data_L6M # _chem_comp.id L6M _chem_comp.name "5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H37 N5 O10" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-02-07 _chem_comp.pdbx_modified_date 2020-02-07 _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 627.642 _chem_comp.one_letter_code ? _chem_comp.three_letter_code L6M _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 6NWN _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.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 L6M C13 C1 C 0 1 N N N -5.079 -37.163 24.327 2.051 -3.096 0.306 C13 L6M 1 L6M C17 C2 C 0 1 N N R -9.516 -37.642 25.064 6.393 -0.885 -0.273 C17 L6M 2 L6M C21 C3 C 0 1 N N N -10.836 -38.116 23.292 8.149 0.803 -0.215 C21 L6M 3 L6M C22 C4 C 0 1 N N R -11.748 -37.984 24.621 6.875 1.250 -0.966 C22 L6M 4 L6M C24 C5 C 0 1 N N N -12.645 -35.635 24.595 6.669 3.563 -1.737 C24 L6M 5 L6M C26 C6 C 0 1 N N N -14.222 -37.606 24.276 6.294 3.078 0.531 C26 L6M 6 L6M C28 C7 C 0 1 N N N -15.173 -35.242 24.262 6.094 5.268 -0.177 C28 L6M 7 L6M C02 C8 C 0 1 N N N 1.623 -33.410 21.923 -5.748 -0.758 -0.867 C02 L6M 8 L6M C03 C9 C 0 1 N N R 1.613 -34.689 22.733 -4.606 -0.691 -1.849 C03 L6M 9 L6M C04 C10 C 0 1 N N S 0.254 -35.588 22.247 -3.693 -1.933 -1.703 C04 L6M 10 L6M C05 C11 C 0 1 N N N -0.889 -34.866 22.948 -2.656 -1.717 -0.599 C05 L6M 11 L6M C06 C12 C 0 1 N N N -1.438 -35.499 24.231 -1.865 -2.984 -0.398 C06 L6M 12 L6M C08 C13 C 0 1 N N S -2.788 -37.161 25.436 -0.120 -4.260 0.726 C08 L6M 13 L6M C09 C14 C 0 1 N N N -1.628 -37.947 26.029 -0.861 -5.172 1.669 C09 L6M 14 L6M C12 C15 C 0 1 N N N -4.084 -37.993 25.247 1.249 -3.918 1.317 C12 L6M 15 L6M C14 C16 C 0 1 N N N -6.465 -36.902 25.031 3.399 -2.759 0.889 C14 L6M 16 L6M C16 C17 C 0 1 N N N -8.943 -36.365 24.812 5.592 -1.707 0.738 C16 L6M 17 L6M C19 C18 C 0 1 N N S -9.651 -38.455 23.765 7.825 -0.634 0.251 C19 L6M 18 L6M C25 C19 C 0 1 N N N -13.801 -34.706 24.481 6.417 4.871 -1.490 C25 L6M 19 L6M C33 C20 C 0 1 N N N 0.451 -36.803 22.693 -3.007 -2.018 -3.090 C33 L6M 20 L6M C34 C21 C 0 1 N N N 2.061 -36.914 22.848 -4.117 -1.620 -4.085 C34 L6M 21 L6M C35 C22 C 0 1 N N N 2.648 -35.481 22.479 -5.134 -0.777 -3.296 C35 L6M 22 L6M C36 C23 C 0 1 Y N N 2.413 -32.190 22.446 -6.462 0.471 -0.484 C36 L6M 23 L6M C37 C24 C 0 1 Y N N 3.123 -32.260 23.644 -7.521 0.413 0.427 C37 L6M 24 L6M C38 C25 C 0 1 Y N N 3.849 -31.162 24.102 -8.185 1.569 0.781 C38 L6M 25 L6M C39 C26 C 0 1 Y N N 3.854 -29.994 23.338 -7.806 2.783 0.236 C39 L6M 26 L6M C40 C27 C 0 1 N N N 4.672 -28.735 23.777 -8.537 4.042 0.629 C40 L6M 27 L6M C41 C28 C 0 1 N N N 4.338 -28.205 25.160 -7.869 4.657 1.831 C41 L6M 28 L6M C44 C29 C 0 1 Y N N 3.155 -29.942 22.142 -6.758 2.849 -0.666 C44 L6M 29 L6M C45 C30 C 0 1 Y N N 2.423 -31.035 21.688 -6.080 1.703 -1.025 C45 L6M 30 L6M N07 N1 N 0 1 N N N -2.353 -36.684 24.165 -0.889 -3.029 0.531 N07 L6M 31 L6M N15 N2 N 0 1 N N N -7.625 -36.599 24.184 4.281 -2.035 0.171 N15 L6M 32 L6M N23 N3 N 0 1 N N N -12.857 -37.082 24.481 6.605 2.668 -0.712 N23 L6M 33 L6M N27 N4 N 0 1 N N N -15.379 -36.670 24.160 6.043 4.360 0.789 N27 L6M 34 L6M N29 N5 N 0 1 N N N -16.291 -34.352 24.152 5.833 6.590 0.102 N29 L6M 35 L6M O01 O1 O 0 1 N N N 1.053 -33.335 20.879 -6.078 -1.824 -0.393 O01 L6M 36 L6M O10 O2 O 0 1 N N N -1.314 -37.762 27.244 -1.923 -4.828 2.132 O10 L6M 37 L6M O11 O3 O 0 1 N N N -0.978 -38.734 25.283 -0.342 -6.365 1.997 O11 L6M 38 L6M O18 O4 O 0 1 N N N -10.974 -37.502 25.567 5.818 0.431 -0.420 O18 L6M 39 L6M O20 O5 O 0 1 N N N -9.607 -39.908 24.103 8.740 -1.567 -0.327 O20 L6M 40 L6M O30 O6 O 0 1 N N N -14.399 -38.761 24.199 6.240 2.262 1.436 O30 L6M 41 L6M O31 O7 O 0 1 N N N -6.555 -36.947 26.223 3.690 -3.139 2.003 O31 L6M 42 L6M O32 O8 O 0 1 N N N -1.167 -35.060 25.306 -2.106 -3.963 -1.072 O32 L6M 43 L6M O42 O9 O 0 1 N N N 3.451 -27.331 25.238 -6.898 4.128 2.320 O42 L6M 44 L6M O43 O10 O 0 1 N N N 4.946 -28.632 26.164 -8.351 5.792 2.360 O43 L6M 45 L6M H1 H1 H 0 1 N N N -4.615 -36.195 24.088 2.184 -3.674 -0.608 H1 L6M 46 L6M H2 H2 H 0 1 N N N -5.254 -37.725 23.398 1.513 -2.175 0.078 H2 L6M 47 L6M H3 H3 H 0 1 N N N -8.925 -38.210 25.798 6.426 -1.396 -1.236 H3 L6M 48 L6M H4 H4 H 0 1 N N N -11.229 -38.894 22.621 9.007 0.802 -0.886 H4 L6M 49 L6M H5 H5 H 0 1 N N N -10.785 -37.158 22.753 8.333 1.450 0.643 H5 L6M 50 L6M H6 H6 H 0 1 N N N -12.116 -38.990 24.870 6.982 1.070 -2.036 H6 L6M 51 L6M H7 H7 H 0 1 N N N -11.652 -35.245 24.761 6.915 3.234 -2.736 H7 L6M 52 L6M H8 H8 H 0 1 N N N 1.499 -34.458 23.802 -4.034 0.225 -1.706 H8 L6M 53 L6M H10 H10 H 0 1 N N N 0.155 -35.513 21.154 -4.284 -2.827 -1.507 H10 L6M 54 L6M H12 H12 H 0 1 N N N -0.535 -33.856 23.203 -1.983 -0.910 -0.885 H12 L6M 55 L6M H13 H13 H 0 1 N N N -1.722 -34.793 22.233 -3.164 -1.455 0.329 H13 L6M 56 L6M H14 H14 H 0 1 N N N -3.015 -36.313 26.099 0.014 -4.761 -0.233 H14 L6M 57 L6M H15 H15 H 0 1 N N N -4.551 -38.181 26.225 1.787 -4.838 1.545 H15 L6M 58 L6M H16 H16 H 0 1 N N N -3.844 -38.952 24.765 1.115 -3.339 2.231 H16 L6M 59 L6M H17 H17 H 0 1 N N N -9.588 -35.789 24.133 6.130 -2.628 0.966 H17 L6M 60 L6M H18 H18 H 0 1 N N N -8.819 -35.814 25.756 5.458 -1.129 1.652 H18 L6M 61 L6M H19 H19 H 0 1 N N N -8.827 -38.199 23.083 7.849 -0.698 1.339 H19 L6M 62 L6M H20 H20 H 0 1 N N N -13.645 -33.640 24.557 6.463 5.598 -2.288 H20 L6M 63 L6M H21 H21 H 0 1 N N N -0.045 -36.947 23.664 -2.175 -1.317 -3.147 H21 L6M 64 L6M H22 H22 H 0 1 N N N 0.076 -37.548 21.975 -2.666 -3.034 -3.285 H22 L6M 65 L6M H23 H23 H 0 1 N N N 2.326 -37.179 23.882 -3.695 -1.031 -4.899 H23 L6M 66 L6M H24 H24 H 0 1 N N N 2.458 -37.676 22.161 -4.600 -2.513 -4.482 H24 L6M 67 L6M H25 H25 H 0 1 N N N 2.941 -35.429 21.420 -6.110 -1.260 -3.310 H25 L6M 68 L6M H26 H26 H 0 1 N N N 3.511 -35.227 23.112 -5.205 0.222 -3.728 H26 L6M 69 L6M H27 H27 H 0 1 N N N 3.110 -33.172 24.222 -7.819 -0.534 0.852 H27 L6M 70 L6M H28 H28 H 0 1 N N N 4.398 -31.214 25.031 -9.003 1.526 1.484 H28 L6M 71 L6M H29 H29 H 0 1 N N N 5.740 -28.999 23.761 -8.514 4.749 -0.201 H29 L6M 72 L6M H30 H30 H 0 1 N N N 4.482 -27.933 23.049 -9.571 3.800 0.872 H30 L6M 73 L6M H31 H31 H 0 1 N N N 3.179 -29.038 21.552 -6.468 3.800 -1.086 H31 L6M 74 L6M H32 H32 H 0 1 N N N 1.873 -30.981 20.760 -5.260 1.756 -1.725 H32 L6M 75 L6M H33 H33 H 0 1 N N N -2.635 -37.104 23.302 -0.696 -2.246 1.070 H33 L6M 76 L6M H34 H34 H 0 1 N N N -7.525 -36.551 23.190 4.048 -1.731 -0.720 H34 L6M 77 L6M H35 H35 H 0 1 N N N -17.210 -34.719 24.005 5.871 7.251 -0.607 H35 L6M 78 L6M H36 H36 H 0 1 N N N -16.152 -33.364 24.222 5.611 6.860 1.007 H36 L6M 79 L6M H37 H37 H 0 1 N N N -0.267 -39.125 25.777 -0.854 -6.915 2.605 H37 L6M 80 L6M H38 H38 H 0 1 N N N -9.690 -40.421 23.308 9.654 -1.454 -0.032 H38 L6M 81 L6M H39 H39 H 0 1 N N N 4.623 -28.192 26.941 -7.890 6.149 3.131 H39 L6M 82 # # 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 L6M C13 C12 SING N N 1 L6M C13 C14 SING N N 2 L6M C17 C16 SING N N 3 L6M C17 C19 SING N N 4 L6M C17 O18 SING N N 5 L6M C21 C22 SING N N 6 L6M C21 C19 SING N N 7 L6M C22 N23 SING N N 8 L6M C22 O18 SING N N 9 L6M C24 C25 DOUB N N 10 L6M C24 N23 SING N N 11 L6M C26 N23 SING N N 12 L6M C26 N27 SING N N 13 L6M C26 O30 DOUB N N 14 L6M C28 C25 SING N N 15 L6M C28 N27 DOUB N N 16 L6M C28 N29 SING N N 17 L6M C02 C03 SING N N 18 L6M C02 C36 SING N N 19 L6M C02 O01 DOUB N N 20 L6M C03 C35 SING N N 21 L6M C04 C05 SING N N 22 L6M C04 C33 SING N N 23 L6M C05 C06 SING N N 24 L6M C06 N07 SING N N 25 L6M C06 O32 DOUB N N 26 L6M C08 C09 SING N N 27 L6M C08 C12 SING N N 28 L6M C08 N07 SING N N 29 L6M C09 O10 DOUB N N 30 L6M C09 O11 SING N N 31 L6M C14 N15 SING N N 32 L6M C14 O31 DOUB N N 33 L6M C16 N15 SING N N 34 L6M C19 O20 SING N N 35 L6M C33 C34 SING N N 36 L6M C34 C35 SING N N 37 L6M C36 C37 DOUB Y N 38 L6M C36 C45 SING Y N 39 L6M C37 C38 SING Y N 40 L6M C38 C39 DOUB Y N 41 L6M C39 C40 SING N N 42 L6M C39 C44 SING Y N 43 L6M C40 C41 SING N N 44 L6M C41 O42 DOUB N N 45 L6M C41 O43 SING N N 46 L6M C44 C45 DOUB Y N 47 L6M C13 H1 SING N N 48 L6M C13 H2 SING N N 49 L6M C17 H3 SING N N 50 L6M C21 H4 SING N N 51 L6M C21 H5 SING N N 52 L6M C22 H6 SING N N 53 L6M C24 H7 SING N N 54 L6M C03 H8 SING N N 55 L6M C04 H10 SING N N 56 L6M C05 H12 SING N N 57 L6M C05 H13 SING N N 58 L6M C08 H14 SING N N 59 L6M C12 H15 SING N N 60 L6M C12 H16 SING N N 61 L6M C16 H17 SING N N 62 L6M C16 H18 SING N N 63 L6M C19 H19 SING N N 64 L6M C25 H20 SING N N 65 L6M C33 H21 SING N N 66 L6M C33 H22 SING N N 67 L6M C34 H23 SING N N 68 L6M C34 H24 SING N N 69 L6M C35 H25 SING N N 70 L6M C35 H26 SING N N 71 L6M C37 H27 SING N N 72 L6M C38 H28 SING N N 73 L6M C40 H29 SING N N 74 L6M C40 H30 SING N N 75 L6M C44 H31 SING N N 76 L6M C45 H32 SING N N 77 L6M N07 H33 SING N N 78 L6M N15 H34 SING N N 79 L6M N29 H35 SING N N 80 L6M N29 H36 SING N N 81 L6M O11 H37 SING N N 82 L6M O20 H38 SING N N 83 L6M O43 H39 SING N N 84 L6M C03 C04 SING N N 85 # # 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 L6M SMILES ACDLabs 12.01 "C(CC(C(=O)O)NC(CC2C(C(c1ccc(CC(=O)O)cc1)=O)CCC2)=O)C(NCC4C(CC(N3C=CC(=NC3=O)N)O4)O)=O" L6M InChI InChI 1.03 "InChI=1S/C30H37N5O10/c31-23-10-11-35(30(44)34-23)26-14-21(36)22(45-26)15-32-24(37)9-8-20(29(42)43)33-25(38)13-18-2-1-3-19(18)28(41)17-6-4-16(5-7-17)12-27(39)40/h4-7,10-11,18-22,26,36H,1-3,8-9,12-15H2,(H,32,37)(H,33,38)(H,39,40)(H,42,43)(H2,31,34,44)/t18-,19+,20-,21-,22+,26+/m0/s1" L6M InChIKey InChI 1.03 JVRVDICAIPFWFZ-BONAQRLYSA-N L6M SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CNC(=O)CC[C@H](NC(=O)C[C@@H]3CCC[C@H]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2" L6M SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CNC(=O)CC[CH](NC(=O)C[CH]3CCC[CH]3C(=O)c4ccc(CC(O)=O)cc4)C(O)=O)O2" L6M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)N[C@@H](CCC(=O)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=NC4=O)N)O)C(=O)O" L6M SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1CC(=O)O)C(=O)C2CCCC2CC(=O)NC(CCC(=O)NCC3C(CC(O3)N4C=CC(=NC4=O)N)O)C(=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 L6M "SYSTEMATIC NAME" ACDLabs 12.01 "5'-{[N-({(1S,2R)-2-[4-(carboxymethyl)benzene-1-carbonyl]cyclopentyl}acetyl)-L-gamma-glutamyl]amino}-2',5'-dideoxycytidine" L6M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-5-[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methylamino]-2-[2-[2-[4-(2-hydroxy-2-oxoethyl)phenyl]carbonylcyclopentyl]ethanoylamino]-5-oxidanylidene-pentanoic 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 L6M "Create component" 2019-02-07 RCSB L6M "Modify linking type" 2019-02-08 RCSB L6M "Initial release" 2020-02-12 RCSB ##