data_0KX
#
_chem_comp.id 0KX
_chem_comp.name "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H17 N4 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-02-06
_chem_comp.pdbx_modified_date 2012-05-04
_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 466.172
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 0KX
_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 4DL2
_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
0KX PG PG P 0 1 N N N 54.987 2.589 7.209 5.387 1.955 -0.387 PG 0KX 1
0KX O1G O1G O 0 1 N N N 54.705 1.700 8.382 6.000 1.561 -1.823 O1G 0KX 2
0KX O2G O2G O 0 1 N N N 54.845 1.780 5.983 6.322 1.533 0.680 O2G 0KX 3
0KX O3G O3G O 0 1 N N N 56.356 3.058 7.312 5.173 3.549 -0.314 O3G 0KX 4
0KX PB PB P 0 1 N N N 52.843 4.118 6.233 3.542 -0.277 0.244 PB 0KX 5
0KX O1B O1B O 0 1 N N N 52.211 5.423 6.660 4.144 -1.335 -0.810 O1B 0KX 6
0KX O2B O2B O 0 1 N N N 53.325 4.307 4.871 4.070 -0.572 1.595 O2B 0KX 7
0KX O3B O3B O 0 1 N N N 54.033 3.832 7.233 3.973 1.213 -0.186 O3B 0KX 8
0KX PA PA P 0 1 N N N 51.341 2.051 4.940 1.371 -1.940 0.706 PA 0KX 9
0KX O1A O1A O 0 1 N N N 52.715 1.761 4.122 1.906 -2.926 -0.259 O1A 0KX 10
0KX O2A O2A O 0 1 N N N 50.789 0.631 5.310 1.926 -2.276 2.180 O2A 0KX 11
0KX N3A N3A N 0 1 N N N 51.708 2.890 6.363 1.864 -0.394 0.260 N3A 0KX 12
0KX "O5'" "O5'" O 0 1 N N N 50.357 2.885 4.008 -0.238 -2.011 0.709 "O5'" 0KX 13
0KX "C5'" "C5'" C 0 1 N N N 50.810 3.931 3.182 -1.016 -2.072 -0.487 "C5'" 0KX 14
0KX "C4'" "C4'" C 0 1 N N R 49.955 5.079 3.129 -2.502 -2.129 -0.126 "C4'" 0KX 15
0KX "O4'" "O4'" O 0 1 N N N 48.630 4.631 2.742 -2.935 -0.865 0.422 "O4'" 0KX 16
0KX "C3'" "C3'" C 0 1 N N S 49.803 5.596 4.494 -3.358 -2.322 -1.398 "C3'" 0KX 17
0KX "O3'" "O3'" O 0 1 N N N 50.704 6.549 4.749 -3.715 -3.696 -1.558 "O3'" 0KX 18
0KX "C2'" "C2'" C 0 1 N N N 48.437 6.133 4.527 -4.615 -1.462 -1.139 "C2'" 0KX 19
0KX "C1'" "C1'" C 0 1 N N R 47.687 5.280 3.566 -4.370 -0.852 0.259 "C1'" 0KX 20
0KX N1 N1 N 0 1 N N N 46.849 4.382 4.318 -4.877 0.522 0.312 N1 0KX 21
0KX C2 C2 C 0 1 N N N 45.557 4.671 4.546 -4.356 1.459 -0.502 C2 0KX 22
0KX N3 N3 N 0 1 N N N 44.769 3.840 5.230 -4.797 2.715 -0.475 N3 0KX 23
0KX C4 C4 C 0 1 N N N 45.244 2.679 5.722 -5.765 3.076 0.358 C4 0KX 24
0KX C5 C5 C 0 1 N N N 46.574 2.362 5.497 -6.332 2.118 1.223 C5 0KX 25
0KX C6 C6 C 0 1 N N N 47.377 3.242 4.778 -5.877 0.843 1.180 C6 0KX 26
0KX O2 O2 O 0 1 N N N 45.105 5.657 4.133 -3.464 1.153 -1.276 O2 0KX 27
0KX N4 N4 N 0 1 N N N 44.432 1.819 6.439 -6.212 4.376 0.377 N4 0KX 28
0KX H1 H1 H 0 1 N N N 54.500 0.825 8.075 5.440 1.809 -2.571 H1 0KX 29
0KX H2 H2 H 0 1 N N N 56.856 2.741 6.569 5.986 4.061 -0.428 H2 0KX 30
0KX H3 H3 H 0 1 N N N 52.274 6.053 5.952 3.840 -1.201 -1.718 H3 0KX 31
0KX H4 H4 H 0 1 N N N 51.377 -0.035 4.974 1.615 -1.669 2.865 H4 0KX 32
0KX H5 H5 H 0 1 N N N 50.860 3.295 6.705 1.474 -0.134 -0.634 H5 0KX 33
0KX H6 H6 H 0 1 N N N 50.915 3.537 2.160 -0.823 -1.186 -1.092 H6 0KX 34
0KX H7 H7 H 0 1 N N N 51.794 4.256 3.552 -0.745 -2.964 -1.052 H7 0KX 35
0KX H8 H8 H 0 1 N N N 50.341 5.850 2.446 -2.689 -2.936 0.582 H8 0KX 36
0KX H9 H9 H 0 1 N N N 49.885 4.765 5.210 -2.822 -1.960 -2.277 H9 0KX 37
0KX H10 H10 H 0 1 N N N 50.586 6.868 5.636 -4.253 -3.874 -2.342 H10 0KX 38
0KX H11 H11 H 0 1 N N N 48.424 7.185 4.207 -4.701 -0.676 -1.889 H11 0KX 39
0KX H12 H12 H 0 1 N N N 48.010 6.051 5.537 -5.509 -2.085 -1.135 H12 0KX 40
0KX H13 H13 H 0 1 N N N 47.050 5.931 2.949 -4.845 -1.460 1.029 H13 0KX 41
0KX H14 H14 H 0 1 N N N 46.985 1.438 5.877 -7.121 2.395 1.907 H14 0KX 42
0KX H15 H15 H 0 1 N N N 48.415 3.007 4.593 -6.298 0.090 1.829 H15 0KX 43
0KX H16 H16 H 0 1 N N N 43.474 2.054 6.600 -5.819 5.033 -0.219 H16 0KX 44
0KX H17 H17 H 0 1 N N N 44.803 0.962 6.796 -6.920 4.637 0.987 H17 0KX 45
#
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
0KX "O4'" "C4'" SING N N 1
0KX "O4'" "C1'" SING N N 2
0KX "C4'" "C5'" SING N N 3
0KX "C4'" "C3'" SING N N 4
0KX "C5'" "O5'" SING N N 5
0KX "C1'" N1 SING N N 6
0KX "C1'" "C2'" SING N N 7
0KX "O5'" PA SING N N 8
0KX O1A PA DOUB N N 9
0KX O2 C2 DOUB N N 10
0KX N1 C2 SING N N 11
0KX N1 C6 SING N N 12
0KX "C3'" "C2'" SING N N 13
0KX "C3'" "O3'" SING N N 14
0KX C2 N3 SING N N 15
0KX C6 C5 DOUB N N 16
0KX O2B PB DOUB N N 17
0KX PA O2A SING N N 18
0KX PA N3A SING N N 19
0KX N3 C4 DOUB N N 20
0KX C5 C4 SING N N 21
0KX C4 N4 SING N N 22
0KX O2G PG DOUB N N 23
0KX PB N3A SING N N 24
0KX PB O1B SING N N 25
0KX PB O3B SING N N 26
0KX PG O3B SING N N 27
0KX PG O3G SING N N 28
0KX PG O1G SING N N 29
0KX O1G H1 SING N N 30
0KX O3G H2 SING N N 31
0KX O1B H3 SING N N 32
0KX O2A H4 SING N N 33
0KX N3A H5 SING N N 34
0KX "C5'" H6 SING N N 35
0KX "C5'" H7 SING N N 36
0KX "C4'" H8 SING N N 37
0KX "C3'" H9 SING N N 38
0KX "O3'" H10 SING N N 39
0KX "C2'" H11 SING N N 40
0KX "C2'" H12 SING N N 41
0KX "C1'" H13 SING N N 42
0KX C5 H14 SING N N 43
0KX C6 H15 SING N N 44
0KX N4 H16 SING N N 45
0KX N4 H17 SING N N 46
#
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
0KX SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)NP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2O"
0KX InChI InChI 1.03 "InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1"
0KX InChIKey InChI 1.03 STYMTWKSQLVXJN-SHYZEUOFSA-N
0KX SMILES_CANONICAL CACTVS 3.370 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2"
0KX SMILES CACTVS 3.370 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)N[P](O)(=O)O[P](O)(O)=O)O2"
0KX SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O"
0KX SMILES "OpenEye OEToolkits" 1.7.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=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
0KX "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine"
0KX "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-N-[oxidanyl(phosphonooxy)phosphoryl]phosphonamidic 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
0KX "Create component" 2012-02-06 RCSB
#