data_KH3
#
_chem_comp.id KH3
_chem_comp.name "5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C22 H38 N8 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-08-01
_chem_comp.pdbx_modified_date 2013-03-22
_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 494.588
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code KH3
_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 3VV0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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.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
KH3 O O O 0 1 N N N -38.722 6.128 -22.689 0.421 -4.206 -1.749 O KH3 1
KH3 C C C 0 1 N N N -38.245 5.480 -21.726 -0.622 -3.782 -1.310 C KH3 2
KH3 CA CA C 0 1 N N S -38.149 3.980 -21.834 -0.613 -2.731 -0.230 CA KH3 3
KH3 N N N 0 1 N N N -38.466 3.559 -23.190 0.692 -2.733 0.444 N KH3 4
KH3 CB CB C 0 1 N N N -36.734 3.532 -21.479 -0.863 -1.357 -0.853 CB KH3 5
KH3 CG CG C 0 1 N N N -36.690 2.063 -21.086 -0.952 -0.303 0.253 CG KH3 6
KH3 ND ND N 0 1 N N N -37.450 1.933 -19.840 -1.333 0.989 -0.331 ND KH3 7
KH3 CE CE C 0 1 N N N -36.481 1.969 -18.748 -2.690 0.935 -0.891 CE KH3 8
KH3 C11 C11 C 0 1 N N N -36.150 0.556 -18.300 -3.710 0.868 0.248 C11 KH3 9
KH3 N12 N12 N 0 1 N N N -34.973 0.449 -17.428 -5.059 0.712 -0.311 N12 KH3 10
KH3 C13 C13 C 0 1 N N N -35.003 -0.957 -16.965 -6.066 0.644 0.756 C13 KH3 11
KH3 C14 C14 C 0 1 N N N -33.726 -1.393 -16.263 -7.456 0.482 0.136 C14 KH3 12
KH3 C15 C15 C 0 1 N N N -33.944 -2.678 -15.470 -8.505 0.411 1.248 C15 KH3 13
KH3 C16 C16 C 0 1 N N N -34.176 -3.876 -16.379 -9.894 0.249 0.628 C16 KH3 14
KH3 C17 C17 C 0 1 N N N -34.209 -5.170 -15.571 -10.943 0.178 1.740 C17 KH3 15
KH3 C18 C18 C 0 1 N N N -32.819 -5.635 -15.198 -12.333 0.016 1.120 C18 KH3 16
KH3 "C5'" "C5'" C 0 1 N N N -38.230 0.679 -19.798 -0.361 1.415 -1.347 "C5'" KH3 17
KH3 "C4'" "C4'" C 0 1 N N R -39.673 1.051 -20.081 0.889 1.966 -0.658 "C4'" KH3 18
KH3 "O4'" "O4'" O 0 1 N N N -39.782 1.275 -21.489 1.649 0.892 -0.062 "O4'" KH3 19
KH3 "C1'" "C1'" C 0 1 N N R -40.844 0.493 -22.037 2.984 1.417 0.104 "C1'" KH3 20
KH3 "C2'" "C2'" C 0 1 N N R -41.694 0.093 -20.854 3.253 2.226 -1.185 "C2'" KH3 21
KH3 "O2'" "O2'" O 0 1 N N N -42.600 1.166 -20.584 4.003 3.405 -0.889 "O2'" KH3 22
KH3 "C3'" "C3'" C 0 1 N N S -40.686 -0.030 -19.739 1.843 2.595 -1.698 "C3'" KH3 23
KH3 "O3'" "O3'" O 0 1 N N N -41.311 0.207 -18.474 1.679 4.014 -1.734 "O3'" KH3 24
KH3 N9 N9 N 0 1 Y N N -40.279 -0.709 -22.691 3.950 0.323 0.230 N9 KH3 25
KH3 C8 C8 C 0 1 Y N N -39.043 -1.217 -22.525 3.809 -0.939 -0.264 C8 KH3 26
KH3 N7 N7 N 0 1 Y N N -38.860 -2.311 -23.302 4.857 -1.652 0.031 N7 KH3 27
KH3 C5 C5 C 0 1 Y N N -39.997 -2.515 -23.987 5.735 -0.895 0.731 C5 KH3 28
KH3 C6 C6 C 0 1 Y N N -40.481 -3.500 -24.979 7.002 -1.118 1.295 C6 KH3 29
KH3 N6 N6 N 0 1 N N N -39.686 -4.514 -25.404 7.613 -2.356 1.197 N6 KH3 30
KH3 C4 C4 C 0 1 Y N N -40.926 -1.449 -23.588 5.166 0.384 0.863 C4 KH3 31
KH3 N3 N3 N 0 1 Y N N -42.167 -1.416 -24.126 5.838 1.325 1.517 N3 KH3 32
KH3 C2 C2 C 0 1 Y N N -42.542 -2.340 -25.024 7.020 1.068 2.037 C2 KH3 33
KH3 N1 N1 N 0 1 Y N N -41.742 -3.340 -25.440 7.601 -0.113 1.925 N1 KH3 34
KH3 OXT OXT O 0 1 N N N -37.853 6.022 -20.666 -1.788 -4.243 -1.789 OXT KH3 35
KH3 H1 H1 H 0 1 N N N -38.855 3.522 -21.126 -1.397 -2.949 0.495 H1 KH3 36
KH3 H2 H2 H 0 1 N N N -38.400 2.563 -23.254 0.883 -3.632 0.861 H2 KH3 37
KH3 H3 H3 H 0 1 N N N -39.396 3.847 -23.420 1.428 -2.466 -0.192 H3 KH3 38
KH3 H5 H5 H 0 1 N N N -36.082 3.687 -22.351 -0.043 -1.108 -1.526 H5 KH3 39
KH3 H6 H6 H 0 1 N N N -36.369 4.137 -20.636 -1.798 -1.376 -1.413 H6 KH3 40
KH3 H7 H7 H 0 1 N N N -37.147 1.447 -21.874 -1.702 -0.607 0.984 H7 KH3 41
KH3 H8 H8 H 0 1 N N N -35.649 1.744 -20.929 0.016 -0.209 0.744 H8 KH3 42
KH3 H10 H10 H 0 1 N N N -35.562 2.466 -19.092 -2.872 1.827 -1.490 H10 KH3 43
KH3 H11 H11 H 0 1 N N N -36.906 2.529 -17.902 -2.789 0.050 -1.519 H11 KH3 44
KH3 H12 H12 H 0 1 N N N -37.018 0.157 -17.755 -3.481 0.018 0.890 H12 KH3 45
KH3 H13 H13 H 0 1 N N N -35.969 -0.054 -19.197 -3.662 1.787 0.832 H13 KH3 46
KH3 H14 H14 H 0 1 N N N -34.134 0.638 -17.938 -5.270 1.455 -0.960 H14 KH3 47
KH3 H16 H16 H 0 1 N N N -35.843 -1.075 -16.264 -5.855 -0.208 1.402 H16 KH3 48
KH3 H17 H17 H 0 1 N N N -35.160 -1.608 -17.838 -6.035 1.562 1.344 H17 KH3 49
KH3 H18 H18 H 0 1 N N N -32.943 -1.565 -17.016 -7.667 1.334 -0.509 H18 KH3 50
KH3 H19 H19 H 0 1 N N N -33.405 -0.597 -15.575 -7.486 -0.436 -0.451 H19 KH3 51
KH3 H20 H20 H 0 1 N N N -34.822 -2.550 -14.820 -8.293 -0.441 1.893 H20 KH3 52
KH3 H21 H21 H 0 1 N N N -33.055 -2.869 -14.851 -8.474 1.329 1.836 H21 KH3 53
KH3 H22 H22 H 0 1 N N N -33.362 -3.932 -17.117 -10.106 1.101 -0.018 H22 KH3 54
KH3 H23 H23 H 0 1 N N N -35.136 -3.752 -16.901 -9.925 -0.669 0.040 H23 KH3 55
KH3 H24 H24 H 0 1 N N N -34.787 -5.000 -14.650 -10.732 -0.674 2.385 H24 KH3 56
KH3 H25 H25 H 0 1 N N N -34.697 -5.952 -16.171 -10.912 1.095 2.327 H25 KH3 57
KH3 H26 H26 H 0 1 N N N -32.887 -6.567 -14.618 -13.080 -0.035 1.911 H26 KH3 58
KH3 H27 H27 H 0 1 N N N -32.235 -5.814 -16.113 -12.544 0.868 0.474 H27 KH3 59
KH3 H28 H28 H 0 1 N N N -32.324 -4.862 -14.592 -12.363 -0.902 0.532 H28 KH3 60
KH3 H29 H29 H 0 1 N N N -38.147 0.214 -18.805 -0.088 0.562 -1.968 H29 KH3 61
KH3 H30 H30 H 0 1 N N N -37.863 -0.021 -20.563 -0.804 2.191 -1.971 H30 KH3 62
KH3 H31 H31 H 0 1 N N N -39.924 1.968 -19.527 0.612 2.701 0.097 H31 KH3 63
KH3 H32 H32 H 0 1 N N N -41.442 1.076 -22.752 3.030 2.068 0.976 H32 KH3 64
KH3 H33 H33 H 0 1 N N N -42.210 -0.861 -21.036 3.780 1.613 -1.917 H33 KH3 65
KH3 H34 H34 H 0 1 N N N -43.148 0.939 -19.842 4.200 3.951 -1.663 H34 KH3 66
KH3 H35 H35 H 0 1 N N N -40.206 -1.019 -19.769 1.670 2.164 -2.684 H35 KH3 67
KH3 H36 H36 H 0 1 N N N -40.666 0.127 -17.781 2.254 4.460 -2.370 H36 KH3 68
KH3 H37 H37 H 0 1 N N N -38.297 -0.807 -21.861 2.953 -1.296 -0.818 H37 KH3 69
KH3 H38 H38 H 0 1 N N N -40.182 -5.070 -26.071 7.166 -3.082 0.734 H38 KH3 70
KH3 H39 H39 H 0 1 N N N -38.864 -4.137 -25.831 8.488 -2.498 1.591 H39 KH3 71
KH3 H40 H40 H 0 1 N N N -43.539 -2.278 -25.435 7.540 1.855 2.562 H40 KH3 72
KH3 H41 H41 H 0 1 N N N -37.978 6.962 -20.725 -1.743 -4.913 -2.484 H41 KH3 73
#
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
KH3 N1 C2 DOUB Y N 1
KH3 N1 C6 SING Y N 2
KH3 N6 C6 SING N N 3
KH3 C2 N3 SING Y N 4
KH3 C6 C5 DOUB Y N 5
KH3 N3 C4 DOUB Y N 6
KH3 C5 C4 SING Y N 7
KH3 C5 N7 SING Y N 8
KH3 C4 N9 SING Y N 9
KH3 N7 C8 DOUB Y N 10
KH3 N CA SING N N 11
KH3 N9 C8 SING Y N 12
KH3 N9 "C1'" SING N N 13
KH3 O C DOUB N N 14
KH3 "C1'" "O4'" SING N N 15
KH3 "C1'" "C2'" SING N N 16
KH3 CA C SING N N 17
KH3 CA CB SING N N 18
KH3 C OXT SING N N 19
KH3 "O4'" "C4'" SING N N 20
KH3 CB CG SING N N 21
KH3 CG ND SING N N 22
KH3 "C2'" "O2'" SING N N 23
KH3 "C2'" "C3'" SING N N 24
KH3 "C4'" "C5'" SING N N 25
KH3 "C4'" "C3'" SING N N 26
KH3 ND "C5'" SING N N 27
KH3 ND CE SING N N 28
KH3 "C3'" "O3'" SING N N 29
KH3 CE C11 SING N N 30
KH3 C11 N12 SING N N 31
KH3 N12 C13 SING N N 32
KH3 C13 C14 SING N N 33
KH3 C16 C17 SING N N 34
KH3 C16 C15 SING N N 35
KH3 C14 C15 SING N N 36
KH3 C17 C18 SING N N 37
KH3 CA H1 SING N N 38
KH3 N H2 SING N N 39
KH3 N H3 SING N N 40
KH3 CB H5 SING N N 41
KH3 CB H6 SING N N 42
KH3 CG H7 SING N N 43
KH3 CG H8 SING N N 44
KH3 CE H10 SING N N 45
KH3 CE H11 SING N N 46
KH3 C11 H12 SING N N 47
KH3 C11 H13 SING N N 48
KH3 N12 H14 SING N N 49
KH3 C13 H16 SING N N 50
KH3 C13 H17 SING N N 51
KH3 C14 H18 SING N N 52
KH3 C14 H19 SING N N 53
KH3 C15 H20 SING N N 54
KH3 C15 H21 SING N N 55
KH3 C16 H22 SING N N 56
KH3 C16 H23 SING N N 57
KH3 C17 H24 SING N N 58
KH3 C17 H25 SING N N 59
KH3 C18 H26 SING N N 60
KH3 C18 H27 SING N N 61
KH3 C18 H28 SING N N 62
KH3 "C5'" H29 SING N N 63
KH3 "C5'" H30 SING N N 64
KH3 "C4'" H31 SING N N 65
KH3 "C1'" H32 SING N N 66
KH3 "C2'" H33 SING N N 67
KH3 "O2'" H34 SING N N 68
KH3 "C3'" H35 SING N N 69
KH3 "O3'" H36 SING N N 70
KH3 C8 H37 SING N N 71
KH3 N6 H38 SING N N 72
KH3 N6 H39 SING N N 73
KH3 C2 H40 SING N N 74
KH3 OXT H41 SING N N 75
#
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
KH3 SMILES ACDLabs 12.01 "O=C(O)C(N)CCN(CCNCCCCCC)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O"
KH3 InChI InChI 1.03
"InChI=1S/C22H38N8O5/c1-2-3-4-5-7-25-8-10-29(9-6-14(23)22(33)34)11-15-17(31)18(32)21(35-15)30-13-28-16-19(24)26-12-27-20(16)30/h12-15,17-18,21,25,31-32H,2-11,23H2,1H3,(H,33,34)(H2,24,26,27)/t14-,15+,17+,18+,21+/m0/s1"
KH3 InChIKey InChI 1.03 XWQXPIOHEBRBJA-UQEZQTQMSA-N
KH3 SMILES_CANONICAL CACTVS 3.370 "CCCCCCNCCN(CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23"
KH3 SMILES CACTVS 3.370 "CCCCCCNCCN(CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23"
KH3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CCCCCCNCCN(CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O"
KH3 SMILES "OpenEye OEToolkits" 1.7.6 "CCCCCCNCCN(CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O"
#
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
KH3 "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[(3S)-3-amino-3-carboxypropyl][2-(hexylamino)ethyl]amino}-5'-deoxyadenosine"
KH3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-[2-(hexylamino)ethyl]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
KH3 "Create component" 2012-08-01 PDBJ
KH3 "Initial release" 2013-03-27 RCSB
#