data_VNM # _chem_comp.id VNM _chem_comp.name "(2S)-2-({4-[({(6S)-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 2020-08-31 _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 ? _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 7JXF _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 VNM C2 C1 C 0 1 N N N -8.643 55.106 7.753 4.094 0.084 1.831 C2 VNM 1 VNM C4 C2 C 0 1 N N N -9.542 54.562 5.653 3.499 -2.175 1.891 C4 VNM 2 VNM C5 C3 C 0 1 N N N -8.355 55.172 4.995 2.170 -1.822 1.554 C5 VNM 3 VNM C6 C4 C 0 1 N N N -7.386 55.725 5.806 1.863 -0.521 1.364 C6 VNM 4 VNM C7 C5 C 0 1 N N N -8.533 56.385 0.780 1.086 -2.933 -2.358 C7 VNM 5 VNM C8 C6 C 0 1 N N N -9.944 55.736 0.649 2.513 -3.444 -2.575 C8 VNM 6 VNM N10 N1 N 0 1 N N N -8.366 59.848 2.421 -1.416 -2.634 -0.794 N10 VNM 7 VNM C11 C7 C 0 1 N N N -8.187 55.354 3.505 1.113 -2.885 1.403 C11 VNM 8 VNM C12 C8 C 0 1 Y N N -10.884 62.856 3.787 -5.394 -1.419 -0.660 C12 VNM 9 VNM C15 C9 C 0 1 Y N N -9.167 60.815 2.941 -2.745 -2.228 -0.749 C15 VNM 10 VNM C16 C10 C 0 1 Y N N -8.876 62.144 2.660 -3.056 -0.873 -0.687 C16 VNM 11 VNM C17 C11 C 0 1 Y N N -9.718 63.164 3.092 -4.370 -0.468 -0.637 C17 VNM 12 VNM N N2 N 0 1 N N N -13.108 63.727 4.396 -7.106 0.323 -0.542 N VNM 13 VNM CA C12 C 0 1 N N S -14.000 64.706 5.002 -8.507 0.751 -0.495 CA VNM 14 VNM C C13 C 0 1 N N N -11.799 63.950 4.266 -6.804 -0.989 -0.613 C VNM 15 VNM O O1 O 0 1 N N N -11.290 65.024 4.577 -7.694 -1.817 -0.638 O VNM 16 VNM CB C14 C 0 1 N N N -15.247 65.011 4.171 -8.600 2.118 0.186 CB VNM 17 VNM CG C15 C 0 1 N N N -15.923 63.786 3.564 -8.166 1.990 1.648 CG VNM 18 VNM CD C16 C 0 1 N N N -17.344 64.140 3.183 -8.258 3.337 2.318 CD VNM 19 VNM OE1 O2 O 0 1 N N N -17.582 65.280 2.721 -8.632 4.300 1.691 OE1 VNM 20 VNM OE2 O3 O 0 1 N N N -18.231 63.274 3.338 -7.924 3.466 3.612 OE2 VNM 21 VNM "C1'" C17 C 0 1 N N R -6.457 56.277 7.934 2.503 1.843 1.298 "C1'" VNM 22 VNM C13 C18 C 0 1 Y N N -11.187 61.528 4.059 -5.079 -2.779 -0.734 C13 VNM 23 VNM C14 C19 C 0 1 Y N N -10.344 60.516 3.630 -3.763 -3.178 -0.778 C14 VNM 24 VNM 'C2"' C20 C 0 1 Y N N -13.039 56.145 2.747 4.433 -5.777 -0.481 'C2"' VNM 25 VNM "C2'" C21 C 0 1 N N N -5.708 55.305 8.844 2.667 2.619 2.620 "C2'" VNM 26 VNM "C3'" C22 C 0 1 N N S -4.354 55.986 8.943 3.707 3.717 2.290 "C3'" VNM 27 VNM 'C4"' C23 C 0 1 Y N N -11.196 56.692 4.078 2.754 -4.988 0.885 'C4"' VNM 28 VNM "C4'" C24 C 0 1 N N R -4.124 56.484 7.520 3.612 3.800 0.745 "C4'" VNM 29 VNM C4A C25 C 0 1 Y N N -10.380 56.410 2.997 2.275 -4.202 -0.179 C4A VNM 30 VNM "C5'" C26 C 0 1 N N N -3.510 55.417 6.631 4.913 4.348 0.154 "C5'" VNM 31 VNM 'C6"' C27 C 0 1 N N S -8.313 57.297 2.006 1.006 -2.332 -0.949 'C6"' VNM 32 VNM C8A C28 C 0 1 Y N N -10.904 56.017 1.798 2.946 -4.256 -1.382 C8A VNM 33 VNM C9 C29 C 0 1 N N N -9.003 58.647 1.816 -0.344 -1.636 -0.764 C9 VNM 34 VNM CT C30 C 0 1 N N N -14.388 64.200 6.363 -9.049 0.850 -1.897 CT VNM 35 VNM N1 N3 N 0 1 N N N -7.505 55.673 7.137 2.836 0.431 1.505 N1 VNM 36 VNM 'N1"' N4 N 0 1 Y N N -12.240 55.881 1.685 4.009 -5.047 -1.498 'N1"' VNM 37 VNM N3 N5 N 0 1 N N N -9.612 54.572 6.995 4.428 -1.206 2.021 N3 VNM 38 VNM 'N3"' N6 N 0 1 Y N N -12.521 56.543 3.922 3.823 -5.751 0.695 'N3"' VNM 39 VNM N5 N7 N 0 1 N N N -9.001 56.433 2.926 1.140 -3.413 0.032 N5 VNM 40 VNM NA2 N8 N 0 1 N N N -14.380 56.024 2.671 5.545 -6.588 -0.647 NA2 VNM 41 VNM NA4 N9 N 0 1 N N N -10.731 57.094 5.287 2.117 -4.965 2.118 NA4 VNM 42 VNM O1 O4 O 0 1 N N N -14.376 62.960 6.544 -8.339 0.590 -2.839 O1 VNM 43 VNM O1P O5 O 0 1 N N N -1.886 53.251 8.021 5.457 5.029 -3.739 O1P VNM 44 VNM O2 O6 O 0 1 N N N -8.745 55.082 9.008 4.942 0.946 1.951 O2 VNM 45 VNM 'O2"' O7 O 0 1 N N N -14.715 65.021 7.249 -10.321 1.227 -2.100 'O2"' VNM 46 VNM O2P O8 O 0 1 N N N -1.068 53.385 5.662 7.146 4.256 -2.030 O2P VNM 47 VNM "O3'" O9 O 0 1 N N N -4.403 57.117 9.810 3.343 4.961 2.891 "O3'" VNM 48 VNM O3P O10 O 0 1 N N N 0.114 54.644 7.425 6.264 6.610 -1.799 O3P VNM 49 VNM O4 O11 O 0 1 N N N -10.471 54.056 4.982 3.800 -3.342 2.063 O4 VNM 50 VNM "O4'" O12 O 0 1 N N N -5.448 56.836 7.070 3.408 2.427 0.346 "O4'" VNM 51 VNM "O5'" O13 O 0 1 N N N -2.099 55.457 6.806 4.759 4.524 -1.255 "O5'" VNM 52 VNM P P1 P 0 1 N N N -1.220 54.119 6.973 5.933 5.087 -2.202 P VNM 53 VNM H6 H1 H 0 1 N N N -6.525 56.203 5.363 0.855 -0.233 1.106 H6 VNM 54 VNM H71 H2 H 0 1 N N N -7.793 55.572 0.829 0.852 -2.169 -3.098 H71 VNM 55 VNM H72 H3 H 0 1 N N N -8.356 56.988 -0.123 0.381 -3.760 -2.446 H72 VNM 56 VNM H81 H4 H 0 1 N N N -10.405 56.111 -0.277 2.543 -4.068 -3.469 H81 VNM 57 VNM H82 H5 H 0 1 N N N -9.811 54.646 0.577 3.187 -2.597 -2.701 H82 VNM 58 VNM H101 H6 H 0 0 N N N -7.773 59.527 3.160 -1.199 -3.578 -0.846 H101 VNM 59 VNM H1 H7 H 0 1 N N N -8.464 54.411 3.010 1.307 -3.694 2.107 H1 VNM 60 VNM H2 H8 H 0 1 N N N -7.129 55.576 3.303 0.132 -2.455 1.606 H2 VNM 61 VNM H161 H9 H 0 0 N N N -7.986 62.388 2.100 -2.264 -0.138 -0.674 H161 VNM 62 VNM H171 H10 H 0 0 N N N -9.467 64.194 2.888 -4.610 0.583 -0.581 H171 VNM 63 VNM H H11 H 0 1 N N N -13.488 62.862 4.068 -6.396 0.984 -0.522 H VNM 64 VNM HA H12 H 0 1 N N N -13.448 65.648 5.134 -9.090 0.023 0.070 HA VNM 65 VNM HB2 H13 H 0 1 N N N -14.956 65.684 3.351 -7.946 2.824 -0.326 HB2 VNM 66 VNM HB3 H14 H 0 1 N N N -15.976 65.518 4.820 -9.628 2.476 0.142 HB3 VNM 67 VNM HG2 H15 H 0 1 N N N -15.932 62.968 4.300 -8.819 1.284 2.160 HG2 VNM 68 VNM HG3 H16 H 0 1 N N N -15.370 63.467 2.668 -7.137 1.632 1.692 HG3 VNM 69 VNM H3 H17 H 0 1 N N N -19.068 63.624 3.056 -7.999 4.350 3.998 H3 VNM 70 VNM "H1'" H18 H 0 1 N N N -6.887 57.074 8.559 1.478 1.934 0.939 "H1'" VNM 71 VNM H131 H19 H 0 0 N N N -12.084 61.283 4.608 -5.868 -3.516 -0.757 H131 VNM 72 VNM H141 H20 H 0 0 N N N -10.600 59.486 3.830 -3.519 -4.229 -0.827 H141 VNM 73 VNM H2*1 H21 H 0 0 N N N -6.191 55.220 9.829 1.719 3.068 2.918 H2*1 VNM 74 VNM H2*2 H22 H 0 0 N N N -5.626 54.307 8.389 3.042 1.961 3.404 H2*2 VNM 75 VNM "H3'" H23 H 0 1 N N N -3.574 55.268 9.237 4.706 3.413 2.603 "H3'" VNM 76 VNM H4* H24 H 0 1 N N N -3.471 57.369 7.540 2.766 4.417 0.445 H4* VNM 77 VNM H5*1 H25 H 0 0 N N N -3.761 55.618 5.579 5.146 5.307 0.617 H5*1 VNM 78 VNM H5*2 H26 H 0 0 N N N -3.894 54.427 6.917 5.724 3.646 0.347 H5*2 VNM 79 VNM H61 H27 H 0 1 N N N -7.244 57.414 2.237 1.813 -1.612 -0.813 H61 VNM 80 VNM H92 H28 H 0 1 N N N -9.078 58.827 0.733 -0.495 -0.916 -1.568 H92 VNM 81 VNM H91 H29 H 0 1 N N N -10.013 58.562 2.244 -0.357 -1.118 0.195 H91 VNM 82 VNM HN3 H30 H 0 1 N N N -10.411 54.169 7.442 5.340 -1.440 2.252 HN3 VNM 83 VNM HA22 H31 H 0 0 N N N -14.637 55.726 1.752 5.867 -7.129 0.091 HA22 VNM 84 VNM HA21 H32 H 0 0 N N N -14.692 55.349 3.339 6.001 -6.616 -1.503 HA21 VNM 85 VNM HA42 H33 H 0 0 N N N -11.499 57.225 5.914 1.167 -5.151 2.177 HA42 VNM 86 VNM HA41 H34 H 0 0 N N N -10.115 56.398 5.656 2.622 -4.761 2.920 HA41 VNM 87 VNM H4 H35 H 0 1 N N N -2.084 52.400 7.649 6.116 5.354 -4.367 H4 VNM 88 VNM H5 H36 H 0 1 N N N -14.941 64.555 8.045 -10.624 1.276 -3.017 H5 VNM 89 VNM "HO3'" H37 H 0 0 N N N -4.546 56.826 10.703 3.300 4.934 3.856 "HO3'" VNM 90 VNM H7 H38 H 0 1 N N N 0.780 54.405 6.791 5.513 7.212 -1.888 H7 VNM 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 VNM C8 C7 SING N N 1 VNM C8 C8A SING N N 2 VNM C7 'C6"' SING N N 3 VNM 'N1"' C8A DOUB Y N 4 VNM 'N1"' 'C2"' SING Y N 5 VNM C8A C4A SING Y N 6 VNM C9 'C6"' SING N N 7 VNM C9 N10 SING N N 8 VNM 'C6"' N5 SING N N 9 VNM N10 C15 SING N N 10 VNM C16 C15 DOUB Y N 11 VNM C16 C17 SING Y N 12 VNM NA2 'C2"' SING N N 13 VNM OE1 CD DOUB N N 14 VNM 'C2"' 'N3"' DOUB Y N 15 VNM N5 C4A SING N N 16 VNM N5 C11 SING N N 17 VNM C15 C14 SING Y N 18 VNM C4A 'C4"' DOUB Y N 19 VNM C17 C12 DOUB Y N 20 VNM CD OE2 SING N N 21 VNM CD CG SING N N 22 VNM C11 C5 SING N N 23 VNM CG CB SING N N 24 VNM C14 C13 DOUB Y N 25 VNM C12 C13 SING Y N 26 VNM C12 C SING N N 27 VNM 'N3"' 'C4"' SING Y N 28 VNM 'C4"' NA4 SING N N 29 VNM CB CA SING N N 30 VNM C N SING N N 31 VNM C O DOUB N N 32 VNM N CA SING N N 33 VNM O4 C4 DOUB N N 34 VNM C5 C4 SING N N 35 VNM C5 C6 DOUB N N 36 VNM CA CT SING N N 37 VNM C4 N3 SING N N 38 VNM O2P P DOUB N N 39 VNM C6 N1 SING N N 40 VNM CT O1 DOUB N N 41 VNM CT 'O2"' SING N N 42 VNM "C5'" "O5'" SING N N 43 VNM "C5'" "C4'" SING N N 44 VNM "O5'" P SING N N 45 VNM P O3P SING N N 46 VNM P O1P SING N N 47 VNM N3 C2 SING N N 48 VNM "O4'" "C4'" SING N N 49 VNM "O4'" "C1'" SING N N 50 VNM N1 C2 SING N N 51 VNM N1 "C1'" SING N N 52 VNM "C4'" "C3'" SING N N 53 VNM C2 O2 DOUB N N 54 VNM "C1'" "C2'" SING N N 55 VNM "C2'" "C3'" SING N N 56 VNM "C3'" "O3'" SING N N 57 VNM C6 H6 SING N N 58 VNM C7 H71 SING N N 59 VNM C7 H72 SING N N 60 VNM C8 H81 SING N N 61 VNM C8 H82 SING N N 62 VNM N10 H101 SING N N 63 VNM C11 H1 SING N N 64 VNM C11 H2 SING N N 65 VNM C16 H161 SING N N 66 VNM C17 H171 SING N N 67 VNM N H SING N N 68 VNM CA HA SING N N 69 VNM CB HB2 SING N N 70 VNM CB HB3 SING N N 71 VNM CG HG2 SING N N 72 VNM CG HG3 SING N N 73 VNM OE2 H3 SING N N 74 VNM "C1'" "H1'" SING N N 75 VNM C13 H131 SING N N 76 VNM C14 H141 SING N N 77 VNM "C2'" H2*1 SING N N 78 VNM "C2'" H2*2 SING N N 79 VNM "C3'" "H3'" SING N N 80 VNM "C4'" H4* SING N N 81 VNM "C5'" H5*1 SING N N 82 VNM "C5'" H5*2 SING N N 83 VNM 'C6"' H61 SING N N 84 VNM C9 H92 SING N N 85 VNM C9 H91 SING N N 86 VNM N3 HN3 SING N N 87 VNM NA2 HA22 SING N N 88 VNM NA2 HA21 SING N N 89 VNM NA4 HA42 SING N N 90 VNM NA4 HA41 SING N N 91 VNM O1P H4 SING N N 92 VNM 'O2"' H5 SING N N 93 VNM "O3'" "HO3'" SING N N 94 VNM O3P H7 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 VNM SMILES ACDLabs 12.01 "C1(=O)N(C=C(C(N1)=O)CN2c4c(N)nc(nc4CCC2CNc3ccc(C(NC(C(=O)O)CCC(O)=O)=O)cc3)N)C5CC(O)C(COP(O)(=O)O)O5" VNM 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+/m0/s1" VNM InChIKey InChI 1.03 OYTZJQBUPHBEFY-GLOJMNGXSA-N VNM 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" VNM 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" VNM 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" VNM 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 VNM "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-({4-[({(6S)-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)" VNM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[4-[[(6~{S})-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 VNM "Create component" 2020-08-31 RCSB VNM "Initial release" 2021-04-21 RCSB ##