data_CDM
#
_chem_comp.id CDM
_chem_comp.name 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H25 N3 O14 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-05-22
_chem_comp.pdbx_modified_date 2011-06-04
_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 521.308
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CDM
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1INI
_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
CDM N1 N1 N 0 1 N N N 48.972 -15.320 32.129 -0.822 -0.498 -5.725 N1 CDM 1
CDM C2 C2 C 0 1 N N N 47.711 -15.455 32.800 -1.530 0.567 -5.309 C2 CDM 2
CDM N3 N3 N 0 1 N N N 47.604 -16.211 33.929 -2.757 0.801 -5.771 N3 CDM 3
CDM C4 C4 C 0 1 N N N 48.759 -16.883 34.469 -3.318 -0.020 -6.649 C4 CDM 4
CDM C5 C5 C 0 1 N N N 50.037 -16.794 33.854 -2.605 -1.149 -7.101 C5 CDM 5
CDM C6 C6 C 0 1 N N N 50.086 -16.008 32.703 -1.356 -1.370 -6.626 C6 CDM 6
CDM O2 O2 O 0 1 N N N 46.649 -14.916 32.422 -1.036 1.337 -4.502 O2 CDM 7
CDM N4 N4 N 0 1 N N N 48.591 -17.609 35.589 -4.588 0.228 -7.115 N4 CDM 8
CDM "C1'" C1* C 0 1 N N R 49.134 -14.495 30.891 0.527 -0.726 -5.203 "C1'" CDM 9
CDM "C2'" C2* C 0 1 N N R 50.055 -13.319 31.132 1.426 0.512 -5.447 "C2'" CDM 10
CDM "O2'" O2* O 0 1 N N N 49.351 -12.350 31.855 2.025 0.459 -6.744 "O2'" CDM 11
CDM "C3'" C3* C 0 1 N N S 50.529 -12.941 29.743 2.499 0.358 -4.337 "C3'" CDM 12
CDM "C4'" C4* C 0 1 N N R 50.336 -14.252 28.943 1.831 -0.561 -3.297 "C4'" CDM 13
CDM "O4'" O4* O 0 1 N N N 49.735 -15.210 29.845 0.502 -0.846 -3.764 "O4'" CDM 14
CDM "O3'" O3* O 0 1 N N N 49.677 -11.980 29.080 3.681 -0.246 -4.864 "O3'" CDM 15
CDM "C5'" C5* C 0 1 N N N 51.739 -14.679 28.527 1.765 0.147 -1.942 "C5'" CDM 16
CDM "O5'" O5* O 0 1 N N N 52.433 -15.082 29.674 1.138 -0.709 -0.986 "O5'" CDM 17
CDM PA PA P 0 1 N N R 54.056 -15.077 29.828 1.102 0.095 0.407 PA CDM 18
CDM O1A O1A O 0 1 N N N 54.488 -13.616 29.398 2.484 0.423 0.822 O1A CDM 19
CDM O2A O2A O 0 1 N N N 54.346 -15.458 31.470 0.261 1.454 0.220 O2A CDM 20
CDM O3A O3A O 0 1 N N N 54.497 -16.134 28.879 0.405 -0.816 1.535 O3A CDM 21
CDM PB PB P 0 1 N N S 54.585 -17.612 28.672 0.403 0.045 2.895 PB CDM 22
CDM O1B O1B O 0 1 N N N 53.337 -18.265 29.179 -0.426 1.405 2.667 O1B CDM 23
CDM O2B O2B O 0 1 N N N 55.839 -18.087 29.434 1.796 0.374 3.272 O2B CDM 24
CDM O3B O3B O 0 1 N N N 54.687 -18.200 27.300 -0.283 -0.810 4.073 O3B CDM 25
CDM C1M C1M C 0 1 N N N 53.636 -17.827 26.427 -0.254 0.003 5.246 C1M CDM 26
CDM C2M C2M C 0 1 N N R 54.008 -18.440 25.091 -0.896 -0.755 6.410 C2M CDM 27
CDM O2M O2M O 0 1 N N N 53.969 -19.941 25.302 -0.169 -1.961 6.650 O2M CDM 28
CDM C3M C3M C 0 1 N N S 53.045 -18.056 23.911 -0.865 0.117 7.666 C3M CDM 29
CDM C4M C4M C 0 1 N N N 53.514 -18.842 22.709 -1.507 -0.641 8.830 C4M CDM 30
CDM C5M C5M C 0 1 N N N 51.561 -18.347 24.271 0.584 0.456 8.017 C5M CDM 31
CDM O3M O3M O 0 1 N N N 53.182 -16.597 23.532 -1.592 1.323 7.426 O3M CDM 32
CDM O4M O4M O 0 1 N N N 54.967 -18.442 22.335 -1.478 0.173 10.003 O4M CDM 33
CDM H5 H5 H 0 1 N N N 50.934 -17.302 34.245 -3.048 -1.827 -7.816 H5 CDM 34
CDM H6 H6 H 0 1 N N N 51.071 -15.925 32.214 -0.790 -2.228 -6.957 H6 CDM 35
CDM H41 1H4 H 0 1 N N N 49.408 -18.084 35.971 -5.076 1.006 -6.802 H41 CDM 36
CDM H42 2H4 H 0 1 N N N 47.844 -18.288 35.440 -4.995 -0.373 -7.758 H42 CDM 37
CDM "H1'" H1* H 0 1 N N N 48.099 -14.178 30.622 0.967 -1.615 -5.655 "H1'" CDM 38
CDM "H2'" H2* H 0 1 N N N 50.955 -13.504 31.762 0.861 1.434 -5.319 "H2'" CDM 39
CDM "HO'2" 2HO* H 0 0 N N N 49.929 -11.611 32.006 2.569 1.254 -6.833 "HO'2" CDM 40
CDM "H3'" H3* H 0 1 N N N 51.555 -12.509 29.802 2.732 1.327 -3.895 "H3'" CDM 41
CDM "H4'" H4* H 0 1 N N N 49.683 -14.153 28.044 2.398 -1.487 -3.203 "H4'" CDM 42
CDM H3T H3T H 0 1 N N N 49.974 -11.743 28.209 4.018 0.346 -5.549 H3T CDM 43
CDM "H5'1" 1H5* H 0 0 N N N 51.732 -15.461 27.732 1.187 1.066 -2.041 "H5'1" CDM 44
CDM "H5'2" 2H5* H 0 0 N N N 52.277 -13.887 27.955 2.774 0.387 -1.608 "H5'2" CDM 45
CDM HO2A HO2A H 0 0 N N N 55.291 -15.455 31.559 -0.630 1.196 -0.049 HO2A CDM 46
CDM HO1B HO1B H 0 0 N N N 53.392 -19.204 29.047 -1.325 1.147 2.423 HO1B CDM 47
CDM H1M1 1H1M H 0 0 N N N 52.621 -18.113 26.790 -0.809 0.924 5.063 H1M1 CDM 48
CDM H1M2 2H1M H 0 0 N N N 53.449 -16.728 26.385 0.778 0.245 5.496 H1M2 CDM 49
CDM H2M1 1H2M H 0 0 N N N 55.008 -18.053 24.786 -1.929 -0.996 6.160 H2M1 CDM 50
CDM H2M2 2H2M H 0 0 N N N 54.202 -20.325 24.464 0.737 -1.703 6.867 H2M2 CDM 51
CDM H4M1 1H4M H 0 0 N N N 53.413 -19.941 22.866 -2.540 -0.883 8.580 H4M1 CDM 52
CDM H4M2 2H4M H 0 0 N N N 52.817 -18.734 21.844 -0.952 -1.562 9.013 H4M2 CDM 53
CDM H5M1 1H5M H 0 0 N N N 50.877 -18.074 23.433 1.139 -0.463 8.200 H5M1 CDM 54
CDM H5M2 2H5M H 0 0 N N N 51.417 -19.406 24.586 1.041 0.997 7.188 H5M2 CDM 55
CDM H5M3 3H5M H 0 0 N N N 51.264 -17.842 25.220 0.606 1.078 8.912 H5M3 CDM 56
CDM H3M H3M H 0 1 N N N 52.599 -16.364 22.818 -2.499 1.065 7.210 H3M CDM 57
CDM H4M H4M H 0 1 N N N 55.261 -18.936 21.579 -1.891 -0.341 10.711 H4M CDM 58
#
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
CDM N1 C2 SING N N 1
CDM N1 C6 SING N N 2
CDM N1 "C1'" SING N N 3
CDM C2 N3 SING N N 4
CDM C2 O2 DOUB N N 5
CDM N3 C4 DOUB N N 6
CDM C4 C5 SING N N 7
CDM C4 N4 SING N N 8
CDM C5 C6 DOUB N N 9
CDM C5 H5 SING N N 10
CDM C6 H6 SING N N 11
CDM N4 H41 SING N N 12
CDM N4 H42 SING N N 13
CDM "C1'" "C2'" SING N N 14
CDM "C1'" "O4'" SING N N 15
CDM "C1'" "H1'" SING N N 16
CDM "C2'" "O2'" SING N N 17
CDM "C2'" "C3'" SING N N 18
CDM "C2'" "H2'" SING N N 19
CDM "O2'" "HO'2" SING N N 20
CDM "C3'" "C4'" SING N N 21
CDM "C3'" "O3'" SING N N 22
CDM "C3'" "H3'" SING N N 23
CDM "C4'" "O4'" SING N N 24
CDM "C4'" "C5'" SING N N 25
CDM "C4'" "H4'" SING N N 26
CDM "O3'" H3T SING N N 27
CDM "C5'" "O5'" SING N N 28
CDM "C5'" "H5'1" SING N N 29
CDM "C5'" "H5'2" SING N N 30
CDM "O5'" PA SING N N 31
CDM PA O1A DOUB N N 32
CDM PA O2A SING N N 33
CDM PA O3A SING N N 34
CDM O2A HO2A SING N N 35
CDM O3A PB SING N N 36
CDM PB O1B SING N N 37
CDM PB O2B DOUB N N 38
CDM PB O3B SING N N 39
CDM O1B HO1B SING N N 40
CDM O3B C1M SING N N 41
CDM C1M C2M SING N N 42
CDM C1M H1M1 SING N N 43
CDM C1M H1M2 SING N N 44
CDM C2M O2M SING N N 45
CDM C2M C3M SING N N 46
CDM C2M H2M1 SING N N 47
CDM O2M H2M2 SING N N 48
CDM C3M C4M SING N N 49
CDM C3M C5M SING N N 50
CDM C3M O3M SING N N 51
CDM C4M O4M SING N N 52
CDM C4M H4M1 SING N N 53
CDM C4M H4M2 SING N N 54
CDM C5M H5M1 SING N N 55
CDM C5M H5M2 SING N N 56
CDM C5M H5M3 SING N N 57
CDM O3M H3M SING N N 58
CDM O4M H4M SING N N 59
#
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
CDM SMILES ACDLabs 10.04 "O=P(O)(OCC(O)C(O)(C)CO)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O"
CDM SMILES_CANONICAL CACTVS 3.341 "C[C@](O)(CO)[C@H](O)CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=NC2=O)N"
CDM SMILES CACTVS 3.341 "C[C](O)(CO)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=NC2=O)N"
CDM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@](CO)([C@@H](CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=NC2=O)N)O)O)O)O"
CDM SMILES "OpenEye OEToolkits" 1.5.0 "CC(CO)(C(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=CC(=NC2=O)N)O)O)O)O"
CDM InChI InChI 1.03
"InChI=1S/C14H25N3O14P2/c1-14(23,6-18)8(19)5-29-33(26,27)31-32(24,25)28-4-7-10(20)11(21)12(30-7)17-3-2-9(15)16-13(17)22/h2-3,7-8,10-12,18-21,23H,4-6H2,1H3,(H,24,25)(H,26,27)(H2,15,16,22)/t7-,8-,10-,11-,12-,14+/m1/s1"
CDM InChIKey InChI 1.03 YFAUKWZNPVBCFF-XHIBXCGHSA-N
#
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
CDM "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-hydroxy{[(S)-hydroxy{[(2R,3S)-2,3,4-trihydroxy-3-methylbutyl]oxy}phosphoryl]oxy}phosphoryl]cytidine"
CDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3S)-2,3,4-trihydroxy-3-methyl-butoxy]phosphoryl] 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
CDM "Create component" 2001-05-22 RCSB
CDM "Modify descriptor" 2011-06-04 RCSB
#