data_I0C
# 
_chem_comp.id                                    I0C 
_chem_comp.name                                  "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-7~{H}-purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H38 N12 O9" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-07-24 
_chem_comp.pdbx_modified_date                    2024-09-16 
_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                        674.666 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     I0C 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8PWA 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              ? 
# 
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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
I0C N1   N1  N 0 1 Y N N N N N -39.119 40.050 26.835 -7.977 -4.737 1.935  N1   I0C 1  
I0C N3   N2  N 0 1 Y N N N N N -40.542 38.301 27.289 -6.672 -3.950 0.197  N3   I0C 2  
I0C C4   C1  C 0 1 Y N N N N N -41.047 38.336 26.030 -6.616 -2.735 0.733  C4   I0C 3  
I0C C5   C2  C 0 1 Y N N N N N -40.569 39.268 25.133 -7.280 -2.493 1.948  C5   I0C 4  
I0C C6   C3  C 0 1 Y N N N N N -39.574 40.149 25.575 -7.978 -3.556 2.545  C6   I0C 5  
I0C C8   C4  C 0 1 Y N N N N N -42.102 38.076 24.137 -6.331 -0.637 1.349  C8   I0C 6  
I0C N    N3  N 0 1 N N N N N N -41.683 28.699 27.621 -1.694 5.249  1.441  N    I0C 7  
I0C CA   C5  C 0 1 N N S N N N -42.979 29.263 27.870 -3.007 5.085  0.803  CA   I0C 8  
I0C C    C6  C 0 1 N N N N N N -43.987 28.209 28.333 -4.090 5.457  1.783  C    I0C 9  
I0C O    O1  O 0 1 N N N N N N -43.609 27.047 28.610 -3.887 5.371  2.970  O    I0C 10 
I0C CB   C7  C 0 1 N N N N N N -43.537 29.952 26.625 -3.187 3.627  0.374  CB   I0C 11 
I0C OXT  O2  O 0 1 N N N N N N -45.196 28.523 28.458 -5.281 5.885  1.335  OXT  I0C 12 
I0C C2   C8  C 0 1 Y N N N N N -39.612 39.136 27.673 -7.339 -4.916 0.793  C2   I0C 13 
I0C CAK  C9  C 0 1 Y N N N N N -49.667 31.377 22.581 4.901  -0.433 -3.115 CAK  I0C 14 
I0C CAM  C10 C 0 1 Y N N N N N -50.370 35.425 24.236 6.209  0.273  1.059  CAM  I0C 15 
I0C CAN  C11 C 0 1 N N N N N N -44.942 31.628 23.226 0.010  1.340  -0.981 CAN  I0C 16 
I0C CAP  C12 C 0 1 N N N N N N -45.965 31.634 24.440 1.223  0.836  -1.766 CAP  I0C 17 
I0C CAR  C13 C 0 1 N N N N N N -43.545 31.171 23.709 -1.203 1.417  -1.910 CAR  I0C 18 
I0C CAS  C14 C 0 1 N N N N N N -42.573 31.021 26.033 -2.173 3.289  -0.721 CAS  I0C 19 
I0C CAT  C15 C 0 1 N N N N N N -42.622 33.142 24.771 -3.599 1.763  -1.946 CAT  I0C 20 
I0C CBF  C16 C 0 1 Y N N N N N -48.176 32.622 23.831 3.604  0.331  -1.365 CBF  I0C 21 
I0C CBH  C17 C 0 1 Y N N N N N -49.137 33.657 23.916 4.729  0.255  -0.525 CBH  I0C 22 
I0C CBJ  C18 C 0 1 Y N N N N N -50.362 33.470 23.294 5.941  -0.191 -1.079 CBJ  I0C 23 
I0C CBM  C19 C 0 1 N N S N N N -44.047 34.642 26.000 -5.331 0.130  -2.785 CBM  I0C 24 
I0C CBO  C20 C 0 1 N N R N N N -43.781 36.169 25.379 -6.129 -0.946 -2.014 CBO  I0C 25 
I0C CBQ  C21 C 0 1 N N R N N N -42.833 34.058 26.007 -4.035 0.297  -1.962 CBQ  I0C 26 
I0C CBS  C22 C 0 1 N N R N N N -42.743 36.515 26.001 -5.220 -1.301 -0.817 CBS  I0C 27 
I0C N6   N4  N 0 1 N N N N N N -39.023 41.140 24.694 -8.650 -3.378 3.742  N6   I0C 28 
I0C N7   N5  N 0 1 Y N N N N N -41.235 39.071 23.981 -7.066 -1.194 2.268  N7   I0C 29 
I0C N9   N6  N 0 1 Y N N N N N -41.996 37.631 25.387 -6.027 -1.547 0.381  N9   I0C 30 
I0C NAV  N7  N 0 1 Y N N N N N -48.477 31.522 23.164 3.740  -0.020 -2.639 NAV  I0C 31 
I0C NAX  N8  N 0 1 Y N N N N N -50.598 32.328 22.639 5.981  -0.520 -2.366 NAX  I0C 32 
I0C NAZ  N9  N 0 1 Y N N N N N -49.184 34.872 24.484 4.962  0.521  0.782  NAZ  I0C 33 
I0C NBA  N10 N 0 1 N N N N N N -46.876 32.761 24.454 2.384  0.763  -0.876 NBA  I0C 34 
I0C NBT  N11 N 0 1 N N N N N N -43.322 31.847 25.034 -2.368 1.900  -1.157 NBT  I0C 35 
I0C NBV  N12 N 0 1 Y N N N N N -51.096 34.581 23.514 6.855  -0.168 -0.057 NBV  I0C 36 
I0C OAG  O3  O 0 1 N N N N N N -44.518 34.836 27.336 -5.030 -0.321 -4.107 OAG  I0C 37 
I0C OAI  O4  O 0 1 N N N N N N -44.920 37.034 25.718 -6.345 -2.094 -2.837 OAI  I0C 38 
I0C OBC  O5  O 0 1 N N N N N N -41.827 35.168 25.864 -4.384 -0.138 -0.630 OBC  I0C 39 
I0C H81  H1  H 0 1 N N N N N N -42.774 37.695 23.382 -6.009 0.394  1.354  H81  I0C 40 
I0C H1   H2  H 0 1 N N N N N N -41.057 29.419 27.322 -1.524 6.216  1.675  H1   I0C 41 
I0C H2   H3  H 0 1 N N N N N N -41.334 28.282 28.460 -1.610 4.660  2.255  H2   I0C 42 
I0C HA   H5  H 0 1 N N N N N N -42.894 30.019 28.664 -3.070 5.732  -0.072 HA   I0C 43 
I0C HB3  H6  H 0 1 N N N N N N -43.726 29.187 25.857 -3.026 2.974  1.232  HB3  I0C 44 
I0C HB2  H7  H 0 1 N N N N N N -44.484 30.444 26.892 -4.197 3.483  -0.009 HB2  I0C 45 
I0C H3   H8  H 0 1 N N N N N N -45.688 27.772 28.770 -5.945 6.112  2.001  H3   I0C 46 
I0C H21  H9  H 0 1 N N N N N N -39.237 39.085 28.684 -7.364 -5.892 0.331  H21  I0C 47 
I0C HAK1 H10 H 0 0 N N N N N N -49.882 30.463 22.047 4.966  -0.713 -4.156 HAK1 I0C 48 
I0C HAM1 H11 H 0 0 N N N N N N -50.689 36.402 24.569 6.665  0.400  2.030  HAM1 I0C 49 
I0C HAN2 H12 H 0 0 N N N N N N -45.303 30.937 22.450 -0.203 0.654  -0.161 HAN2 I0C 50 
I0C HAN1 H13 H 0 0 N N N N N N -44.868 32.643 22.808 0.223  2.331  -0.579 HAN1 I0C 51 
I0C HAP1 H14 H 0 0 N N N N N N -46.561 30.711 24.391 1.010  -0.154 -2.167 HAP1 I0C 52 
I0C HAP2 H15 H 0 0 N N N N N N -45.387 31.648 25.376 1.436  1.523  -2.585 HAP2 I0C 53 
I0C HAR1 H16 H 0 0 N N N N N N -43.521 30.078 23.829 -0.990 2.103  -2.730 HAR1 I0C 54 
I0C HAR2 H17 H 0 0 N N N N N N -42.772 31.478 22.989 -1.416 0.426  -2.312 HAR2 I0C 55 
I0C HAS2 H18 H 0 0 N N N N N N -41.726 30.522 25.539 -2.317 3.960  -1.569 HAS2 I0C 56 
I0C HAS1 H19 H 0 0 N N N N N N -42.198 31.668 26.840 -1.163 3.410  -0.331 HAS1 I0C 57 
I0C HAT1 H20 H 0 0 N N N N N N -43.045 33.620 23.875 -3.416 2.099  -2.967 HAT1 I0C 58 
I0C HAT2 H21 H 0 0 N N N N N N -41.548 32.962 24.618 -4.386 2.371  -1.500 HAT2 I0C 59 
I0C HBM1 H22 H 0 0 N N N N N N -44.784 34.123 25.369 -5.887 1.067  -2.817 HBM1 I0C 60 
I0C HBO1 H23 H 0 0 N N N N N N -43.659 36.085 24.289 -7.079 -0.540 -1.666 HBO1 I0C 61 
I0C HBQ1 H24 H 0 0 N N N N N N -42.641 33.486 26.927 -3.242 -0.329 -2.372 HBQ1 I0C 62 
I0C HBS1 H25 H 0 0 N N N N N N -42.908 36.711 27.071 -4.610 -2.174 -1.050 HBS1 I0C 63 
I0C H62  H26 H 0 1 N N N N N N -38.320 41.662 25.177 -9.129 -4.119 4.144  H62  I0C 64 
I0C H61  H27 H 0 1 N N N N N N -38.616 40.690 23.899 -8.643 -2.511 4.177  H61  I0C 65 
I0C HBA1 H29 H 0 0 N N N N N N -47.034 32.998 25.413 2.297  1.017  0.056  HBA1 I0C 66 
I0C HAG1 H42 H 0 0 N N N N N N -44.686 33.992 27.739 -5.811 -0.500 -4.649 HAG1 I0C 67 
I0C HAI1 H33 H 0 0 N N N N N N -44.773 37.904 25.367 -6.860 -1.914 -3.636 HAI1 I0C 68 
I0C C10  C23 C 0 1 N N N N N N ?       ?      ?      8.267  -0.549 -0.147 C10  I0C 69 
I0C O1   O6  O 0 1 N N N N N N ?       ?      ?      9.033  0.089  0.897  O1   I0C 70 
I0C C3   C24 C 0 1 N N N N N N ?       ?      ?      10.232 -0.685 1.070  C3   I0C 71 
I0C C7   C25 C 0 1 N N N N N N ?       ?      ?      9.915  -2.126 0.628  C7   I0C 72 
I0C C9   C26 C 0 1 N N N N N N ?       ?      ?      8.445  -2.060 0.146  C9   I0C 73 
I0C H7   H41 H 0 1 N N N N N N ?       ?      ?      11.031 -0.275 0.452  H7   I0C 74 
I0C O4   O7  O 0 1 N N N N N N ?       ?      ?      10.775 -2.522 -0.443 O4   I0C 75 
I0C O3   O8  O 0 1 N N N N N N ?       ?      ?      7.551  -2.489 1.175  O3   I0C 76 
I0C C1   C27 C 0 1 N N N N N N ?       ?      ?      10.651 -0.672 2.542  C1   I0C 77 
I0C O2   O9  O 0 1 N N N N N N ?       ?      ?      11.039 0.651  2.915  O2   I0C 78 
I0C H10  H31 H 0 1 N N N N N N ?       ?      ?      11.318 0.734  3.838  H10  I0C 79 
I0C H8   H32 H 0 1 N N N N N N ?       ?      ?      11.714 -2.524 -0.212 H8   I0C 80 
I0C H9   H34 H 0 1 N N N N N N ?       ?      ?      7.685  -3.404 1.456  H9   I0C 81 
I0C H11  H35 H 0 1 N N N N N N ?       ?      ?      8.669  -0.295 -1.128 H11  I0C 82 
I0C H5   H36 H 0 1 N N N N N N ?       ?      ?      10.010 -2.813 1.469  H5   I0C 83 
I0C H6   H37 H 0 1 N N N N N N ?       ?      ?      8.306  -2.651 -0.760 H6   I0C 84 
I0C H12  H38 H 0 1 N N N N N N ?       ?      ?      9.814  -0.994 3.161  H12  I0C 85 
I0C H13  H39 H 0 1 N N N N N N ?       ?      ?      11.491 -1.352 2.686  H13  I0C 86 
# 
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 
I0C N   CA   SING N N 1  
I0C CA  C    SING N N 2  
I0C CA  CB   SING N N 3  
I0C CAK NAV  DOUB Y N 4  
I0C CAK NAX  SING Y N 5  
I0C CAM NAZ  DOUB Y N 6  
I0C CAM NBV  SING Y N 7  
I0C CAN CAP  SING N N 8  
I0C CAN CAR  SING N N 9  
I0C CAP NBA  SING N N 10 
I0C CAR NBT  SING N N 11 
I0C CAS NBT  SING N N 12 
I0C CAS CB   SING N N 13 
I0C CAT CBQ  SING N N 14 
I0C CAT NBT  SING N N 15 
I0C C   O    DOUB N N 16 
I0C C   OXT  SING N N 17 
I0C NAV CBF  SING Y N 18 
I0C NAX CBJ  DOUB Y N 19 
I0C NAZ CBH  SING Y N 20 
I0C OAG CBM  SING N N 21 
I0C OAI CBO  SING N N 22 
I0C CBF CBH  DOUB Y N 23 
I0C CBF NBA  SING N N 24 
I0C CBH CBJ  SING Y N 25 
I0C CBJ NBV  SING Y N 26 
I0C CBM CBO  SING N N 27 
I0C CBM CBQ  SING N N 28 
I0C CBO CBS  SING N N 29 
I0C CBQ OBC  SING N N 30 
I0C CBS OBC  SING N N 31 
I0C CBS N9   SING N N 32 
I0C N1  C2   DOUB Y N 33 
I0C N1  C6   SING Y N 34 
I0C C2  N3   SING Y N 35 
I0C N3  C4   DOUB Y N 36 
I0C C4  C5   SING Y N 37 
I0C C4  N9   SING Y N 38 
I0C C5  C6   DOUB Y N 39 
I0C C5  N7   SING Y N 40 
I0C C6  N6   SING N N 41 
I0C N7  C8   DOUB Y N 42 
I0C C8  N9   SING Y N 43 
I0C C8  H81  SING N N 44 
I0C N   H1   SING N N 45 
I0C N   H2   SING N N 46 
I0C CA  HA   SING N N 47 
I0C CB  HB3  SING N N 48 
I0C CB  HB2  SING N N 49 
I0C OXT H3   SING N N 50 
I0C C2  H21  SING N N 51 
I0C CAK HAK1 SING N N 52 
I0C CAM HAM1 SING N N 53 
I0C CAN HAN2 SING N N 54 
I0C CAN HAN1 SING N N 55 
I0C CAP HAP1 SING N N 56 
I0C CAP HAP2 SING N N 57 
I0C CAR HAR1 SING N N 58 
I0C CAR HAR2 SING N N 59 
I0C CAS HAS2 SING N N 60 
I0C CAS HAS1 SING N N 61 
I0C CAT HAT1 SING N N 62 
I0C CAT HAT2 SING N N 63 
I0C CBM HBM1 SING N N 64 
I0C CBO HBO1 SING N N 65 
I0C CBQ HBQ1 SING N N 66 
I0C CBS HBS1 SING N N 67 
I0C N6  H62  SING N N 68 
I0C N6  H61  SING N N 69 
I0C NBA HBA1 SING N N 70 
I0C OAG HAG1 SING N N 71 
I0C OAI HAI1 SING N N 72 
I0C C10 O1   SING N N 73 
I0C O1  C3   SING N N 74 
I0C C3  C7   SING N N 75 
I0C C7  C9   SING N N 76 
I0C C9  C10  SING N N 77 
I0C NBV C10  SING N N 78 
I0C C3  H7   SING N N 79 
I0C C7  O4   SING N N 80 
I0C C9  O3   SING N N 81 
I0C C3  C1   SING N N 82 
I0C C1  O2   SING N N 83 
I0C O2  H10  SING N N 84 
I0C O4  H8   SING N N 85 
I0C O3  H9   SING N N 86 
I0C C10 H11  SING N N 87 
I0C C7  H5   SING N N 88 
I0C C9  H6   SING N N 89 
I0C C1  H12  SING N N 90 
I0C C1  H13  SING N N 91 
# 
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 
I0C SMILES           ACDLabs              14.52 "O=C(O)C(N)CCN(CC1OC(n2cnc3c(N)ncnc32)C(O)C1O)CCCNc1ncnc2c1ncn2C1OC(CO)C(O)C1O"                                                                                                                                                                                                                  
I0C InChI            InChI                1.06  "InChI=1S/C27H38N12O9/c28-12(27(45)46)2-5-37(6-13-17(41)19(43)25(47-13)38-10-35-15-21(29)31-8-33-23(15)38)4-1-3-30-22-16-24(34-9-32-22)39(11-36-16)26-20(44)18(42)14(7-40)48-26/h8-14,17-20,25-26,40-44H,1-7,28H2,(H,45,46)(H2,29,31,33)(H,30,32,34)/t12-,13+,14?,17+,18?,19+,20?,25+,26?/m0/s1" 
I0C InChIKey         InChI                1.06  BNMNWGQODJWABC-MAYUJHHQSA-N                                                                                                                                                                                                                                                                      
I0C SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCN(CCCNc1ncnc2n(cnc12)C3OC(CO)C(O)C3O)C[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)C(O)=O"                                                                                                                                                                                          
I0C SMILES           CACTVS               3.385 "N[CH](CCN(CCCNc1ncnc2n(cnc12)C3OC(CO)C(O)C3O)C[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)C(O)=O"                                                                                                                                                                                                 
I0C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CCCNc4c5c(ncn4)n(cn5)[C@H]6[C@@H]([C@@H]([C@H](O6)CO)O)O)CC[C@@H](C(=O)O)N)O)O)N"                                                                                                                                                             
I0C SMILES           "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCCNc4c5c(ncn4)n(cn5)C6C(C(C(O6)CO)O)O)CCC(C(=O)O)N)O)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 
I0C "SYSTEMATIC NAME" ACDLabs              14.52 "(2S)-2-amino-4-({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl}[3-({9-[3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-9H-purin-6-yl}amino)propyl]amino)butanoic acid (non-preferred name)"                      
I0C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[3-[[9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-6-yl]amino]propyl]amino]-2-azanyl-butanoic 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 
I0C "Create component"   2023-07-24 PDBE 
I0C "Modify coordinates" 2023-07-24 PDBE 
I0C "Initial release"    2023-11-08 RCSB 
I0C "Modify formula"     2024-09-16 RCSB 
# 
