data_VLD # _chem_comp.id VLD _chem_comp.name "(2S)-2-({4-[({(6R)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C30 H38 N9 O13 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-08-27 _chem_comp.pdbx_modified_date 2021-04-16 _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 763.649 _chem_comp.one_letter_code ? _chem_comp.three_letter_code VLD _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 7JX1 _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 VLD N1 N1 N 0 1 N N N -43.816 33.972 -6.821 -3.490 1.109 1.144 N1 VLD 1 VLD C2 C1 C 0 1 N N N -42.995 34.869 -7.562 -3.045 1.803 0.081 C2 VLD 2 VLD C4 C2 C 0 1 N N N -41.538 35.088 -5.776 -0.914 0.873 0.312 C4 VLD 3 VLD C5 C3 C 0 1 N N N -42.620 34.660 -4.834 -1.372 0.129 1.426 C5 VLD 4 VLD C8 C4 C 0 1 N N N -46.273 33.648 -3.113 -1.367 -3.756 -0.737 C8 VLD 5 VLD C11 C5 C 0 1 N N N -43.424 35.925 -4.617 -0.436 -0.791 2.167 C11 VLD 6 VLD C12 C6 C 0 1 Y N N -46.778 40.879 -4.228 6.150 -0.368 -1.617 C12 VLD 7 VLD O1 O1 O 0 1 N N N -48.252 45.919 -7.110 10.028 -1.866 -1.201 O1 VLD 8 VLD O2 O2 O 0 1 N N N -43.270 35.187 -8.735 -3.805 2.544 -0.512 O2 VLD 9 VLD N N2 N 0 1 N N N -47.262 43.148 -5.015 8.378 0.116 -0.732 N VLD 10 VLD CA C7 C 0 1 N N S -48.173 44.177 -5.501 9.789 0.461 -0.917 CA VLD 11 VLD C C8 C 0 1 N N N -47.720 41.930 -4.736 7.571 -0.021 -1.804 C VLD 12 VLD O O3 O 0 1 N N N -48.900 41.647 -4.863 8.015 0.143 -2.924 O VLD 13 VLD CB C9 C 0 1 N N N -48.496 45.038 -4.282 10.316 1.148 0.344 CB VLD 14 VLD CG C10 C 0 1 N N N -47.363 46.008 -3.963 9.594 2.484 0.536 CG VLD 15 VLD CD C11 C 0 1 N N N -47.596 46.605 -2.596 10.113 3.161 1.778 CD VLD 16 VLD OE1 O4 O 0 1 N N N -48.566 46.189 -1.923 10.972 2.630 2.442 OE1 VLD 17 VLD OE2 O5 O 0 1 N N N -46.807 47.488 -2.189 9.621 4.354 2.148 OE2 VLD 18 VLD "C1'" C12 C 0 1 N N R -45.039 33.415 -7.433 -4.883 1.253 1.572 "C1'" VLD 19 VLD C13 C13 C 0 1 Y N N -45.417 40.920 -4.524 5.312 -0.510 -2.727 C13 VLD 20 VLD C14 C14 C 0 1 Y N N -44.566 39.932 -4.030 3.987 -0.835 -2.550 C14 VLD 21 VLD C15 C15 C 0 1 Y N N -45.083 38.906 -3.240 3.480 -1.021 -1.267 C15 VLD 22 VLD C16 C16 C 0 1 Y N N -46.445 38.873 -2.950 4.311 -0.881 -0.160 C16 VLD 23 VLD C17 C17 C 0 1 Y N N -47.291 39.855 -3.443 5.639 -0.562 -0.330 C17 VLD 24 VLD 'C2"' C18 C 0 1 Y N N -48.169 34.967 -6.063 -4.146 -3.776 1.669 'C2"' VLD 25 VLD "C2'" C19 C 0 1 N N N -44.788 32.300 -8.444 -5.135 2.692 2.062 "C2'" VLD 26 VLD "C3'" C20 C 0 1 N N S -46.119 31.567 -8.409 -6.272 3.210 1.149 "C3'" VLD 27 VLD 'C4"' C21 C 0 1 Y N N -46.208 36.246 -5.818 -2.520 -2.468 2.643 'C4"' VLD 28 VLD "C4'" C22 C 0 1 N N R -46.548 31.666 -6.947 -6.902 1.891 0.634 "C4'" VLD 29 VLD C4A C23 C 0 1 Y N N -45.868 35.478 -4.709 -1.693 -2.687 1.526 C4A VLD 30 VLD "C5'" C24 C 0 1 N N N -46.053 30.474 -6.130 -7.614 2.118 -0.701 "C5'" VLD 31 VLD C6 C25 C 0 1 N N N -43.394 33.525 -5.481 -2.655 0.265 1.825 C6 VLD 32 VLD 'C6"' C26 C 0 1 N N R -44.591 35.529 -2.516 0.152 -2.016 0.167 'C6"' VLD 33 VLD C7 C27 C 0 1 N N N -45.685 34.567 -2.044 0.101 -3.404 -0.483 C7 VLD 34 VLD C8A C28 C 0 1 Y N N -46.700 34.462 -4.309 -2.176 -3.472 0.502 C8A VLD 35 VLD C9 C29 C 0 1 N N N -44.917 36.895 -1.922 1.605 -1.546 0.258 C9 VLD 36 VLD CT C30 C 0 1 N N N -47.546 45.033 -6.569 10.584 -0.794 -1.175 CT VLD 37 VLD 'N1"' N3 N 0 1 Y N N -47.842 34.210 -4.989 -3.394 -3.998 0.605 'N1"' VLD 38 VLD N10 N4 N 0 1 N N N -44.289 37.924 -2.740 2.140 -1.349 -1.091 N10 VLD 39 VLD N3 N5 N 0 1 N N N -41.889 35.392 -7.025 -1.769 1.690 -0.335 N3 VLD 40 VLD 'N3"' N6 N 0 1 Y N N -47.360 35.975 -6.475 -3.724 -3.024 2.675 'N3"' VLD 41 VLD N5 N7 N 0 1 N N N -44.693 35.659 -3.968 -0.421 -2.106 1.513 N5 VLD 42 VLD NA2 N8 N 0 1 N N N -49.319 34.712 -6.733 -5.409 -4.346 1.735 NA2 VLD 43 VLD NA4 N9 N 0 1 N N N -45.416 37.259 -6.249 -2.082 -1.680 3.698 NA4 VLD 44 VLD O1P O6 O 0 1 N N N -45.246 27.986 -7.823 -8.289 1.182 -3.605 O1P VLD 45 VLD 'O2"' O7 O 0 1 N N N -46.346 44.826 -6.873 11.909 -0.720 -1.375 'O2"' VLD 46 VLD O2P O8 O 0 1 N N N -45.416 27.411 -5.410 -10.413 1.774 -2.376 O2P VLD 47 VLD "O3'" O9 O 0 1 N N N -47.080 32.242 -9.241 -7.222 3.970 1.899 "O3'" VLD 48 VLD O3P O10 O 0 1 N N N -47.302 26.878 -6.922 -9.635 -0.723 -2.641 O3P VLD 49 VLD O4 O11 O 0 1 N N N -40.511 35.593 -5.295 0.239 0.766 -0.066 O4 VLD 50 VLD "O4'" O12 O 0 1 N N N -45.928 32.861 -6.449 -5.763 1.020 0.460 "O4'" VLD 51 VLD "O5'" O13 O 0 1 N N N -46.851 29.317 -6.398 -8.283 0.919 -1.095 "O5'" VLD 52 VLD P P1 P 0 1 N N N -46.180 27.862 -6.641 -9.136 0.797 -2.455 P VLD 53 VLD H2 H2 H 0 1 N N N -45.513 32.915 -3.423 -1.747 -3.155 -1.563 H2 VLD 54 VLD H3 H3 H 0 1 N N N -47.145 33.120 -2.701 -1.449 -4.813 -0.990 H3 VLD 55 VLD H4 H4 H 0 1 N N N -42.841 36.613 -3.987 0.569 -0.370 2.159 H4 VLD 56 VLD H5 H5 H 0 1 N N N -43.616 36.395 -5.593 -0.775 -0.901 3.197 H5 VLD 57 VLD H6 H6 H 0 1 N N N -46.292 43.357 -4.891 8.023 -0.015 0.161 H6 VLD 58 VLD H7 H7 H 0 1 N N N -49.098 43.722 -5.884 9.890 1.135 -1.768 H7 VLD 59 VLD H8 H8 H 0 1 N N N -49.412 45.613 -4.484 10.134 0.510 1.209 H8 VLD 60 VLD H9 H9 H 0 1 N N N -48.659 44.382 -3.414 11.387 1.325 0.241 H9 VLD 61 VLD H10 H10 H 0 1 N N N -46.404 45.470 -3.972 9.776 3.122 -0.329 H10 VLD 62 VLD H11 H11 H 0 1 N N N -47.341 46.809 -4.716 8.524 2.307 0.638 H11 VLD 63 VLD H12 H12 H 0 1 N N N -47.067 47.769 -1.320 9.985 4.749 2.952 H12 VLD 64 VLD H13 H13 H 0 1 N N N -45.560 34.229 -7.959 -5.099 0.545 2.373 H13 VLD 65 VLD H14 H14 H 0 1 N N N -45.021 41.717 -5.136 5.705 -0.365 -3.723 H14 VLD 66 VLD H15 H15 H 0 1 N N N -43.511 39.961 -4.258 3.339 -0.944 -3.407 H15 VLD 67 VLD H16 H16 H 0 1 N N N -46.844 38.078 -2.338 3.915 -1.026 0.835 H16 VLD 68 VLD H17 H17 H 0 1 N N N -48.347 39.823 -3.217 6.285 -0.458 0.529 H17 VLD 69 VLD H18 H18 H 0 1 N N N -44.576 32.703 -9.445 -5.453 2.690 3.105 H18 VLD 70 VLD H19 H19 H 0 1 N N N -43.960 31.648 -8.128 -4.239 3.300 1.937 H19 VLD 71 VLD H20 H20 H 0 1 N N N -45.990 30.515 -8.703 -5.871 3.798 0.323 H20 VLD 72 VLD H21 H21 H 0 1 N N N -47.644 31.732 -6.884 -7.592 1.481 1.371 H21 VLD 73 VLD H22 H22 H 0 1 N N N -45.007 30.262 -6.396 -8.343 2.921 -0.591 H22 VLD 74 VLD H23 H23 H 0 1 N N N -46.117 30.718 -5.059 -6.883 2.394 -1.461 H23 VLD 75 VLD H25 H24 H 0 1 N N N -43.599 32.562 -5.038 -3.020 -0.288 2.677 H25 VLD 76 VLD H26 H26 H 0 1 N N N -43.596 35.184 -2.199 -0.424 -1.311 -0.431 H26 VLD 77 VLD H28 H27 H 0 1 N N N -46.506 35.169 -1.628 0.545 -4.141 0.185 H28 VLD 78 VLD H27 H28 H 0 1 N N N -45.258 33.933 -1.253 0.644 -3.388 -1.428 H27 VLD 79 VLD H29 H29 H 0 1 N N N -46.007 37.044 -1.913 1.648 -0.605 0.807 H29 VLD 80 VLD H30 H30 H 0 1 N N N -44.530 36.953 -0.894 2.198 -2.297 0.778 H30 VLD 81 VLD H31 H31 H 0 1 N N N -43.857 37.466 -3.516 1.559 -1.446 -1.862 H31 VLD 82 VLD H32 H32 H 0 1 N N N -41.322 36.015 -7.563 -1.465 2.197 -1.104 H32 VLD 83 VLD H33 H33 H 0 1 N N N -49.793 33.944 -6.303 -5.730 -4.899 1.006 H33 VLD 84 VLD H34 H34 H 0 1 N N N -49.906 35.521 -6.708 -5.971 -4.191 2.510 H34 VLD 85 VLD H35 H35 H 0 1 N N N -45.831 37.690 -7.050 -2.621 -0.933 4.002 H35 VLD 86 VLD H36 H36 H 0 1 N N N -45.316 37.937 -5.521 -1.236 -1.876 4.131 H36 VLD 87 VLD H37 H37 H 0 1 N N N -46.082 45.433 -7.554 12.376 -1.551 -1.536 H37 VLD 88 VLD H38 H38 H 0 1 N N N -44.499 27.296 -5.630 -11.013 1.579 -1.644 H38 VLD 89 VLD H39 H39 H 0 1 N N N -47.907 31.776 -9.212 -6.853 4.759 2.317 H39 VLD 90 VLD H40 H40 H 0 1 N N N -47.201 26.524 -7.798 -10.157 -0.871 -3.441 H40 VLD 91 # # 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 VLD N1 C2 SING N N 1 VLD N1 "C1'" SING N N 2 VLD N1 C6 SING N N 3 VLD C2 O2 DOUB N N 4 VLD C2 N3 SING N N 5 VLD C4 C5 SING N N 6 VLD C4 N3 SING N N 7 VLD C4 O4 DOUB N N 8 VLD C5 C11 SING N N 9 VLD C5 C6 DOUB N N 10 VLD C8 C7 SING N N 11 VLD C8 C8A SING N N 12 VLD C11 N5 SING N N 13 VLD C12 C SING N N 14 VLD C12 C13 DOUB Y N 15 VLD C12 C17 SING Y N 16 VLD O1 CT DOUB N N 17 VLD N CA SING N N 18 VLD N C SING N N 19 VLD CA CB SING N N 20 VLD CA CT SING N N 21 VLD C O DOUB N N 22 VLD CB CG SING N N 23 VLD CG CD SING N N 24 VLD CD OE1 DOUB N N 25 VLD CD OE2 SING N N 26 VLD "C1'" "C2'" SING N N 27 VLD "C1'" "O4'" SING N N 28 VLD C13 C14 SING Y N 29 VLD C14 C15 DOUB Y N 30 VLD C15 C16 SING Y N 31 VLD C15 N10 SING N N 32 VLD C16 C17 DOUB Y N 33 VLD 'C2"' 'N1"' DOUB Y N 34 VLD 'C2"' 'N3"' SING Y N 35 VLD 'C2"' NA2 SING N N 36 VLD "C2'" "C3'" SING N N 37 VLD "C3'" "C4'" SING N N 38 VLD "C3'" "O3'" SING N N 39 VLD 'C4"' C4A SING Y N 40 VLD 'C4"' 'N3"' DOUB Y N 41 VLD 'C4"' NA4 SING N N 42 VLD "C4'" "C5'" SING N N 43 VLD "C4'" "O4'" SING N N 44 VLD C4A C8A DOUB Y N 45 VLD C4A N5 SING N N 46 VLD "C5'" "O5'" SING N N 47 VLD 'C6"' C7 SING N N 48 VLD 'C6"' C9 SING N N 49 VLD 'C6"' N5 SING N N 50 VLD C8A 'N1"' SING Y N 51 VLD C9 N10 SING N N 52 VLD CT 'O2"' SING N N 53 VLD O1P P DOUB N N 54 VLD O2P P SING N N 55 VLD O3P P SING N N 56 VLD "O5'" P SING N N 57 VLD C8 H2 SING N N 58 VLD C8 H3 SING N N 59 VLD C11 H4 SING N N 60 VLD C11 H5 SING N N 61 VLD N H6 SING N N 62 VLD CA H7 SING N N 63 VLD CB H8 SING N N 64 VLD CB H9 SING N N 65 VLD CG H10 SING N N 66 VLD CG H11 SING N N 67 VLD OE2 H12 SING N N 68 VLD "C1'" H13 SING N N 69 VLD C13 H14 SING N N 70 VLD C14 H15 SING N N 71 VLD C16 H16 SING N N 72 VLD C17 H17 SING N N 73 VLD "C2'" H18 SING N N 74 VLD "C2'" H19 SING N N 75 VLD "C3'" H20 SING N N 76 VLD "C4'" H21 SING N N 77 VLD "C5'" H22 SING N N 78 VLD "C5'" H23 SING N N 79 VLD C6 H25 SING N N 80 VLD 'C6"' H26 SING N N 81 VLD C7 H28 SING N N 82 VLD C7 H27 SING N N 83 VLD C9 H29 SING N N 84 VLD C9 H30 SING N N 85 VLD N10 H31 SING N N 86 VLD N3 H32 SING N N 87 VLD NA2 H33 SING N N 88 VLD NA2 H34 SING N N 89 VLD NA4 H35 SING N N 90 VLD NA4 H36 SING N N 91 VLD 'O2"' H37 SING N N 92 VLD O2P H38 SING N N 93 VLD "O3'" H39 SING N N 94 VLD O3P H40 SING N N 95 # # 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 VLD SMILES ACDLabs 12.01 "N4(C(=O)NC(C(CN2c3c(nc(nc3CCC2CNc1ccc(C(NC(CCC(=O)O)C(=O)O)=O)cc1)N)N)=C4)=O)C5CC(C(COP(=O)(O)O)O5)O" VLD InChI InChI 1.03 "InChI=1S/C30H38N9O13P/c31-25-24-18(35-29(32)36-25)6-5-17(10-33-16-3-1-14(2-4-16)26(43)34-19(28(45)46)7-8-23(41)42)38(24)11-15-12-39(30(47)37-27(15)44)22-9-20(40)21(52-22)13-51-53(48,49)50/h1-4,12,17,19-22,33,40H,5-11,13H2,(H,34,43)(H,41,42)(H,45,46)(H,37,44,47)(H2,48,49,50)(H4,31,32,35,36)/t17-,19+,20+,21-,22-/m1/s1" VLD InChIKey InChI 1.03 OYTZJQBUPHBEFY-WHCFWRGISA-N VLD SMILES_CANONICAL CACTVS 3.385 "Nc1nc(N)c2N(CC3=CN([C@H]4C[C@H](O)[C@@H](CO[P](O)(O)=O)O4)C(=O)NC3=O)[C@H](CCc2n1)CNc5ccc(cc5)C(=O)N[C@@H](CCC(O)=O)C(O)=O" VLD SMILES CACTVS 3.385 "Nc1nc(N)c2N(CC3=CN([CH]4C[CH](O)[CH](CO[P](O)(O)=O)O4)C(=O)NC3=O)[CH](CCc2n1)CNc5ccc(cc5)C(=O)N[CH](CCC(O)=O)C(O)=O" VLD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2CCc3c(c(nc(n3)N)N)N2CC4=CN(C(=O)NC4=O)[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O" VLD SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CCc3c(c(nc(n3)N)N)N2CC4=CN(C(=O)NC4=O)C5CC(C(O5)COP(=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 VLD "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-({4-[({(6R)-2,4-diamino-5-[(1-{(2R,4S,5R)-4-hydroxy-5-[(phosphonooxy)methyl]tetrahydrofuran-2-yl}-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl]-5,6,7,8-tetrahydropyrido[3,2-d]pyrimidin-6-yl}methyl)amino]benzoyl}amino)pentanedioic acid (non-preferred name)" VLD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[4-[[(6~{R})-2,4-bis(azanyl)-5-[[2,4-bis(oxidanylidene)-1-[(2~{R},4~{S},5~{R})-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidin-5-yl]methyl]-7,8-dihydro-6~{H}-pyrido[3,2-d]pyrimidin-6-yl]methylamino]phenyl]carbonylamino]pentanedioic 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 VLD "Create component" 2020-08-27 RCSB VLD "Other modification" 2020-08-31 RCSB VLD "Initial release" 2021-04-21 RCSB ##