data_VNR
#
_chem_comp.id VNR
_chem_comp.name "1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H35 N4 O16 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2011-06-15
_chem_comp.pdbx_modified_date 2011-10-28
_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 716.462
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VNR
_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 3B03
_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
VNR P P P 0 1 N N N 28.509 41.464 17.751 9.629 -2.083 -0.197 P VNR 1
VNR N1 N1 N 0 1 N N N 20.580 44.161 20.282 2.001 2.917 -0.422 N1 VNR 2
VNR C2 C2 C 0 1 N N N 19.387 44.133 20.913 1.919 4.233 -0.191 C2 VNR 3
VNR O2 O2 O 0 1 N N N 19.381 44.091 22.155 2.794 4.964 -0.616 O2 VNR 4
VNR N3 N3 N 0 1 N N N 18.241 44.385 20.246 0.898 4.770 0.498 N3 VNR 5
VNR C4 C4 C 0 1 N N N 18.190 44.381 18.901 -0.180 4.033 0.823 C4 VNR 6
VNR O4 O4 O 0 1 N N N 17.083 44.479 18.317 -1.068 4.526 1.484 O4 VNR 7
VNR N5 N5 N 0 1 N N N 19.534 43.950 16.897 -0.769 1.737 1.455 N5 VNR 8
VNR C6 C6 C 0 1 Y N N 20.565 44.067 14.798 -1.564 -0.522 1.835 C6 VNR 9
VNR C7 C7 C 0 1 Y N N 21.634 43.514 14.126 -1.468 -1.880 1.583 C7 VNR 10
VNR C8 C8 C 0 1 Y N N 22.953 43.457 14.814 -0.494 -2.360 0.727 C8 VNR 11
VNR C9 C9 C 0 1 Y N N 23.011 43.540 16.190 0.396 -1.491 0.122 C9 VNR 12
VNR "C1'" "C1'" C 0 1 N N N 23.066 44.105 19.123 2.368 0.234 -0.967 "C1'" VNR 13
VNR C10 C10 C 0 1 N N N 20.625 44.253 18.932 1.040 2.092 -0.105 C10 VNR 14
VNR N10 N10 N 0 1 N N N 21.855 43.980 18.306 1.220 0.755 -0.221 N10 VNR 15
VNR C11 C11 C 0 1 N N N 19.362 46.074 17.582 -1.278 2.535 -0.791 C11 VNR 16
VNR C12 C12 C 0 1 N N N 17.452 48.191 17.792 -4.389 1.331 -0.710 C12 VNR 17
VNR C13 C13 C 0 1 N N N 18.438 48.073 18.964 -3.588 2.099 0.344 C13 VNR 18
VNR C14 C14 C 0 1 N N N 19.576 47.160 18.582 -2.626 3.036 -0.341 C14 VNR 19
VNR C15 C15 C 0 1 N N N 20.822 47.262 19.029 -2.962 4.286 -0.544 C15 VNR 20
VNR O15 O15 O 0 1 N N N 17.295 49.549 17.344 -5.301 0.442 -0.061 O15 VNR 21
VNR C16 C16 C 0 1 N N N 21.223 48.294 20.035 -4.310 4.786 -0.094 C16 VNR 22
VNR O1P O1P O 0 1 N N N 28.846 39.995 17.916 10.540 -2.395 1.093 O1P VNR 23
VNR "C2'" "C2'" C 0 1 N N S 23.695 42.711 19.170 3.554 0.053 -0.018 "C2'" VNR 24
VNR "O2'" "O2'" O 0 1 N N N 22.804 41.846 19.859 3.896 1.314 0.562 "O2'" VNR 25
VNR O22 O22 O 0 1 N N N 12.586 48.795 17.516 -8.662 -2.873 -1.212 O22 VNR 26
VNR O2P O2P O 0 1 N N N 29.745 42.316 17.719 10.372 -1.001 -1.130 O2P VNR 27
VNR "C3'" "C3'" C 0 1 N N S 25.065 42.707 19.851 4.753 -0.491 -0.797 "C3'" VNR 28
VNR "O3'" "O3'" O 0 1 N N N 24.914 43.075 21.236 4.411 -1.752 -1.377 "O3'" VNR 29
VNR O33 O33 O 0 1 N N N 13.127 51.043 18.581 -8.865 -3.051 1.297 O33 VNR 30
VNR O3P O3P O 0 1 N N N 27.506 41.776 16.682 9.415 -3.331 -0.963 O3P VNR 31
VNR "C4'" "C4'" C 0 1 N N R 26.063 43.642 19.171 5.939 -0.672 0.153 "C4'" VNR 32
VNR "O4'" "O4'" O 0 1 N N N 25.805 43.618 17.758 6.281 0.588 0.733 "O4'" VNR 33
VNR O44 O44 O 0 1 N N N 13.164 48.923 19.975 -6.817 -4.083 0.012 O44 VNR 34
VNR C4A C4A C 0 1 N N R 19.445 44.658 18.139 -0.291 2.609 0.376 C4A VNR 35
VNR "C5'" "C5'" C 0 1 N N N 27.532 43.259 19.466 7.138 -1.217 -0.626 "C5'" VNR 36
VNR "O5'" "O5'" O 0 1 N N N 27.810 41.885 19.146 8.208 -1.495 0.279 "O5'" VNR 37
VNR P55 P55 P 0 1 N N N 13.321 49.538 18.600 -7.875 -2.870 0.041 P55 VNR 38
VNR C5A C5A C 0 1 Y N N 20.630 44.132 16.172 -0.682 0.352 1.227 C5A VNR 39
VNR O66 O66 O 0 1 N N N 14.906 49.323 18.255 -7.086 -1.473 0.175 O66 VNR 40
VNR O77 O77 O 0 1 N N N 16.118 51.600 18.249 -7.369 0.366 -1.682 O77 VNR 41
VNR C7M C7M C 0 1 N N N 21.576 43.480 12.617 -2.427 -2.837 2.243 C7M VNR 42
VNR O88 O88 O 0 1 N N N 15.329 50.499 16.027 -5.532 -1.361 -1.811 O88 VNR 43
VNR C8M C8M C 0 1 N N N 24.209 43.050 14.070 -0.400 -3.838 0.452 C8M VNR 44
VNR P99 P99 P 0 1 N N N 15.885 50.343 17.423 -6.305 -0.525 -0.865 P99 VNR 45
VNR C9A C9A C 0 1 Y N N 21.913 44.001 16.888 0.310 -0.129 0.370 C9A VNR 46
VNR HN3 HN3 H 0 1 N N N 17.408 44.580 20.764 0.938 5.702 0.764 HN3 VNR 47
VNR HN5 HN5 H 0 1 N N N 19.486 42.975 17.113 -1.127 2.097 2.282 HN5 VNR 48
VNR H6 H6 H 0 1 N N N 19.703 44.438 14.263 -2.325 -0.148 2.504 H6 VNR 49
VNR H9 H9 H 0 1 N N N 23.907 43.247 16.716 1.156 -1.872 -0.543 H9 VNR 50
VNR "H1'" "H1'" H 0 1 N N N 23.762 44.828 18.674 2.107 -0.728 -1.410 "H1'" VNR 51
VNR "H1'A" "H1'A" H 0 0 N N N 22.815 44.450 20.137 2.638 0.936 -1.756 "H1'A" VNR 52
VNR H11 H11 H 0 1 N N N 18.357 46.206 17.156 -1.368 1.502 -1.126 H11 VNR 53
VNR H11A H11A H 0 0 N N N 20.138 46.174 16.809 -0.916 3.153 -1.612 H11A VNR 54
VNR H12 H12 H 0 1 N N N 17.832 47.588 16.954 -4.945 2.035 -1.328 H12 VNR 55
VNR H12A H12A H 0 0 N N N 16.472 47.816 18.121 -3.707 0.757 -1.337 H12A VNR 56
VNR H13 H13 H 0 1 N N N 18.835 49.069 19.209 -4.270 2.673 0.971 H13 VNR 57
VNR H13A H13A H 0 0 N N N 17.916 47.660 19.840 -3.031 1.395 0.962 H13A VNR 58
VNR H15 H15 H 0 1 N N N 21.570 46.578 18.655 -2.273 4.957 -1.035 H15 VNR 59
VNR H16 H16 H 0 1 N N N 22.296 48.193 20.257 -5.095 4.218 -0.594 H16 VNR 60
VNR H16A H16A H 0 0 N N N 21.025 49.297 19.630 -4.403 4.661 0.985 H16A VNR 61
VNR H16B H16B H 0 0 N N N 20.643 48.151 20.958 -4.409 5.842 -0.347 H16B VNR 62
VNR HO1P HO1P H 0 0 N N N 28.348 39.483 17.290 11.413 -2.752 0.881 HO1P VNR 63
VNR "H2'" "H2'" H 0 1 N N N 23.859 42.368 18.138 3.284 -0.649 0.771 "H2'" VNR 64
VNR "HO2'" "HO2'" H 0 0 N N N 23.177 40.973 19.899 4.147 1.988 -0.083 "HO2'" VNR 65
VNR HO2P HO2P H 0 0 N N N 29.685 42.935 17.001 10.544 -0.156 -0.692 HO2P VNR 66
VNR "H3'" "H3'" H 0 1 N N N 25.471 41.688 19.768 5.023 0.210 -1.586 "H3'" VNR 67
VNR "HO3'" "HO3'" H 0 0 N N N 25.764 43.073 21.659 4.160 -2.427 -0.732 "HO3'" VNR 68
VNR HO33 HO33 H 0 0 N N N 12.553 51.280 17.862 -9.374 -3.873 1.282 HO33 VNR 69
VNR "H4'" "H4'" H 0 1 N N N 25.928 44.657 19.573 5.669 -1.374 0.942 "H4'" VNR 70
VNR "HO4'" "HO4'" H 0 0 N N N 26.379 42.986 17.341 6.532 1.263 0.088 "HO4'" VNR 71
VNR HO44 HO44 H 0 0 N N N 12.613 48.152 19.916 -6.265 -4.143 0.804 HO44 VNR 72
VNR "H5'" "H5'" H 0 1 N N N 28.190 43.900 18.860 6.850 -2.133 -1.141 "H5'" VNR 73
VNR "H5'A" "H5'A" H 0 0 N N N 27.726 43.415 20.537 7.463 -0.476 -1.357 "H5'A" VNR 74
VNR HO77 HO77 H 0 0 N N N 15.866 52.363 17.743 -7.911 0.940 -1.125 HO77 VNR 75
VNR H7M H7M H 0 1 N N N 21.832 44.472 12.217 -3.304 -2.966 1.609 H7M VNR 76
VNR H7MA H7MA H 0 0 N N N 22.293 42.736 12.239 -1.938 -3.800 2.386 H7MA VNR 77
VNR H7MB H7MB H 0 0 N N N 20.560 43.207 12.295 -2.732 -2.437 3.209 H7MB VNR 78
VNR H8M H8M H 0 1 N N N 24.744 43.950 13.734 -1.022 -4.089 -0.407 H8M VNR 79
VNR H8MA H8MA H 0 0 N N N 24.858 42.466 14.739 0.636 -4.104 0.241 H8MA VNR 80
VNR H8MB H8MB H 0 0 N N N 23.936 42.438 13.197 -0.746 -4.392 1.325 H8MB VNR 81
#
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
VNR P O1P SING N N 1
VNR P O2P SING N N 2
VNR P O3P DOUB N N 3
VNR P "O5'" SING N N 4
VNR N1 C2 SING N N 5
VNR N1 C10 DOUB N N 6
VNR C2 O2 DOUB N N 7
VNR C2 N3 SING N N 8
VNR N3 C4 SING N N 9
VNR C4 O4 DOUB N N 10
VNR C4 C4A SING N N 11
VNR N5 C4A SING N N 12
VNR N5 C5A SING N N 13
VNR C6 C7 SING Y N 14
VNR C6 C5A DOUB Y N 15
VNR C7 C8 DOUB Y N 16
VNR C7 C7M SING N N 17
VNR C8 C9 SING Y N 18
VNR C8 C8M SING N N 19
VNR C9 C9A DOUB Y N 20
VNR "C1'" N10 SING N N 21
VNR "C1'" "C2'" SING N N 22
VNR C10 N10 SING N N 23
VNR C10 C4A SING N N 24
VNR N10 C9A SING N N 25
VNR C11 C14 SING N N 26
VNR C11 C4A SING N N 27
VNR C12 C13 SING N N 28
VNR C12 O15 SING N N 29
VNR C13 C14 SING N N 30
VNR C14 C15 DOUB N Z 31
VNR C15 C16 SING N N 32
VNR O15 P99 SING N N 33
VNR "C2'" "O2'" SING N N 34
VNR "C2'" "C3'" SING N N 35
VNR O22 P55 DOUB N N 36
VNR "C3'" "O3'" SING N N 37
VNR "C3'" "C4'" SING N N 38
VNR O33 P55 SING N N 39
VNR "C4'" "O4'" SING N N 40
VNR "C4'" "C5'" SING N N 41
VNR O44 P55 SING N N 42
VNR "C5'" "O5'" SING N N 43
VNR P55 O66 SING N N 44
VNR C5A C9A SING Y N 45
VNR O66 P99 SING N N 46
VNR O77 P99 SING N N 47
VNR O88 P99 DOUB N N 48
VNR N3 HN3 SING N N 49
VNR N5 HN5 SING N N 50
VNR C6 H6 SING N N 51
VNR C9 H9 SING N N 52
VNR "C1'" "H1'" SING N N 53
VNR "C1'" "H1'A" SING N N 54
VNR C11 H11 SING N N 55
VNR C11 H11A SING N N 56
VNR C12 H12 SING N N 57
VNR C12 H12A SING N N 58
VNR C13 H13 SING N N 59
VNR C13 H13A SING N N 60
VNR C15 H15 SING N N 61
VNR C16 H16 SING N N 62
VNR C16 H16A SING N N 63
VNR C16 H16B SING N N 64
VNR O1P HO1P SING N N 65
VNR "C2'" "H2'" SING N N 66
VNR "O2'" "HO2'" SING N N 67
VNR O2P HO2P SING N N 68
VNR "C3'" "H3'" SING N N 69
VNR "O3'" "HO3'" SING N N 70
VNR O33 HO33 SING N N 71
VNR "C4'" "H4'" SING N N 72
VNR "O4'" "HO4'" SING N N 73
VNR O44 HO44 SING N N 74
VNR "C5'" "H5'" SING N N 75
VNR "C5'" "H5'A" SING N N 76
VNR O77 HO77 SING N N 77
VNR C7M H7M SING N N 78
VNR C7M H7MA SING N N 79
VNR C7M H7MB SING N N 80
VNR C8M H8M SING N N 81
VNR C8M H8MA SING N N 82
VNR C8M H8MB SING N N 83
#
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
VNR SMILES ACDLabs 12.01 "O=P(O)(O)OCC(O)C(O)C(O)CN2C3=NC(=O)NC(=O)C3(Nc1cc(c(cc12)C)C)CC(=C/C)/CCOP(=O)(O)OP(=O)(O)O"
VNR InChI InChI 1.03
;InChI=1S/C23H35N4O16P3/c1-4-14(5-6-41-46(39,40)43-45(36,37)38)9-23-20(24-22(32)25-21(23)31)27(16-8-13(3)12(2)7-15(16)26-23)10-17(28)19(30)18(29)11-42-44(33,34)35/h4,7-8,17-19,26,28-30H,5-6,9-11H2,1-3H3,(H,39,40)(H,25,31,32)(H2,33,34,35)(H2,36,37,38)/b14-4+/t17-,18+,19-,23+/m0/s1
;
VNR InChIKey InChI 1.03 OAOWJIIZSRFUAL-QCJQWHCGSA-N
VNR SMILES_CANONICAL CACTVS 3.370 "C/C=C(CCO[P](O)(=O)O[P](O)(O)=O)/C[C@@]12Nc3cc(C)c(C)cc3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O"
VNR SMILES CACTVS 3.370 "CC=C(CCO[P](O)(=O)O[P](O)(O)=O)C[C]12Nc3cc(C)c(C)cc3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)C1=NC(=O)NC2=O"
VNR SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C/C=C(\CCO[P@](=O)(O)OP(=O)(O)O)/C[C@]12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O"
VNR SMILES "OpenEye OEToolkits" 1.7.2 "CC=C(CCOP(=O)(O)OP(=O)(O)O)CC12C(=O)NC(=O)N=C1N(c3cc(c(cc3N2)C)C)CC(C(C(COP(=O)(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
VNR "SYSTEMATIC NAME" ACDLabs 12.01 "1-deoxy-1-[(4aR)-4a-[(2Z)-2-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)but-2-en-1-yl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-5-O-phosphono-D-ribitol"
VNR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "[(Z)-3-[[(4aR)-7,8-dimethyl-2,4-bis(oxidanylidene)-10-[(2S,3S,4R)-2,3,4-tris(oxidanyl)-5-phosphonooxy-pentyl]-5H-benzo[g]pteridin-4a-yl]methyl]pent-3-enyl] phosphono hydrogen 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
VNR "Create component" 2011-06-15 PDBJ
#