data_2JV # _chem_comp.id 2JV _chem_comp.name "N-(8-aminopyren-1-yl)-2'-deoxy-5'-O-(trihydroxy-lambda~5~-phosphanyl)guanosine" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C26 H25 N6 O7 P" _chem_comp.mon_nstd_parent_comp_id DG _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-11-12 _chem_comp.pdbx_modified_date 2015-09-11 _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 564.486 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 2JV _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 4NF3 _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 2JV C2 C2 C 0 1 N N N 12.453 70.531 47.597 1.523 2.878 -0.465 C2 2JV 1 2JV C5 C5 C 0 1 Y N N 12.644 69.628 50.205 -0.971 3.766 0.124 C5 2JV 2 2JV C6 C6 C 0 1 N N N 11.369 70.106 49.648 0.080 4.695 -0.062 C6 2JV 3 2JV C4 C4 C 0 1 Y N N 13.804 69.646 49.314 -0.689 2.401 -0.002 C4 2JV 4 2JV O6 O6 O 0 1 N N N 10.337 70.118 50.346 -0.120 5.893 0.039 O6 2JV 5 2JV N7 N7 N 0 1 Y N N 13.062 69.156 51.387 -2.289 3.879 0.419 N7 2JV 6 2JV C8 C8 C 0 1 Y N N 14.382 68.886 51.268 -2.820 2.693 0.479 C8 2JV 7 2JV N9 N9 N 0 1 Y N N 14.830 69.186 50.027 -1.869 1.747 0.226 N9 2JV 8 2JV CAQ CAQ C 0 1 N N R 16.204 69.045 49.458 -2.075 0.297 0.201 CAQ 2JV 9 2JV OAP OAP O 0 1 N N N 16.573 67.655 49.368 -3.460 0.004 -0.046 OAP 2JV 10 2JV CAR CAR C 0 1 N N N 17.271 69.768 50.276 -1.717 -0.306 1.573 CAR 2JV 11 2JV CAT CAT C 0 1 N N S 18.379 68.741 50.349 -3.021 -1.003 2.033 CAT 2JV 12 2JV OAS OAS O 0 1 N N N 19.265 68.901 49.229 -2.737 -2.263 2.644 OAS 2JV 13 2JV CAU CAU C 0 1 N N R 17.642 67.416 50.278 -3.776 -1.196 0.693 CAU 2JV 14 2JV CAV CAV C 0 1 N N N 16.994 67.066 51.601 -5.283 -1.298 0.935 CAV 2JV 15 2JV OAB OAB O 0 1 N N N 17.773 66.262 52.455 -5.954 -1.487 -0.313 OAB 2JV 16 2JV PAD PAD P 0 1 N N N 17.291 66.281 53.990 -7.663 -1.618 -0.176 PAD 2JV 17 2JV OAC OAC O 0 1 N N N 18.365 65.743 54.863 -8.624 -1.849 -1.584 OAC 2JV 18 2JV OAA OAA O 0 1 N N N 16.914 67.795 54.409 -7.518 -3.323 0.003 OAA 2JV 19 2JV N1 N1 N 0 1 N N N 11.350 70.522 48.384 1.311 4.220 -0.355 N1 2JV 20 2JV N3 N3 N 0 1 N N N 13.655 70.094 48.046 0.555 2.006 -0.294 N3 2JV 21 2JV N2 N2 N 0 1 N N N 12.267 70.997 46.333 2.783 2.426 -0.768 N2 2JV 22 2JV CBD CBD C 0 1 Y N N 13.185 71.128 45.324 2.991 1.107 -1.000 CBD 2JV 23 2JV CBC CBC C 0 1 Y N N 12.711 71.358 44.013 4.052 0.530 -0.486 CBC 2JV 24 2JV CAX CAX C 0 1 Y N N 13.612 71.448 42.947 4.276 -0.906 -0.733 CAX 2JV 25 2JV CBG CBG C 0 1 Y N N 14.975 71.292 43.184 3.304 -1.656 -1.551 CBG 2JV 26 2JV CBF CBF C 0 1 Y N N 15.442 71.053 44.472 2.146 -0.917 -2.083 CBF 2JV 27 2JV CBE CBE C 0 1 Y N N 14.563 70.968 45.532 2.020 0.366 -1.816 CBE 2JV 28 2JV CBB CBB C 0 1 Y N N 11.340 71.518 43.738 5.023 1.278 0.330 CBB 2JV 29 2JV CBA CBA C 0 1 Y N N 10.887 71.746 42.439 6.079 0.668 0.833 CBA 2JV 30 2JV CAZ CAZ C 0 1 Y N N 11.785 71.840 41.372 6.297 -0.767 0.582 CAZ 2JV 31 2JV CAY CAY C 0 1 Y N N 13.149 71.692 41.632 5.320 -1.510 -0.235 CAY 2JV 32 2JV CBM CBM C 0 1 Y N N 11.365 72.078 40.059 7.336 -1.404 1.068 CBM 2JV 33 2JV NAW NAW N 0 1 N N N 10.066 72.227 39.746 8.233 -0.720 1.819 NAW 2JV 34 2JV CBL CBL C 0 1 Y N N 12.293 72.167 39.014 7.556 -2.835 0.823 CBL 2JV 35 2JV CBK CBK C 0 1 Y N N 13.642 72.011 39.282 6.734 -3.570 0.106 CBK 2JV 36 2JV CBJ CBJ C 0 1 Y N N 14.066 71.771 40.582 5.538 -2.947 -0.487 CBJ 2JV 37 2JV CBI CBI C 0 1 Y N N 15.441 71.622 40.845 4.676 -3.618 -1.212 CBI 2JV 38 2JV CBH CBH C 0 1 Y N N 15.890 71.386 42.140 3.493 -2.934 -1.777 CBH 2JV 39 2JV H1 H1 H 0 1 N N N 14.997 68.484 52.059 -3.858 2.488 0.697 H1 2JV 40 2JV H2 H2 H 0 1 N N N 16.204 69.479 48.447 -1.454 -0.152 -0.574 H2 2JV 41 2JV H3 H3 H 0 1 N N N 17.610 70.683 49.768 -0.911 -1.033 1.472 H3 2JV 42 2JV H4 H4 H 0 1 N N N 16.898 70.023 51.279 -1.437 0.480 2.274 H4 2JV 43 2JV H5 H5 H 0 1 N N N 18.918 68.827 51.304 -3.586 -0.363 2.710 H5 2JV 44 2JV H6 H6 H 0 1 N N N 19.959 68.254 49.279 -2.189 -2.201 3.439 H6 2JV 45 2JV H7 H7 H 0 1 N N N 18.310 66.610 49.940 -3.409 -2.078 0.169 H7 2JV 46 2JV H8 H8 H 0 1 N N N 16.769 68.005 52.129 -5.490 -2.145 1.589 H8 2JV 47 2JV H9 H9 H 0 1 N N N 16.057 66.530 51.390 -5.640 -0.381 1.404 H9 2JV 48 2JV H10 H10 H 0 1 N N N 18.075 65.757 55.768 -9.572 -1.911 -1.408 H10 2JV 49 2JV H11 H11 H 0 1 N N N 16.629 67.812 55.315 -8.363 -3.780 0.115 H11 2JV 50 2JV H13 H13 H 0 1 N N N 11.335 71.282 46.110 3.524 3.049 -0.816 H13 2JV 51 2JV H14 H14 H 0 1 N N N 16.501 70.933 44.644 1.408 -1.423 -2.687 H14 2JV 52 2JV H15 H15 H 0 1 N N N 14.938 70.777 46.527 1.164 0.894 -2.208 H15 2JV 53 2JV H16 H16 H 0 1 N N N 10.627 71.463 44.547 4.870 2.330 0.518 H16 2JV 54 2JV H17 H17 H 0 1 N N N 9.828 71.851 42.255 6.787 1.223 1.430 H17 2JV 55 2JV H18 H18 H 0 1 N N N 9.511 72.143 40.574 8.102 0.225 1.990 H18 2JV 56 2JV H19 H19 H 0 1 N N N 9.923 73.129 39.339 9.007 -1.177 2.186 H19 2JV 57 2JV H20 H20 H 0 1 N N N 11.958 72.356 38.005 8.429 -3.305 1.252 H20 2JV 58 2JV H21 H21 H 0 1 N N N 14.364 72.076 38.481 6.935 -4.620 -0.049 H21 2JV 59 2JV H22 H22 H 0 1 N N N 16.152 71.691 40.035 4.829 -4.671 -1.395 H22 2JV 60 2JV H23 H23 H 0 1 N N N 16.947 71.276 42.335 2.783 -3.487 -2.375 H23 2JV 61 2JV OP3 OP3 O 0 1 N Y N ? ? ? -7.808 0.086 -0.356 OP3 2JV 62 2JV H24 H24 H 0 1 N N N ? ? ? -8.303 -1.534 1.144 H24 2JV 63 2JV H25 H25 H 0 1 N N N 10.484 70.842 47.998 2.047 4.838 -0.487 H25 2JV 64 2JV H12 H12 H 0 1 N N N ? ? ? -8.720 0.408 -0.326 H12 2JV 65 # 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 2JV CBL CBK DOUB Y N 1 2JV CBL CBM SING Y N 2 2JV CBK CBJ SING Y N 3 2JV NAW CBM SING N N 4 2JV CBM CAZ DOUB Y N 5 2JV CBJ CBI DOUB Y N 6 2JV CBJ CAY SING Y N 7 2JV CBI CBH SING Y N 8 2JV CAZ CAY SING Y N 9 2JV CAZ CBA SING Y N 10 2JV CAY CAX DOUB Y N 11 2JV CBH CBG DOUB Y N 12 2JV CBA CBB DOUB Y N 13 2JV CAX CBG SING Y N 14 2JV CAX CBC SING Y N 15 2JV CBG CBF SING Y N 16 2JV CBB CBC SING Y N 17 2JV CBC CBD DOUB Y N 18 2JV CBF CBE DOUB Y N 19 2JV CBD CBE SING Y N 20 2JV CBD N2 SING N N 21 2JV N2 C2 SING N N 22 2JV C2 N3 DOUB N N 23 2JV C2 N1 SING N N 24 2JV N3 C4 SING N N 25 2JV N1 C6 SING N N 26 2JV OAS CAT SING N N 27 2JV C4 N9 SING Y N 28 2JV C4 C5 DOUB Y N 29 2JV OAP CAQ SING N N 30 2JV OAP CAU SING N N 31 2JV CAQ N9 SING N N 32 2JV CAQ CAR SING N N 33 2JV C6 C5 SING N N 34 2JV C6 O6 DOUB N N 35 2JV N9 C8 SING Y N 36 2JV C5 N7 SING Y N 37 2JV CAR CAT SING N N 38 2JV CAU CAT SING N N 39 2JV CAU CAV SING N N 40 2JV C8 N7 DOUB Y N 41 2JV CAV OAB SING N N 42 2JV OAB PAD SING N N 43 2JV PAD OAA SING N N 44 2JV PAD OAC SING N N 45 2JV C8 H1 SING N N 46 2JV CAQ H2 SING N N 47 2JV CAR H3 SING N N 48 2JV CAR H4 SING N N 49 2JV CAT H5 SING N N 50 2JV OAS H6 SING N N 51 2JV CAU H7 SING N N 52 2JV CAV H8 SING N N 53 2JV CAV H9 SING N N 54 2JV OAC H10 SING N N 55 2JV OAA H11 SING N N 56 2JV N2 H13 SING N N 57 2JV CBF H14 SING N N 58 2JV CBE H15 SING N N 59 2JV CBB H16 SING N N 60 2JV CBA H17 SING N N 61 2JV NAW H18 SING N N 62 2JV NAW H19 SING N N 63 2JV CBL H20 SING N N 64 2JV CBK H21 SING N N 65 2JV CBI H22 SING N N 66 2JV CBH H23 SING N N 67 2JV PAD OP3 SING N N 68 2JV PAD H24 SING N N 69 2JV N1 H25 SING N N 70 2JV OP3 H12 SING N N 71 # 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 2JV SMILES ACDLabs 12.01 "O=C5c6ncn(c6N=C(Nc4c1c3c2c(cc1)c(N)ccc2ccc3cc4)N5)C7OC(C(O)C7)COP(O)(O)O" 2JV InChI InChI 1.03 "InChI=1S/C26H25N6O7P/c27-16-7-3-12-1-2-13-4-8-17(15-6-5-14(16)21(12)22(13)15)29-26-30-24-23(25(34)31-26)28-11-32(24)20-9-18(33)19(39-20)10-38-40(35,36)37/h1-8,11,18-20,33,35-37,40H,9-10,27H2,(H2,29,30,31,34)/t18-,19+,20+/m0/s1" 2JV InChIKey InChI 1.03 AFDQKKAHJUXROA-XUVXKRRUSA-N 2JV SMILES_CANONICAL CACTVS 3.385 "Nc1ccc2ccc3ccc(NC4=Nc5n(cnc5C(=O)N4)[C@H]6C[C@H](O)[C@@H](CO[PH](O)(O)O)O6)c7ccc1c2c37" 2JV SMILES CACTVS 3.385 "Nc1ccc2ccc3ccc(NC4=Nc5n(cnc5C(=O)N4)[CH]6C[CH](O)[CH](CO[PH](O)(O)O)O6)c7ccc1c2c37" 2JV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1cc2ccc(c3c2c4c1ccc(c4cc3)N)NC5=Nc6c(ncn6[C@H]7C[C@@H]([C@H](O7)COP(O)(O)O)O)C(=O)N5" 2JV SMILES "OpenEye OEToolkits" 1.7.6 "c1cc2ccc(c3c2c4c1ccc(c4cc3)N)NC5=Nc6c(ncn6C7CC(C(O7)COP(O)(O)O)O)C(=O)N5" # 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 2JV "SYSTEMATIC NAME" ACDLabs 12.01 "N-(8-aminopyren-1-yl)-2'-deoxy-5'-O-(trihydroxy-lambda~5~-phosphanyl)guanosine" 2JV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-[(8-azanylpyren-1-yl)amino]-9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1H-purin-6-one" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 2JV "Create component" 2013-11-12 RCSB 2JV "Other modification" 2013-12-13 RCSB 2JV "Initial release" 2015-09-16 RCSB #