.536 -1.398 CAH K38 14
K38 CAI C14 C 0 1 N N R N N N 15.493 9.611 9.853 -2.508 -1.746 -0.926 CAI K38 15
K38 CAJ C15 C 0 1 N N N N N N 14.148 9.839 10.636 -1.432 -1.744 -2.014 CAJ K38 16
K38 CAL C16 C 0 1 N N N N N N 14.598 10.587 13.070 0.837 -1.072 -2.523 CAL K38 17
K38 CAM C17 C 0 1 N N N N N N 15.998 10.923 12.923 2.035 -0.414 -1.976 CAM K38 18
K38 CAN C18 C 0 1 N N N N N N 17.107 11.121 12.813 2.990 0.111 -1.540 CAN K38 19
K38 CAO C19 C 0 1 Y N N N N N 18.488 11.273 12.747 4.155 0.752 -1.008 CAO K38 20
K38 CAQ C20 C 0 1 Y N N N N N 20.541 11.026 12.916 5.899 1.204 0.275 CAQ K38 21
K38 CAS C21 C 0 1 Y N N N N N 22.730 11.406 12.687 7.763 2.290 1.068 CAS K38 22
K38 CAU C22 C 0 1 Y N N N N N 21.317 12.962 11.808 6.753 3.187 -0.803 CAU K38 23
K38 CAV C23 C 0 1 Y N N N N N 20.295 12.176 12.263 5.794 2.158 -0.753 CAV K38 24
K38 N3 N2 N 0 1 Y N N N N N 19.068 6.248 8.569 -6.709 0.542 1.673 N3 K38 25
K38 N6 N3 N 0 1 N N N N N N 17.949 2.915 6.700 -8.139 4.108 0.242 N6 K38 26
K38 N7 N4 N 0 1 Y N N N N N 16.142 5.244 7.316 -5.805 2.547 -1.010 N7 K38 27
K38 N9 N5 N 0 1 Y N N N N N 16.830 6.981 8.303 -5.078 0.650 -0.211 N9 K38 28
K38 NAK N6 N 0 1 N N N N N N 14.184 9.564 12.084 -0.219 -1.093 -1.503 NAK K38 29
K38 NAP N7 N 0 1 Y N N N N N 19.415 10.490 13.215 4.858 0.328 0.093 NAP K38 30
K38 NAR N8 N 0 1 Y N N N N N 21.775 10.662 13.114 6.891 1.308 1.153 NAR K38 31
K38 NAT N9 N 0 1 Y N N N N N 22.534 12.557 12.022 7.705 3.211 0.123 NAT K38 32
K38 NAW N10 N 0 1 Y N N N N N 19.030 12.273 12.194 4.718 1.830 -1.501 NAW K38 33
K38 NAX N11 N 0 1 N N N N N N 21.100 14.059 11.174 6.700 4.157 -1.789 NAX K38 34
K38 "O2'" O1 O 0 1 N N N N N N 18.780 9.651 16.159 3.739 0.072 3.047 "O2'" K38 35
K38 "O3'" O2 O 0 1 N N N N N N 19.472 7.178 15.608 3.272 -2.468 3.366 "O3'" K38 36
K38 "O4'" O3 O 0 1 N N N N N N 18.719 8.511 12.959 4.115 -1.947 0.101 "O4'" K38 37
K38 "O5'" O4 O 0 1 N N N N N N 16.182 7.422 13.063 2.785 -4.365 -0.820 "O5'" K38 38
K38 OBH O5 O 0 1 N N N N N N 15.740 8.335 9.690 -2.990 -0.405 -0.693 OBH K38 39
K38 OBI O6 O 0 1 N N N N N N 15.451 11.343 8.192 -3.727 -3.864 -0.872 OBI K38 40
K38 OBJ O7 O 0 1 N N N N N N 17.809 10.207 8.052 -5.692 -2.558 0.086 OBJ K38 41
K38 H1 H1 H 0 1 N N N N N N 20.896 5.390 8.632 -8.174 0.740 3.117 H1 K38 42
K38 H2 H2 H 0 1 N N N N N N 20.292 8.861 14.185 5.421 -1.126 1.515 H2 K38 43
K38 H3 H3 H 0 1 N N N N N N 17.327 9.483 14.673 2.587 0.039 1.312 H3 K38 44
K38 H4 H4 H 0 1 N N N N N N 17.404 7.166 15.342 1.708 -2.000 2.081 H4 K38 45
K38 H5 H5 H 0 1 N N N N N N 19.451 6.666 13.367 4.039 -3.602 1.356 H5 K38 46
K38 H6 H6 H 0 1 N N N N N N 17.230 5.696 13.286 1.609 -4.063 0.852 H6 K38 47
K38 H7 H7 H 0 1 N N N N N N 17.542 6.626 11.781 1.640 -2.720 -0.316 H7 K38 48
K38 H8 H8 H 0 1 N N N N N N 14.805 6.829 7.710 -4.189 1.572 -1.964 H8 K38 49
K38 H9 H9 H 0 1 N N N N N N 17.776 8.389 9.542 -4.157 -0.815 0.992 H9 K38 50
K38 H10 H10 H 0 1 N N N N N N 16.616 8.930 6.928 -5.581 -1.371 -1.617 H10 K38 51
K38 H11 H11 H 0 1 N N N N N N 14.596 9.500 7.912 -3.798 -2.556 -2.486 H11 K38 52
K38 H12 H12 H 0 1 N N N N N N 16.305 10.150 10.363 -2.113 -2.175 -0.005 H12 K38 53
K38 H13 H13 H 0 1 N N N N N N 13.855 10.891 10.501 -1.202 -2.770 -2.299 H13 K38 54
K38 H14 H14 H 0 1 N N N N N N 13.384 9.186 10.189 -1.798 -1.199 -2.885 H14 K38 55
K38 H15 H15 H 0 1 N N N N N N 13.994 11.494 12.920 0.488 -0.522 -3.397 H15 K38 56
K38 H16 H16 H 0 1 N N N N N N 14.428 10.197 14.084 1.084 -2.094 -2.812 H16 K38 57
K38 H17 H17 H 0 1 N N N N N N 23.746 11.090 12.872 8.557 2.345 1.798 H17 K38 58
K38 H18 H18 H 0 1 N N N N N N 18.754 2.325 6.634 -7.744 4.520 -0.542 H18 K38 59
K38 H19 H19 H 0 1 N N N N N N 17.230 2.442 7.209 -8.881 4.539 0.694 H19 K38 60
K38 H20 H20 H 0 1 N N N N N N 13.257 9.289 12.339 -0.421 -0.161 -1.172 H20 K38 61
K38 H22 H22 H 0 1 N N N N N N 21.973 14.474 10.917 7.362 4.865 -1.809 H22 K38 62
K38 H23 H23 H 0 1 N N N N N N 20.567 13.868 10.350 6.000 4.129 -2.460 H23 K38 63
K38 H24 H24 H 0 1 N N N N N N 18.124 9.542 16.838 3.010 0.267 3.652 H24 K38 64
K38 H25 H25 H 0 1 N N N N N N 19.390 7.333 16.542 2.968 -3.358 3.589 H25 K38 65
K38 H26 H26 H 0 1 N N N N N N 15.462 6.973 12.636 2.119 -4.816 -1.357 H26 K38 66
K38 H27 H27 H 0 1 N N N N N N 14.628 11.707 8.495 -4.512 -4.386 -1.087 H27 K38 67
K38 H28 H28 H 0 1 N N N N N N 18.597 9.767 7.755 -6.080 -3.344 -0.323 H28 K38 68
#
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
K38 N6 C6 SING N N 1
K38 C6 C5 DOUB Y N 2
K38 C6 N1 SING Y N 3
K38 N7 C5 SING Y N 4
K38 N7 C8 DOUB Y N 5
K38 C5 C4 SING Y N 6
K38 N1 C2 DOUB Y N 7
K38 C8 N9 SING Y N 8
K38 CAG OBJ SING N N 9
K38 CAG CAH SING N N 10
K38 CAG CAF SING N N 11
K38 OBI CAH SING N N 12
K38 C4 N9 SING Y N 13
K38 C4 N3 DOUB Y N 14
K38 N9 CAF SING N N 15
K38 C2 N3 SING Y N 16
K38 CAH CAI SING N N 17
K38 CAF OBH SING N N 18
K38 OBH CAI SING N N 19
K38 CAI CAJ SING N N 20
K38 CAJ NAK SING N N 21
K38 NAX CAU SING N N 22
K38 CAU NAT DOUB Y N 23
K38 CAU CAV SING Y N 24
K38 NAT CAS SING Y N 25
K38 NAK CAL SING N N 26
K38 NAW CAV SING Y N 27
K38 NAW CAO DOUB Y N 28
K38 CAV CAQ DOUB Y N 29
K38 CAS NAR DOUB Y N 30
K38 CAO CAN SING N N 31
K38 CAO NAP SING Y N 32
K38 CAN CAM TRIP N N 33
K38 "C5'" "O5'" SING N N 34
K38 "C5'" "C4'" SING N N 35
K38 CAQ NAR SING Y N 36
K38 CAQ NAP SING Y N 37
K38 CAM CAL SING N N 38
K38 "O4'" "C4'" SING N N 39
K38 "O4'" "C1'" SING N N 40
K38 NAP "C1'" SING N N 41
K38 "C4'" "C3'" SING N N 42
K38 "C1'" "C2'" SING N N 43
K38 "C2'" "C3'" SING N N 44
K38 "C2'" "O2'" SING N N 45
K38 "C3'" "O3'" SING N N 46
K38 C2 H1 SING N N 47
K38 "C1'" H2 SING N N 48
K38 "C2'" H3 SING N N 49
K38 "C3'" H4 SING N N 50
K38 "C4'" H5 SING N N 51
K38 "C5'" H6 SING N N 52
K38 "C5'" H7 SING N N 53
K38 C8 H8 SING N N 54
K38 CAF H9 SING N N 55
K38 CAG H10 SING N N 56
K38 CAH H11 SING N N 57
K38 CAI H12 SING N N 58
K38 CAJ H13 SING N N 59
K38 CAJ H14 SING N N 60
K38 CAL H15 SING N N 61
K38 CAL H16 SING N N 62
K38 CAS H17 SING N N 63
K38 N6 H18 SING N N 64
K38 N6 H19 SING N N 65
K38 NAK H20 SING N N 66
K38 NAX H22 SING N N 67
K38 NAX H23 SING N N 68
K38 "O2'" H24 SING N N 69
K38 "O3'" H25 SING N N 70
K38 "O5'" H26 SING N N 71
K38 OBI H27 SING N N 72
K38 OBJ H28 SING N N 73
#
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
K38 InChI InChI 1.03 InChI=1S/C23H27N11O7/c24-18-12-20(29-6-27-18)33(8-31-12)22-16(38)14(36)9(40-22)4-26-3-1-2-11-32-13-19(25)28-7-30-21(13)34(11)23-17(39)15(37)10(5-35)41-23/h6-10,14-17,22-23,26,35-39H,3-5H2,(H2,24,27,29)(H2,25,28,30)/t9-,10-,14-,15-,16-,17-,22-,23-/m1/s1
K38 InChIKey InChI 1.03 CGSYXPCXDPYUKS-MKWZPUSRSA-N
K38 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CNCC#Cc4nc5c(N)ncnc5n4[C@@H]6O[C@H](CO)[C@@H](O)[C@H]6O)[C@@H](O)[C@H]3O"
K38 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CNCC#Cc4nc5c(N)ncnc5n4[CH]6O[CH](CO)[CH](O)[CH]6O)[CH](O)[CH]3O"
K38 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNCC#Cc4nc5c(ncnc5n4[C@H]6[C@@H]([C@@H]([C@H](O6)CO)O)O)N)O)O)N"
K38 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNCC#Cc4nc5c(ncnc5n4C6C(C(C(O6)CO)O)O)N)O)O)N"
#
_pdbx_chem_comp_identifier.comp_id K38
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier
(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynylamino]methyl]oxolane-3,4-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
K38 'Create component' 2019-04-16 RCSB
K38 'Initial release' 2020-02-19 RCSB
#
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
K38 N1 N 20.100 -8.358 1
K38 C2 C 18.608 -8.204 2
K38 C4 C 18.876 -5.620 3
K38 C5 C 20.368 -5.774 4
K38 C6 C 20.980 -7.143 5
K38 "C1'" C 7.483 3.304 6
K38 "C2'" C 8.911 3.765 7
K38 "C3'" C 8.913 5.265 8
K38 "C4'" C 7.487 5.731 9
K38 "C5'" C 7.027 7.159 10
K38 C8 C 19.858 -3.414 11
K38 CAF C 17.196 -3.551 12
K38 CAG C 15.897 -4.301 13
K38 CAH C 14.783 -3.297 14
K38 CAI C 15.393 -1.927 15
K38 CAJ C 14.643 -0.628 16
K38 CAL C 12.393 0.671 17
K38 CAM C 10.893 0.671 18
K38 CAN C 9.393 0.671 19
K38 CAO C 7.893 0.671 20
K38 CAQ C 5.598 1.421 21
K38 CAS C 3.000 1.421 22
K38 CAU C 4.299 -0.829 23
K38 CAV C 5.598 -0.079 24
K38 N3 N 17.996 -6.835 25
K38 N6 N 22.472 -7.297 26
K38 N7 N 20.968 -4.409 27
K38 N9 N 18.567 -4.161 28
K38 NAK N 13.143 -0.628 29
K38 NAP N 7.018 1.878 30
K38 NAR N 4.299 2.171 31
K38 NAT N 3.000 -0.079 32
K38 NAW N 7.018 -0.536 33
K38 NAX N 4.299 -2.329 34
K38 "O2'" O 10.123 2.881 35
K38 "O3'" O 10.129 6.145 36
K38 "O4'" O 6.604 4.519 37
K38 "O5'" O 5.560 7.473 38
K38 OBH O 16.885 -2.083 39
K38 OBI O 13.316 -3.609 40
K38 OBJ O 15.741 -5.792 41
#
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
K38 N6 C6 SINGLE NONE 1
K38 C6 C5 SINGLE NONE 2
K38 C6 N1 DOUBLE NONE 3
K38 N7 C5 SINGLE NONE 4
K38 N7 C8 DOUBLE NONE 5
K38 C5 C4 DOUBLE NONE 6
K38 N1 C2 SINGLE NONE 7
K38 C8 N9 SINGLE NONE 8
K38 CAG OBJ SINGLE BEGINDASH 9
K38 CAG CAH SINGLE NONE 10
K38 CAG CAF SINGLE NONE 11
K38 CAH OBI SINGLE BEGINDASH 12
K38 C4 N9 SINGLE NONE 13
K38 C4 N3 SINGLE NONE 14
K38 CAF N9 SINGLE BEGINWEDGE 15
K38 C2 N3 DOUBLE NONE 16
K38 CAH CAI SINGLE NONE 17
K38 CAF OBH SINGLE NONE 18
K38 OBH CAI SINGLE NONE 19
K38 CAI CAJ SINGLE BEGINWEDGE 20
K38 CAJ NAK SINGLE NONE 21
K38 NAX CAU SINGLE NONE 22
K38 CAU NAT SINGLE NONE 23
K38 CAU CAV DOUBLE NONE 24
K38 NAT CAS DOUBLE NONE 25
K38 NAK CAL SINGLE NONE 26
K38 NAW CAV SINGLE NONE 27
K38 NAW CAO DOUBLE NONE 28
K38 CAV CAQ SINGLE NONE 29
K38 CAS NAR SINGLE NONE 30
K38 CAO CAN SINGLE NONE 31
K38 CAO NAP SINGLE NONE 32
K38 CAN CAM TRIPLE NONE 33
K38 "C5'" "O5'" SINGLE NONE 34
K38 "C4'" "C5'" SINGLE BEGINDASH 35
K38 CAQ NAR DOUBLE NONE 36
K38 CAQ NAP SINGLE NONE 37
K38 CAM CAL SINGLE NONE 38
K38 "O4'" "C4'" SINGLE NONE 39
K38 "O4'" "C1'" SINGLE NONE 40
K38 "C1'" NAP SINGLE BEGINDASH 41
K38 "C4'" "C3'" SINGLE NONE 42
K38 "C1'" "C2'" SINGLE NONE 43
K38 "C2'" "C3'" SINGLE NONE 44
K38 "C2'" "O2'" SINGLE BEGINWEDGE 45
K38 "C3'" "O3'" SINGLE BEGINWEDGE 46
#
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
K38 MurckoScaffold S1 scaffold 'C(#Cc1nc2cncnc2n1[C@H]1CCCO1)CNC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C22H23N9O2/c1(3-18-29-17-11-25-13-27-22(17)31(18)20-4-2-8-32-20)7-23-9-15-5-6-19(33-15)30-14-28-16-10-24-12-26-21(16)30/h10-15,19-20,23H,2,4-9H2/t15-,19+,20+/m0/s1 AQDJRWGHEKTEKO-CWFSZBLJSA-N
K38 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
K38 imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
K38 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
K38 pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
K38 ribose F5 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
K38 Z1362754425 F6 fragment Cc1nccn1CC(C)O InChI=1S/C7H12N2O/c1-6(10)5-9-4-3-8-7(9)2/h3-4,6,10H,5H2,1-2H3 VUFBCWUJICCKDU-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
K38 N1 S1 1
K38 C2 S1 1
K38 C4 S1 1
K38 C5 S1 1
K38 C6 S1 1
K38 "C1'" S1 1
K38 "C2'" S1 1
K38 "C3'" S1 1
K38 "C4'" S1 1
K38 C8 S1 1
K38 CAF S1 1
K38 CAG S1 1
K38 CAH S1 1
K38 CAI S1 1
K38 CAJ S1 1
K38 CAL S1 1
K38 CAM S1 1
K38 CAN S1 1
K38 CAO S1 1
K38 CAQ S1 1
K38 CAS S1 1
K38 CAU S1 1
K38 CAV S1 1
K38 N3 S1 1
K38 N7 S1 1
K38 N9 S1 1
K38 NAK S1 1
K38 NAP S1 1
K38 NAR S1 1
K38 NAT S1 1
K38 NAW S1 1
K38 "O4'" S1 1
K38 OBH S1 1
K38 N1 F1 1
K38 C6 F1 1
K38 C5 F1 1
K38 C4 F1 1
K38 N3 F1 1
K38 C2 F1 1
K38 N9 F1 1
K38 C8 F1 1
K38 N7 F1 1
K38 N6 F1 1
K38 NAT F1 2
K38 CAU F1 2
K38 CAV F1 2
K38 CAQ F1 2
K38 NAR F1 2
K38 CAS F1 2
K38 NAP F1 2
K38 CAO F1 2
K38 NAW F1 2
K38 NAX F1 2
K38 C4 F2 1
K38 C5 F2 1
K38 N7 F2 1
K38 C8 F2 1
K38 N9 F2 1
K38 CAQ F2 2
K38 CAV F2 2
K38 NAW F2 2
K38 CAO F2 2
K38 NAP F2 2
K38 N7 F3 1
K38 C8 F3 1
K38 N9 F3 1
K38 C4 F3 1
K38 C5 F3 1
K38 C6 F3 1
K38 N1 F3 1
K38 C2 F3 1
K38 N3 F3 1
K38 NAW F3 2
K38 CAO F3 2
K38 NAP F3 2
K38 CAQ F3 2
K38 CAV F3 2
K38 CAU F3 2
K38 NAT F3 2
K38 CAS F3 2
K38 NAR F3 2
K38 C5 F4 1
K38 C6 F4 1
K38 N1 F4 1
K38 C2 F4 1
K38 N3 F4 1
K38 C4 F4 1
K38 CAV F4 2
K38 CAU F4 2
K38 NAT F4 2
K38 CAS F4 2
K38 NAR F4 2
K38 CAQ F4 2
K38 "C2'" F5 1
K38 "C3'" F5 1
K38 "C4'" F5 1
K38 "O4'" F5 1
K38 "C1'" F5 1
K38 "C5'" F5 1
K38 "O5'" F5 1
K38 "O3'" F5 1
K38 "O2'" F5 1
K38 "C3'" F6 1
K38 "C2'" F6 1
K38 "O2'" F6 1
K38 "C1'" F6 1
K38 NAP F6 1
K38 CAQ F6 1
K38 CAV F6 1
K38 NAW F6 1
K38 CAO F6 1
K38 CAN F6 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K38
_pdbe_chem_comp_rdkit_properties.exactmw 569.209
_pdbe_chem_comp_rdkit_properties.amw 569.539
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 18
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 10
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 13
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 41
_pdbe_chem_comp_rdkit_properties.NumAtoms 68
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 18
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.478
_pdbe_chem_comp_rdkit_properties.NumRings 6
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 4
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 6
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 8
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 268.826
_pdbe_chem_comp_rdkit_properties.tpsa 270.880
_pdbe_chem_comp_rdkit_properties.CrippenClogP -5.670
_pdbe_chem_comp_rdkit_properties.CrippenMR 131.826
_pdbe_chem_comp_rdkit_properties.chi0v 19.277
_pdbe_chem_comp_rdkit_properties.chi1v 10.506
_pdbe_chem_comp_rdkit_properties.chi2v 5.139
_pdbe_chem_comp_rdkit_properties.chi3v 5.139
_pdbe_chem_comp_rdkit_properties.chi4v 3.389
_pdbe_chem_comp_rdkit_properties.chi0n 46.277
_pdbe_chem_comp_rdkit_properties.chi1n 23.284
_pdbe_chem_comp_rdkit_properties.chi2n 5.139
_pdbe_chem_comp_rdkit_properties.chi3n 5.139
_pdbe_chem_comp_rdkit_properties.chi4n 3.389
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -4.060
_pdbe_chem_comp_rdkit_properties.kappa1 10.039
_pdbe_chem_comp_rdkit_properties.kappa2 10.732
_pdbe_chem_comp_rdkit_properties.kappa3 4.593
_pdbe_chem_comp_rdkit_properties.Phi 2.628
#
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
K38 UniChem ChEMBL CHEMBL5080064
K38 UniChem PDBe K38
K38 UniChem SureChEMBL SCHEMBL10004509
K38 UniChem 'PubChem TPHARMA' 136957743
K38 UniChem PubChem 57411420
#
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
K38 N1 7.867 -0.390 -0.433 ETKDGv3 1
K38 C2 6.456 -0.211 -0.712 ETKDGv3 2
K38 C4 6.197 0.584 1.493 ETKDGv3 3
K38 C5 7.463 0.420 1.769 ETKDGv3 4
K38 C6 8.369 -0.104 0.740 ETKDGv3 5
K38 "C1'" -3.777 -0.634 -0.388 ETKDGv3 6
K38 "C2'" -3.382 0.832 -0.449 ETKDGv3 7
K38 "C3'" -4.011 1.391 0.806 ETKDGv3 8
K38 "C4'" -5.186 0.433 1.061 ETKDGv3 9
K38 "C5'" -6.532 1.064 0.682 ETKDGv3 10
K38 C8 6.528 0.872 3.653 ETKDGv3 11
K38 CAF 4.058 0.704 2.931 ETKDGv3 12
K38 CAG 3.206 1.660 2.116 ETKDGv3 13
K38 CAH 1.922 0.885 1.951 ETKDGv3 14
K38 CAI 2.387 -0.577 2.064 ETKDGv3 15
K38 CAJ 2.381 -1.289 0.703 ETKDGv3 16
K38 CAL 1.006 -1.962 -1.162 ETKDGv3 17
K38 CAM -0.343 -1.855 -1.721 ETKDGv3 18
K38 CAN -1.463 -1.738 -2.147 ETKDGv3 19
K38 CAO -2.810 -1.562 -2.614 ETKDGv3 20
K38 CAQ -4.974 -1.046 -2.639 ETKDGv3 21
K38 CAS -7.052 -0.416 -3.531 ETKDGv3 22
K38 CAU -5.295 -1.154 -5.000 ETKDGv3 23
K38 CAV -4.504 -1.338 -3.944 ETKDGv3 24
K38 N3 5.651 0.243 0.212 ETKDGv3 25
K38 N6 9.756 -0.307 1.004 ETKDGv3 26
K38 N7 7.701 0.596 3.161 ETKDGv3 27
K38 N9 5.482 0.913 2.672 ETKDGv3 28
K38 NAK 1.012 -1.380 0.182 ETKDGv3 29
K38 NAP -3.899 -1.204 -1.732 ETKDGv3 30
K38 NAR -6.161 -0.579 -2.403 ETKDGv3 31
K38 NAT -6.641 -0.687 -4.749 ETKDGv3 32
K38 NAW -3.120 -1.653 -3.881 ETKDGv3 33
K38 NAX -4.838 -1.375 -6.334 ETKDGv3 34
K38 "O2'" -1.985 0.980 -0.461 ETKDGv3 35
K38 "O3'" -3.112 1.398 1.893 ETKDGv3 36
K38 "O4'" -5.003 -0.745 0.301 ETKDGv3 37
K38 "O5'" -6.818 2.134 1.540 ETKDGv3 38
K38 OBH 3.696 -0.615 2.596 ETKDGv3 39
K38 OBI 1.024 1.190 2.989 ETKDGv3 40
K38 OBJ 3.019 2.873 2.797 ETKDGv3 41
K38 H1 6.065 -0.469 -1.686 ETKDGv3 42
K38 H2 -3.013 -1.211 0.181 ETKDGv3 43
K38 H3 -3.837 1.316 -1.347 ETKDGv3 44
K38 H4 -4.345 2.437 0.627 ETKDGv3 45
K38 H5 -5.230 0.154 2.138 ETKDGv3 46
K38 H6 -6.500 1.419 -0.373 ETKDGv3 47
K38 H7 -7.332 0.295 0.772 ETKDGv3 48
K38 H8 6.361 1.029 4.710 ETKDGv3 49
K38 H9 3.855 0.859 4.016 ETKDGv3 50
K38 H10 3.665 1.840 1.116 ETKDGv3 51
K38 H11 1.460 1.128 0.965 ETKDGv3 52
K38 H12 1.719 -1.141 2.754 ETKDGv3 53
K38 H13 2.810 -2.309 0.822 ETKDGv3 54
K38 H14 3.024 -0.718 -0.003 ETKDGv3 55
K38 H15 1.698 -1.407 -1.832 ETKDGv3 56
K38 H16 1.304 -3.032 -1.128 ETKDGv3 57
K38 H17 -8.060 -0.061 -3.371 ETKDGv3 58
K38 H18 10.386 -0.685 0.262 ETKDGv3 59
K38 H19 10.159 -0.079 1.940 ETKDGv3 60
K38 H20 0.467 -2.017 0.812 ETKDGv3 61
K38 H22 -5.480 -1.209 -7.140 ETKDGv3 62
K38 H23 -3.865 -1.706 -6.525 ETKDGv3 63
K38 H24 -1.807 1.938 -0.653 ETKDGv3 64
K38 H25 -2.813 0.465 2.056 ETKDGv3 65
K38 H26 -7.689 2.503 1.237 ETKDGv3 66
K38 H27 0.144 0.818 2.718 ETKDGv3 67
K38 H28 2.580 3.490 2.155 ETKDGv3 68
#