data_LVR # _chem_comp.id LVR _chem_comp.name "1-{[2-({6-[(2-aminoethyl)amino]-5,10-dioxo-5,10-dihydrobenzo[g]isoquinolin-9-yl}amino)ethyl]amino}-1,2-dideoxy-5-O-(dihydroxyphosphanyl)-L-threo-pentitol" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C22 H30 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-03-07 _chem_comp.pdbx_modified_date 2023-03-21 _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 523.476 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LVR _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 7U38 _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 LVR OP1 O1 O 0 1 N N N 44.685 41.718 32.098 10.715 -1.157 -1.168 OP1 LVR 1 LVR P P1 P 0 1 N N N 43.554 40.764 32.056 10.600 -0.002 -0.250 P LVR 2 LVR OP2 O2 O 0 1 N N N 42.264 41.087 32.679 11.629 1.150 -0.706 OP2 LVR 3 LVR "O5'" O3 O 0 1 N N N 43.217 40.358 30.503 9.097 0.573 -0.297 "O5'" LVR 4 LVR "C5'" C1 C 0 1 N N N 44.295 40.011 29.661 7.946 -0.237 -0.049 "C5'" LVR 5 LVR "C4'" C2 C 0 1 N N S 43.825 39.551 28.258 6.684 0.618 -0.172 "C4'" LVR 6 LVR "O4'" O4 O 0 1 N N N 42.414 39.395 28.192 6.677 1.610 0.857 "O4'" LVR 7 LVR "C3'" C3 C 0 1 N N S 44.509 38.232 27.965 5.448 -0.273 -0.030 "C3'" LVR 8 LVR "O3'" O5 O 0 1 N N N 43.599 37.290 27.433 5.524 -1.001 1.197 "O3'" LVR 9 LVR "C2'" C4 C 0 1 N N N 45.699 38.420 27.029 4.189 0.598 -0.029 "C2'" LVR 10 LVR "C1'" C5 C 0 1 N N N 46.294 37.122 26.545 2.950 -0.299 -0.012 "C1'" LVR 11 LVR NAT N1 N 0 1 N N N 47.598 37.069 26.439 1.741 0.537 -0.011 NAT LVR 12 LVR CAP C6 C 0 1 N N N 48.048 35.665 26.313 0.528 -0.292 0.005 CAP LVR 13 LVR CAR C7 C 0 1 N N N 48.105 34.988 27.660 -0.706 0.612 0.006 CAR LVR 14 LVR NAV N2 N 0 1 N N N 49.228 34.029 27.691 -1.916 -0.215 0.022 NAV LVR 15 LVR CAZ C8 C 0 1 Y N N 50.450 34.392 28.039 -3.166 0.386 0.025 CAZ LVR 16 LVR CAJ C9 C 0 1 Y N N 50.778 35.729 27.851 -3.276 1.774 0.148 CAJ LVR 17 LVR CAI C10 C 0 1 Y N N 52.058 36.141 28.107 -4.500 2.378 0.152 CAI LVR 18 LVR CBF C11 C 0 1 Y N N 51.371 33.401 28.528 -4.319 -0.394 -0.100 CBF LVR 19 LVR CBB C12 C 0 1 N N N 51.034 32.027 28.797 -4.224 -1.858 -0.235 CBB LVR 20 LVR OAB O6 O 0 1 N N N 49.910 31.565 28.580 -3.156 -2.386 -0.481 OAB LVR 21 LVR CBD C13 C 0 1 Y N N 51.972 31.141 29.334 -5.442 -2.676 -0.067 CBD LVR 22 LVR CAX C14 C 0 1 Y N N 51.618 29.806 29.575 -5.371 -4.056 0.090 CAX LVR 23 LVR NAH N3 N 0 1 Y N N 52.595 28.886 30.098 -6.474 -4.766 0.238 NAH LVR 24 LVR CAG C15 C 0 1 Y N N 53.911 29.334 30.336 -7.672 -4.215 0.245 CAG LVR 25 LVR CAW C16 C 0 1 Y N N 54.225 30.686 30.109 -7.836 -2.846 0.094 CAW LVR 26 LVR CBC C17 C 0 1 Y N N 53.263 31.565 29.588 -6.705 -2.053 -0.064 CBC LVR 27 LVR CBA C18 C 0 1 N N N 53.605 32.893 29.369 -6.804 -0.586 -0.226 CBA LVR 28 LVR OAA O7 O 0 1 N N N 54.759 33.218 29.664 -7.875 -0.063 -0.464 OAA LVR 29 LVR CBE C19 C 0 1 Y N N 52.660 33.836 28.840 -5.585 0.230 -0.096 CBE LVR 30 LVR CAY C20 C 0 1 Y N N 52.976 35.213 28.604 -5.669 1.620 0.034 CAY LVR 31 LVR NAU N4 N 0 1 N N N 54.204 35.652 28.915 -6.907 2.245 0.040 NAU LVR 32 LVR CAQ C21 C 0 1 N N N 54.538 37.094 28.945 -6.989 3.707 0.030 CAQ LVR 33 LVR CAO C22 C 0 1 N N N 55.043 37.518 27.560 -8.458 4.136 0.040 CAO LVR 34 LVR NAS N5 N 0 1 N N N 56.390 38.115 27.656 -8.540 5.602 0.029 NAS LVR 35 LVR H2 H2 H 0 1 N N N 42.309 41.950 33.073 12.556 0.873 -0.701 H2 LVR 36 LVR H3 H3 H 0 1 N N N 44.860 39.192 30.130 7.908 -1.048 -0.776 H3 LVR 37 LVR H4 H4 H 0 1 N N N 44.949 40.888 29.545 8.005 -0.654 0.957 H4 LVR 38 LVR H5 H5 H 0 1 N N N 44.158 40.295 27.520 6.670 1.106 -1.147 H5 LVR 39 LVR H6 H6 H 0 1 N N N 41.994 40.227 28.377 6.689 1.246 1.753 H6 LVR 40 LVR H7 H7 H 0 1 N N N 44.900 37.845 28.918 5.406 -0.971 -0.865 H7 LVR 41 LVR H8 H8 H 0 1 N N N 42.866 37.186 28.028 5.565 -0.442 1.985 H8 LVR 42 LVR H9 H9 H 0 1 N N N 46.478 38.982 27.565 4.189 1.235 0.856 H9 LVR 43 LVR H10 H10 H 0 1 N N N 45.366 38.998 26.154 4.176 1.219 -0.924 H10 LVR 44 LVR H11 H11 H 0 1 N N N 45.871 36.913 25.551 2.950 -0.936 -0.896 H11 LVR 45 LVR H12 H12 H 0 1 N N N 45.986 36.333 27.247 2.963 -0.920 0.883 H12 LVR 46 LVR H13 H13 H 0 1 N N N 48.012 37.476 27.253 1.738 1.168 -0.798 H13 LVR 47 LVR H15 H15 H 0 1 N N N 47.345 35.119 25.667 0.512 -0.929 -0.879 H15 LVR 48 LVR H16 H16 H 0 1 N N N 49.050 35.649 25.860 0.525 -0.913 0.900 H16 LVR 49 LVR H17 H17 H 0 1 N N N 48.250 35.746 28.444 -0.690 1.249 0.890 H17 LVR 50 LVR H18 H18 H 0 1 N N N 47.162 34.451 27.839 -0.702 1.233 -0.890 H18 LVR 51 LVR H19 H19 H 0 1 N N N 48.960 33.305 28.326 -1.843 -1.182 0.030 H19 LVR 52 LVR H20 H20 H 0 1 N N N 50.034 36.433 27.508 -2.384 2.376 0.240 H20 LVR 53 LVR H21 H21 H 0 1 N N N 52.353 37.165 27.928 -4.566 3.451 0.248 H21 LVR 54 LVR H22 H22 H 0 1 N N N 50.613 29.468 29.369 -4.410 -4.549 0.091 H22 LVR 55 LVR H23 H23 H 0 1 N N N 54.667 28.648 30.688 -8.542 -4.843 0.369 H23 LVR 56 LVR H24 H24 H 0 1 N N N 55.215 31.051 30.338 -8.822 -2.406 0.100 H24 LVR 57 LVR H25 H25 H 0 1 N N N 54.404 35.299 29.829 -7.718 1.713 0.051 H25 LVR 58 LVR H26 H26 H 0 1 N N N 55.322 37.276 29.695 -6.488 4.105 0.913 H26 LVR 59 LVR H27 H27 H 0 1 N N N 53.641 37.675 29.204 -6.504 4.092 -0.867 H27 LVR 60 LVR H28 H28 H 0 1 N N N 54.350 38.258 27.134 -8.958 3.737 -0.843 H28 LVR 61 LVR H29 H29 H 0 1 N N N 55.085 36.635 26.905 -8.942 3.751 0.937 H29 LVR 62 LVR H30 H30 H 0 1 N N N 56.701 38.385 26.745 -8.042 5.987 -0.759 H30 LVR 63 LVR H31 H31 H 0 1 N N N 56.356 38.920 28.248 -9.500 5.911 0.035 H31 LVR 64 LVR OP3 OP3 O 0 1 N Y N ? ? ? 10.949 -0.471 1.250 OP3 LVR 65 LVR HO3 HO3 H 0 1 N Y N ? ? ? 10.894 0.236 1.906 HO3 LVR 66 # 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 LVR CAP NAT SING N N 1 LVR CAP CAR SING N N 2 LVR NAT "C1'" SING N N 3 LVR "C1'" "C2'" SING N N 4 LVR "C2'" "C3'" SING N N 5 LVR "O3'" "C3'" SING N N 6 LVR CAO NAS SING N N 7 LVR CAO CAQ SING N N 8 LVR CAR NAV SING N N 9 LVR NAV CAZ SING N N 10 LVR CAJ CAZ DOUB Y N 11 LVR CAJ CAI SING Y N 12 LVR "C3'" "C4'" SING N N 13 LVR CAZ CBF SING Y N 14 LVR CAI CAY DOUB Y N 15 LVR "O4'" "C4'" SING N N 16 LVR "C4'" "C5'" SING N N 17 LVR CBF CBB SING N N 18 LVR CBF CBE DOUB Y N 19 LVR OAB CBB DOUB N N 20 LVR CAY CBE SING Y N 21 LVR CAY NAU SING N N 22 LVR CBB CBD SING N N 23 LVR CBE CBA SING N N 24 LVR NAU CAQ SING N N 25 LVR CBD CAX DOUB Y N 26 LVR CBD CBC SING Y N 27 LVR CBA CBC SING N N 28 LVR CBA OAA DOUB N N 29 LVR CAX NAH SING Y N 30 LVR CBC CAW DOUB Y N 31 LVR "C5'" "O5'" SING N N 32 LVR NAH CAG DOUB Y N 33 LVR CAW CAG SING Y N 34 LVR "O5'" P SING N N 35 LVR P OP1 DOUB N N 36 LVR P OP2 SING N N 37 LVR OP2 H2 SING N N 38 LVR "C5'" H3 SING N N 39 LVR "C5'" H4 SING N N 40 LVR "C4'" H5 SING N N 41 LVR "O4'" H6 SING N N 42 LVR "C3'" H7 SING N N 43 LVR "O3'" H8 SING N N 44 LVR "C2'" H9 SING N N 45 LVR "C2'" H10 SING N N 46 LVR "C1'" H11 SING N N 47 LVR "C1'" H12 SING N N 48 LVR NAT H13 SING N N 49 LVR CAP H15 SING N N 50 LVR CAP H16 SING N N 51 LVR CAR H17 SING N N 52 LVR CAR H18 SING N N 53 LVR NAV H19 SING N N 54 LVR CAJ H20 SING N N 55 LVR CAI H21 SING N N 56 LVR CAX H22 SING N N 57 LVR CAG H23 SING N N 58 LVR CAW H24 SING N N 59 LVR NAU H25 SING N N 60 LVR CAQ H26 SING N N 61 LVR CAQ H27 SING N N 62 LVR CAO H28 SING N N 63 LVR CAO H29 SING N N 64 LVR NAS H30 SING N N 65 LVR NAS H31 SING N N 66 LVR P OP3 SING N N 67 LVR OP3 HO3 SING N N 68 # 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 LVR SMILES ACDLabs 12.01 "O=P(O)(O)OCC(O)C(O)CCNCCNc1ccc(NCCN)c2c1C(=O)c1cnccc1C2=O" LVR InChI InChI 1.06 "InChI=1S/C22H30N5O8P/c23-5-8-26-15-1-2-16(20-19(15)21(30)13-3-6-25-11-14(13)22(20)31)27-10-9-24-7-4-17(28)18(29)12-35-36(32,33)34/h1-3,6,11,17-18,24,26-29H,4-5,7-10,12,23H2,(H2,32,33,34)/t17-,18-/m0/s1" LVR InChIKey InChI 1.06 BJAOHGRBCOQHHR-ROUUACIJSA-N LVR SMILES_CANONICAL CACTVS 3.385 "NCCNc1ccc(NCCNCC[C@H](O)[C@@H](O)CO[P](O)(O)=O)c2C(=O)c3cnccc3C(=O)c12" LVR SMILES CACTVS 3.385 "NCCNc1ccc(NCCNCC[CH](O)[CH](O)CO[P](O)(O)=O)c2C(=O)c3cnccc3C(=O)c12" LVR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c2c(c1NCCN)C(=O)c3ccncc3C2=O)NCCNCC[C@@H]([C@H](COP(=O)(O)O)O)O" LVR SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c2c(c1NCCN)C(=O)c3ccncc3C2=O)NCCNCCC(C(COP(=O)(O)O)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 LVR "SYSTEMATIC NAME" ACDLabs 12.01 "1-{[2-({6-[(2-aminoethyl)amino]-5,10-dioxo-5,10-dihydrobenzo[g]isoquinolin-9-yl}amino)ethyl]amino}-1,2-dideoxy-5-O-phosphono-L-threo-pentitol" LVR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{S},3~{S})-5-[2-[[6-(2-azanylethylamino)-5,10-bis(oxidanylidene)benzo[g]isoquinolin-9-yl]amino]ethylamino]-2,3-bis(oxidanyl)pentyl] dihydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site LVR "Create component" 2022-03-07 RCSB LVR "Initial release" 2023-03-15 RCSB LVR "Other modification" 2023-03-21 RCSB #