data_3JY
#
_chem_comp.id 3JY
_chem_comp.name "[(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H19 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-08-28
_chem_comp.pdbx_modified_date 2015-03-06
_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 362.272
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 3JY
_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 4R5P
_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
3JY N21 N21 N 0 1 N N N -28.781 -49.937 -5.547 -4.487 1.052 0.983 N21 3JY 1
3JY N6 N6 N 0 1 N N N -26.994 -48.516 -6.002 -3.118 -0.448 -0.183 N6 3JY 2
3JY C2 C2 C 0 1 N N N -29.542 -48.903 -5.115 -5.500 0.822 0.124 C2 3JY 3
3JY C22 C22 C 0 1 N N N -27.529 -49.743 -5.983 -3.309 0.420 0.827 C22 3JY 4
3JY C7 C7 C 0 1 N N R -25.613 -48.328 -6.514 -1.825 -1.121 -0.327 C7 3JY 5
3JY C20 C20 C 0 1 N N N -25.616 -47.265 -7.579 -0.682 -0.081 -0.430 C20 3JY 6
3JY C10 C10 C 0 1 N N S -24.504 -46.306 -7.265 0.557 -0.888 0.032 C10 3JY 7
3JY C12 C12 C 0 1 N N R -25.930 -44.335 -7.170 2.642 0.210 -0.408 C12 3JY 8
3JY C13 C13 C 0 1 N N N -25.883 -43.201 -6.220 3.195 1.599 -0.217 C13 3JY 9
3JY C9 C9 C 0 1 N N N -24.216 -46.488 -5.805 0.025 -1.778 1.174 C9 3JY 10
3JY C8 C8 C 0 1 N N N -24.570 -47.905 -5.476 -1.490 -1.926 0.946 C8 3JY 11
3JY C5 C5 C 0 1 N N N -27.709 -47.447 -5.588 -4.125 -0.718 -1.069 C5 3JY 12
3JY C3 C3 C 0 1 N N N -29.014 -47.617 -5.123 -5.315 -0.094 -0.939 C3 3JY 13
3JY C4 C4 C 0 1 N N N -29.844 -46.464 -4.645 -6.436 -0.379 -1.906 C4 3JY 14
3JY O1 O1 O 0 1 N N N -30.801 -49.100 -4.676 -6.565 1.397 0.262 O1 3JY 15
3JY O11 O11 O 0 1 N N N -24.773 -45.014 -7.522 1.574 -0.009 0.516 O11 3JY 16
3JY O18 O18 O 0 1 N N N -25.266 -43.930 -9.765 4.735 -0.628 1.084 O18 3JY 17
3JY O19 O19 O 0 1 N N N -27.689 -44.307 -9.338 3.302 -2.466 0.115 O19 3JY 18
3JY O17 O17 O 0 1 N N N -26.595 -42.119 -8.634 4.938 -1.066 -1.394 O17 3JY 19
3JY O14 O14 O 0 1 N N N -25.194 -42.225 -6.381 2.500 2.466 0.256 O14 3JY 20
3JY O15 O15 O 0 1 N N N -26.586 -43.229 -5.243 4.460 1.872 -0.573 O15 3JY 21
3JY O23 O23 O 0 1 N N N -26.890 -50.667 -6.351 -2.404 0.638 1.609 O23 3JY 22
3JY P16 P16 P 0 1 N N N -26.380 -43.641 -8.816 3.960 -1.015 -0.116 P16 3JY 23
3JY H1 H1 H 0 1 N N N -29.161 -50.862 -5.540 -4.606 1.679 1.714 H1 3JY 24
3JY H2 H2 H 0 1 N N N -25.277 -49.272 -6.968 -1.830 -1.773 -1.200 H2 3JY 25
3JY H3 H3 H 0 1 N N N -26.580 -46.735 -7.578 -0.560 0.259 -1.459 H3 3JY 26
3JY H4 H4 H 0 1 N N N -25.450 -47.722 -8.566 -0.864 0.762 0.237 H4 3JY 27
3JY H5 H5 H 0 1 N N N -23.614 -46.625 -7.828 0.939 -1.502 -0.784 H5 3JY 28
3JY H6 H6 H 0 1 N N N -26.741 -45.027 -6.898 2.268 0.105 -1.427 H6 3JY 29
3JY H7 H7 H 0 1 N N N -23.150 -46.305 -5.602 0.505 -2.756 1.140 H7 3JY 30
3JY H8 H8 H 0 1 N N N -24.827 -45.795 -5.208 0.212 -1.302 2.136 H8 3JY 31
3JY H9 H9 H 0 1 N N N -24.992 -47.969 -4.462 -2.037 -1.523 1.798 H9 3JY 32
3JY H10 H10 H 0 1 N N N -23.680 -48.548 -5.544 -1.745 -2.976 0.801 H10 3JY 33
3JY H11 H11 H 0 1 N N N -27.271 -46.460 -5.617 -3.964 -1.417 -1.877 H11 3JY 34
3JY H12 H12 H 0 1 N N N -30.832 -46.829 -4.327 -7.038 -1.206 -1.530 H12 3JY 35
3JY H13 H13 H 0 1 N N N -29.342 -45.978 -3.795 -7.062 0.508 -2.008 H13 3JY 36
3JY H14 H14 H 0 1 N N N -29.967 -45.738 -5.462 -6.020 -0.643 -2.877 H14 3JY 37
3JY H15 H15 H 0 1 N N N -27.511 -44.761 -10.153 2.825 -2.553 0.952 H15 3JY 38
3JY H16 H16 H 0 1 N N N -25.969 -41.644 -9.168 5.370 -0.224 -1.593 H16 3JY 39
3JY C1 C1 C 0 1 N N N ? ? ? 4.926 3.231 -0.360 C1 3JY 40
3JY H17 H17 H 0 1 N N N ? ? ? 4.306 3.921 -0.932 H17 3JY 41
3JY H18 H18 H 0 1 N N N ? ? ? 4.861 3.475 0.700 H18 3JY 42
3JY H19 H19 H 0 1 N N N ? ? ? 5.962 3.315 -0.690 H19 3JY 43
#
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
3JY O18 P16 DOUB N N 1
3JY O19 P16 SING N N 2
3JY P16 O17 SING N N 3
3JY P16 C12 SING N N 4
3JY C20 C10 SING N N 5
3JY C20 C7 SING N N 6
3JY O11 C10 SING N N 7
3JY O11 C12 SING N N 8
3JY C10 C9 SING N N 9
3JY C12 C13 SING N N 10
3JY C7 N6 SING N N 11
3JY C7 C8 SING N N 12
3JY O14 C13 DOUB N N 13
3JY O23 C22 DOUB N N 14
3JY C13 O15 SING N N 15
3JY N6 C22 SING N N 16
3JY N6 C5 SING N N 17
3JY C22 N21 SING N N 18
3JY C9 C8 SING N N 19
3JY C5 C3 DOUB N N 20
3JY N21 C2 SING N N 21
3JY C3 C2 SING N N 22
3JY C3 C4 SING N N 23
3JY C2 O1 DOUB N N 24
3JY N21 H1 SING N N 25
3JY C7 H2 SING N N 26
3JY C20 H3 SING N N 27
3JY C20 H4 SING N N 28
3JY C10 H5 SING N N 29
3JY C12 H6 SING N N 30
3JY C9 H7 SING N N 31
3JY C9 H8 SING N N 32
3JY C8 H9 SING N N 33
3JY C8 H10 SING N N 34
3JY C5 H11 SING N N 35
3JY C4 H12 SING N N 36
3JY C4 H13 SING N N 37
3JY C4 H14 SING N N 38
3JY O19 H15 SING N N 39
3JY O17 H16 SING N N 40
3JY O15 C1 SING N N 41
3JY C1 H17 SING N N 42
3JY C1 H18 SING N N 43
3JY C1 H19 SING N N 44
#
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
3JY SMILES ACDLabs 12.01 "O=C(OC)C(OC2CC(N1C=C(C(=O)NC1=O)C)CC2)P(=O)(O)O"
3JY InChI InChI 1.03 "InChI=1S/C13H19N2O8P/c1-7-6-15(13(18)14-10(7)16)8-3-4-9(5-8)23-12(11(17)22-2)24(19,20)21/h6,8-9,12H,3-5H2,1-2H3,(H,14,16,18)(H2,19,20,21)/t8-,9+,12-/m1/s1"
3JY InChIKey InChI 1.03 VZWKSNLNIFIGPO-VDDIYKPWSA-N
3JY SMILES_CANONICAL CACTVS 3.385 "COC(=O)[C@H](O[C@H]1CC[C@H](C1)N2C=C(C)C(=O)NC2=O)[P](O)(O)=O"
3JY SMILES CACTVS 3.385 "COC(=O)[CH](O[CH]1CC[CH](C1)N2C=C(C)C(=O)NC2=O)[P](O)(O)=O"
3JY SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)[C@@H]2CC[C@@H](C2)O[C@@H](C(=O)OC)P(=O)(O)O"
3JY SMILES "OpenEye OEToolkits" 1.7.6 "CC1=CN(C(=O)NC1=O)C2CCC(C2)OC(C(=O)OC)P(=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
3JY "SYSTEMATIC NAME" ACDLabs 12.01 "[(1R)-2-methoxy-1-{[(1S,3R)-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}-2-oxoethyl]phosphonic acid"
3JY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(1R)-2-methoxy-1-[(1S,3R)-3-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]cyclopentyl]oxy-2-oxidanylidene-ethyl]phosphonic 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
3JY "Create component" 2014-08-28 RCSB
3JY "Initial release" 2015-03-11 RCSB
#