data_CMK
#
_chem_comp.id CMK
_chem_comp.name "CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H26 N3 O15 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-11-21
_chem_comp.pdbx_modified_date 2020-06-17
_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 543.373
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CMK
_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 1GQC
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
# #
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
CMK N1C N1C N 0 1 Y N N 16.133 88.265 67.034 0.311 -0.423 5.611 N1C CMK 1
CMK C2C C2C C 0 1 Y N N 15.872 89.363 66.266 0.727 0.851 5.501 C2C CMK 2
CMK N3C N3C N 0 1 Y N N 15.142 89.208 65.012 1.643 1.349 6.328 N3C CMK 3
CMK C4C C4C C 0 1 Y N N 14.720 88.055 64.586 2.171 0.598 7.286 C4C CMK 4
CMK C5C C5C C 0 1 Y N N 15.015 86.872 65.442 1.761 -0.743 7.425 C5C CMK 5
CMK C6C C6C C 0 1 Y N N 15.694 87.023 66.601 0.824 -1.233 6.580 C6C CMK 6
CMK O2C O2C O 0 1 N N N 16.221 90.490 66.568 0.256 1.562 4.628 O2C CMK 7
CMK N4C N4C N 0 1 N N N 14.067 87.915 63.460 3.117 1.124 8.135 N4C CMK 8
CMK "C1'" C1* C 0 1 N N R 16.882 88.410 68.298 -0.698 -0.943 4.686 "C1'" CMK 9
CMK "C2'" C2* C 0 1 N N R 16.223 87.747 69.530 -1.991 -0.103 4.773 "C2'" CMK 10
CMK "O2'" O2* O 0 1 N N N 15.178 88.593 70.044 -2.956 -0.742 5.612 "O2'" CMK 11
CMK "C3'" C3* C 0 1 N N S 17.402 87.539 70.490 -2.497 -0.043 3.313 "C3'" CMK 12
CMK "C4'" C4* C 0 1 N N R 18.611 87.428 69.531 -1.452 -0.857 2.519 "C4'" CMK 13
CMK "O4'" O4* O 0 1 N N N 18.161 87.797 68.234 -0.252 -0.797 3.320 "O4'" CMK 14
CMK "O3'" O3* O 0 1 N N N 17.608 88.687 71.351 -3.788 -0.645 3.204 "O3'" CMK 15
CMK "C5'" C5* C 0 1 N N N 19.237 86.024 69.418 -1.209 -0.223 1.148 "C5'" CMK 16
CMK "O5'" O5* O 0 1 N N N 18.275 85.007 69.189 -0.187 -0.950 0.461 "O5'" CMK 17
CMK PA PA P 0 1 N N S 18.013 83.587 69.860 0.014 -0.232 -0.965 PA CMK 18
CMK O1A O1A O 0 1 N N N 17.539 83.682 71.280 -1.368 -0.275 -1.788 O1A CMK 19
CMK O2A O2A O 0 1 N N N 16.976 82.864 69.061 0.421 1.174 -0.756 O2A CMK 20
CMK O6 O6 O 0 1 N N N 21.406 81.735 69.291 -0.121 -0.464 -3.668 O6 CMK 21
CMK C2 C2 C 0 1 N N R 20.020 81.921 68.882 1.186 -0.419 -3.099 C2 CMK 22
CMK O2 O2 O 0 1 N N N 19.358 82.739 69.844 1.158 -1.004 -1.796 O2 CMK 23
CMK C3 C3 C 0 1 N N N 19.953 82.559 67.450 2.163 -1.197 -3.984 C3 CMK 24
CMK C4 C4 C 0 1 N N R 20.754 81.676 66.453 2.211 -0.542 -5.370 C4 CMK 25
CMK O4 O4 O 0 1 N N N 20.673 82.265 65.151 3.004 -1.341 -6.250 O4 CMK 26
CMK C5 C5 C 0 1 N N R 22.246 81.572 66.957 0.782 -0.436 -5.912 C5 CMK 27
CMK C6 C6 C 0 1 N N R 22.224 80.917 68.389 -0.090 0.283 -4.881 C6 CMK 28
CMK C7 C7 C 0 1 N N R 23.652 80.780 68.973 -1.512 0.422 -5.428 C7 CMK 29
CMK C1 C1 C 0 1 N N N 19.230 80.590 69.023 1.636 1.014 -2.996 C1 CMK 30
CMK O1X O1X O 0 1 N N N 19.195 80.066 70.236 0.735 1.988 -2.796 O1X CMK 31
CMK O1Y O1Y O 0 1 N N N 18.650 80.041 68.105 2.809 1.288 -3.093 O1Y CMK 32
CMK O5 O5 O 0 1 N N N 22.857 82.882 67.041 0.262 -1.746 -6.150 O5 CMK 33
CMK C8 C8 C 0 1 N N N 23.636 80.640 70.533 -2.386 1.142 -4.398 C8 CMK 34
CMK O8 O8 O 0 1 N N N 22.675 79.645 70.904 -3.714 1.272 -4.908 O8 CMK 35
CMK O7 O7 O 0 1 N N N 24.261 79.614 68.395 -1.485 1.178 -6.640 O7 CMK 36
CMK H5C H5C H 0 1 N N N 14.678 85.869 65.129 2.181 -1.367 8.200 H5C CMK 37
CMK H6C H6C H 0 1 N N N 15.905 86.134 67.219 0.490 -2.257 6.669 H6C CMK 38
CMK H4C1 1H4C H 0 0 N N N 13.709 86.936 63.098 3.401 2.046 8.034 H4C1 CMK 39
CMK H4C2 2H4C H 0 0 N N N 13.849 88.791 62.826 3.499 0.573 8.837 H4C2 CMK 40
CMK "H1'" H1* H 0 1 N N N 17.018 89.496 68.509 -0.910 -1.990 4.906 "H1'" CMK 41
CMK "H2'" H2* H 0 1 N N N 15.797 86.758 69.240 -1.770 0.898 5.142 "H2'" CMK 42
CMK HA HA H 0 1 N N N 14.773 88.186 70.801 -3.758 -0.202 5.576 HA CMK 43
CMK "H3'" H3* H 0 1 N N N 17.275 86.606 71.087 -2.527 0.987 2.959 "H3'" CMK 44
CMK "H4'" H4* H 0 1 N N N 19.397 88.148 69.858 -1.781 -1.890 2.406 "H4'" CMK 45
CMK HB HB H 0 1 N N N 18.338 88.558 71.945 -4.397 -0.096 3.717 HB CMK 46
CMK "H5'1" 1H5* H 0 0 N N N 19.858 85.791 70.315 -2.130 -0.253 0.565 "H5'1" CMK 47
CMK "H5'2" 2H5* H 0 0 N N N 20.032 86.004 68.636 -0.894 0.811 1.277 "H5'2" CMK 48
CMK HO1A HO1A H 0 0 N N N 17.383 82.835 71.680 -1.596 -1.207 -1.902 HO1A CMK 49
CMK H3C1 1H3C H 0 0 N N N 20.297 83.620 67.444 3.156 -1.176 -3.536 H3C1 CMK 50
CMK H3C2 2H3C H 0 0 N N N 18.904 82.730 67.113 1.826 -2.229 -4.080 H3C2 CMK 51
CMK H4 H4 H 0 1 N N N 20.305 80.656 66.423 2.646 0.453 -5.288 H4 CMK 52
CMK HC HC H 0 1 N N N 21.163 81.725 64.542 3.889 -1.390 -5.863 HC CMK 53
CMK H5 H5 H 0 1 N N N 22.833 80.929 66.260 0.786 0.128 -6.844 H5 CMK 54
CMK H6 H6 H 0 1 N N N 21.769 79.902 68.313 0.321 1.273 -4.686 H6 CMK 55
CMK H7 H7 H 0 1 N N N 24.248 81.680 68.693 -1.924 -0.566 -5.625 H7 CMK 56
CMK H1X H1X H 0 1 N N N 18.712 79.252 70.322 1.024 2.908 -2.729 H1X CMK 57
CMK HD HD H 0 1 N N N 22.870 83.277 66.177 0.844 -2.164 -6.798 HD CMK 58
CMK H8C1 1H8C H 0 0 N N N 23.456 81.614 71.044 -2.407 0.566 -3.473 H8C1 CMK 59
CMK H8C2 2H8C H 0 0 N N N 24.648 80.428 70.950 -1.974 2.132 -4.200 H8C2 CMK 60
CMK H8 H8 H 0 1 N N N 22.665 79.560 71.850 -4.230 1.730 -4.230 H8 CMK 61
CMK HE HE H 0 1 N N N 25.137 79.530 68.753 -1.115 2.044 -6.422 HE CMK 62
# #
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
CMK N1C C2C SING Y N 1
CMK N1C C6C SING Y N 2
CMK N1C "C1'" SING N N 3
CMK C2C N3C SING Y N 4
CMK C2C O2C DOUB N N 5
CMK N3C C4C DOUB Y N 6
CMK C4C C5C SING Y N 7
CMK C4C N4C SING N N 8
CMK C5C C6C DOUB Y N 9
CMK C5C H5C SING N N 10
CMK C6C H6C SING N N 11
CMK N4C H4C1 SING N N 12
CMK N4C H4C2 SING N N 13
CMK "C1'" "C2'" SING N N 14
CMK "C1'" "O4'" SING N N 15
CMK "C1'" "H1'" SING N N 16
CMK "C2'" "O2'" SING N N 17
CMK "C2'" "C3'" SING N N 18
CMK "C2'" "H2'" SING N N 19
CMK "O2'" HA SING N N 20
CMK "C3'" "C4'" SING N N 21
CMK "C3'" "O3'" SING N N 22
CMK "C3'" "H3'" SING N N 23
CMK "C4'" "O4'" SING N N 24
CMK "C4'" "C5'" SING N N 25
CMK "C4'" "H4'" SING N N 26
CMK "O3'" HB SING N N 27
CMK "C5'" "O5'" SING N N 28
CMK "C5'" "H5'1" SING N N 29
CMK "C5'" "H5'2" SING N N 30
CMK "O5'" PA SING N N 31
CMK PA O1A SING N N 32
CMK PA O2A DOUB N N 33
CMK PA O2 SING N N 34
CMK O1A HO1A SING N N 35
CMK O6 C2 SING N N 36
CMK O6 C6 SING N N 37
CMK C2 O2 SING N N 38
CMK C2 C3 SING N N 39
CMK C2 C1 SING N N 40
CMK C3 C4 SING N N 41
CMK C3 H3C1 SING N N 42
CMK C3 H3C2 SING N N 43
CMK C4 O4 SING N N 44
CMK C4 C5 SING N N 45
CMK C4 H4 SING N N 46
CMK O4 HC SING N N 47
CMK C5 C6 SING N N 48
CMK C5 O5 SING N N 49
CMK C5 H5 SING N N 50
CMK C6 C7 SING N N 51
CMK C6 H6 SING N N 52
CMK C7 C8 SING N N 53
CMK C7 O7 SING N N 54
CMK C7 H7 SING N N 55
CMK C1 O1X SING N N 56
CMK C1 O1Y DOUB N N 57
CMK O1X H1X SING N N 58
CMK O5 HD SING N N 59
CMK C8 O8 SING N N 60
CMK C8 H8C1 SING N N 61
CMK C8 H8C2 SING N N 62
CMK O8 H8 SING N N 63
CMK O7 HE SING N N 64
# #
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
CMK SMILES ACDLabs 10.04 "O=C(O)C1(OC(C(O)CO)C(O)C(O)C1)OP(=O)(O)OCC3OC(N2C(=O)N=C(N)C=C2)C(O)C3O"
CMK SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[C@]3(C[C@@H](O)[C@@H](O)[C@H](O3)[C@H](O)CO)C(O)=O)[C@@H](O)[C@H]2O"
CMK SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[C]3(C[CH](O)[CH](O)[CH](O3)[CH](O)CO)C(O)=O)[CH](O)[CH]2O"
CMK SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H]([C@H](O[C@@]1(C(=O)O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O)[C@@H](CO)O)O)O"
CMK SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(OC1(C(=O)O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=NC3=O)N)O)O)C(CO)O)O)O"
CMK InChI InChI 1.03 "InChI=1S/C17H26N3O15P/c18-9-1-2-20(16(29)19-9)14-12(26)11(25)8(33-14)5-32-36(30,31)35-17(15(27)28)3-6(22)10(24)13(34-17)7(23)4-21/h1-2,6-8,10-14,21-26H,3-5H2,(H,27,28)(H,30,31)(H2,18,19,29)/t6-,7-,8-,10-,11-,12-,13-,14-,17-/m1/s1"
CMK InChIKey InChI 1.03 YWWJKULNWGRYAS-UOVSKDHASA-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
CMK "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,4R,5R,6R)-2-{[(S)-{[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)"
CMK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4R,5R,6R)-2-[[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-6-[(1R)-1,2-dihydroxyethyl]-4,5-dihydroxy-oxane-2-carboxylic 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
CMK "Create component" 2001-11-21 EBI
CMK "Modify descriptor" 2011-06-04 RCSB
CMK "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id CMK
_pdbx_chem_comp_synonyms.name "CMP-2-KETO-3-DEOXY-OCTULOSONIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##