data_2TM
#
_chem_comp.id 2TM
_chem_comp.name "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H18 N3 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms CMPcPP
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-01-30
_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 481.184
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2TM
_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 4OIO
_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
2TM "O5'" "O5'" O 0 1 N N N -4.777 -3.346 84.515 0.148 -1.185 -0.194 "O5'" 2TM 1
2TM "C5'" "C5'" C 0 1 N N N -3.688 -2.495 84.454 1.261 -1.869 0.386 "C5'" 2TM 2
2TM "C4'" "C4'" C 0 1 N N R -4.006 -1.285 83.669 2.445 -1.829 -0.583 "C4'" 2TM 3
2TM "O4'" "O4'" O 0 1 N N N -2.865 -0.832 82.991 2.913 -0.477 -0.727 "O4'" 2TM 4
2TM "C3'" "C3'" C 0 1 N N S -5.119 -1.477 82.741 3.612 -2.663 -0.019 "C3'" 2TM 5
2TM "O3'" "O3'" O 0 1 N N N -6.298 -1.014 83.300 3.945 -3.726 -0.914 "O3'" 2TM 6
2TM "C2'" "C2'" C 0 1 N N R -4.742 -0.751 81.533 4.782 -1.656 0.086 "C2'" 2TM 7
2TM "O2'" "O2'" O 0 1 N N N -5.359 0.487 81.421 6.012 -2.255 -0.329 "O2'" 2TM 8
2TM "C1'" "C1'" C 0 1 N N R -3.289 -0.577 81.656 4.344 -0.544 -0.906 "C1'" 2TM 9
2TM C5 C5 C 0 1 N N N -1.047 -3.242 80.327 6.431 2.491 -1.081 C5 2TM 10
2TM C6 C6 C 0 1 N N N -1.781 -2.425 81.187 5.860 1.309 -1.414 C6 2TM 11
2TM N1 N1 N 0 1 N N N -2.526 -1.417 80.694 4.969 0.735 -0.558 N1 2TM 12
2TM C2 C2 C 0 1 N N N -2.559 -1.195 79.360 4.659 1.336 0.605 C2 2TM 13
2TM N3 N3 N 0 1 N N N -1.858 -1.970 78.511 5.212 2.499 0.947 N3 2TM 14
2TM C4 C4 C 0 1 N N N -1.105 -2.986 78.958 6.089 3.092 0.148 C4 2TM 15
2TM O3G O3G O 0 1 N N N -7.436 -3.176 90.369 -7.047 2.093 -1.782 O3G 2TM 16
2TM PG PG P 0 1 N N N -8.071 -4.400 89.723 -6.668 1.080 -0.590 PG 2TM 17
2TM O1G O1G O 0 1 N N N -9.541 -4.455 90.075 -6.886 1.747 0.713 O1G 2TM 18
2TM O2G O2G O 0 1 N N N -7.394 -5.647 90.244 -7.599 -0.231 -0.684 O2G 2TM 19
2TM O3B O3B O 0 1 N N N -7.926 -4.304 88.139 -5.122 0.651 -0.721 O3B 2TM 20
2TM PB PB P 0 1 N N N -7.039 -3.191 87.437 -4.070 -0.056 0.271 PB 2TM 21
2TM O1B O1B O 0 1 N N N -7.039 -1.877 88.296 -4.618 -1.512 0.686 O1B 2TM 22
2TM O2B O2B O 0 1 N N N -7.606 -2.888 86.074 -3.902 0.773 1.485 O2B 2TM 23
2TM PA PA P 0 1 N N N -4.812 -4.489 85.619 -1.271 -1.031 0.551 PA 2TM 24
2TM O1A O1A O 0 1 N N N -5.844 -5.603 85.175 -1.775 -2.369 0.933 O1A 2TM 25
2TM O2A O2A O 0 1 N N N -3.447 -5.096 85.746 -1.089 -0.129 1.872 O2A 2TM 26
2TM N4 N4 N 0 1 N N N -0.368 -3.796 78.034 6.654 4.293 0.511 N4 2TM 27
2TM O2 O2 O 0 1 N N N -3.234 -0.275 78.877 3.859 0.808 1.359 O2 2TM 28
2TM C1 C1 C 0 1 N N N -5.321 -3.788 87.230 -2.463 -0.230 -0.572 C1 2TM 29
2TM H1 H1 H 0 1 N N N -2.846 -3.021 83.979 1.540 -1.382 1.321 H1 2TM 30
2TM H2 H2 H 0 1 N N N -3.406 -2.198 85.475 0.988 -2.905 0.583 H2 2TM 31
2TM H3 H3 H 0 1 N N N -4.308 -0.506 84.384 2.143 -2.222 -1.553 H3 2TM 32
2TM H4 H4 H 0 1 N N N -5.207 -2.547 82.504 3.357 -3.059 0.964 H4 2TM 33
2TM H5 H5 H 0 1 N N N -6.498 -1.517 84.080 4.674 -4.283 -0.609 H5 2TM 34
2TM H6 H6 H 0 1 N N N -4.960 -1.371 80.651 4.866 -1.262 1.099 H6 2TM 35
2TM H7 H7 H 0 1 N N N -6.298 0.367 81.342 6.326 -2.955 0.259 H7 2TM 36
2TM H8 H8 H 0 1 N N N -3.062 0.474 81.422 4.589 -0.825 -1.931 H8 2TM 37
2TM H9 H9 H 0 1 N N N -0.448 -4.054 80.713 7.140 2.964 -1.744 H9 2TM 38
2TM H10 H10 H 0 1 N N N -1.752 -2.601 82.252 6.109 0.827 -2.348 H10 2TM 39
2TM H11 H11 H 0 1 N N N -8.095 -2.699 90.860 -7.966 2.394 -1.766 H11 2TM 40
2TM H12 H12 H 0 1 N N N -8.034 -6.197 90.680 -7.507 -0.720 -1.514 H12 2TM 41
2TM H13 H13 H 0 1 N N N -7.395 -1.162 87.782 -4.752 -2.110 -0.062 H13 2TM 42
2TM H14 H14 H 0 1 N N N -3.490 -6.021 85.533 -0.760 0.763 1.697 H14 2TM 43
2TM H15 H15 H 0 1 N N N -0.414 -3.604 77.054 6.411 4.708 1.354 H15 2TM 44
2TM H16 H16 H 0 1 N N N 0.193 -4.553 78.369 7.295 4.725 -0.075 H16 2TM 45
2TM H17 H17 H 0 1 N N N -5.158 -4.569 87.987 -2.586 -0.841 -1.467 H17 2TM 46
2TM H18 H18 H 0 1 N N N -4.657 -2.935 87.434 -2.091 0.755 -0.854 H18 2TM 47
# #
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
2TM N4 C4 SING N N 1
2TM N3 C4 DOUB N N 2
2TM N3 C2 SING N N 3
2TM O2 C2 DOUB N N 4
2TM C4 C5 SING N N 5
2TM C2 N1 SING N N 6
2TM C5 C6 DOUB N N 7
2TM N1 C6 SING N N 8
2TM N1 "C1'" SING N N 9
2TM "O2'" "C2'" SING N N 10
2TM "C2'" "C1'" SING N N 11
2TM "C2'" "C3'" SING N N 12
2TM "C1'" "O4'" SING N N 13
2TM "C3'" "O3'" SING N N 14
2TM "C3'" "C4'" SING N N 15
2TM "O4'" "C4'" SING N N 16
2TM "C4'" "C5'" SING N N 17
2TM "C5'" "O5'" SING N N 18
2TM "O5'" PA SING N N 19
2TM O1A PA DOUB N N 20
2TM PA O2A SING N N 21
2TM PA C1 SING N N 22
2TM O2B PB DOUB N N 23
2TM C1 PB SING N N 24
2TM PB O3B SING N N 25
2TM PB O1B SING N N 26
2TM O3B PG SING N N 27
2TM PG O1G DOUB N N 28
2TM PG O2G SING N N 29
2TM PG O3G SING N N 30
2TM "C5'" H1 SING N N 31
2TM "C5'" H2 SING N N 32
2TM "C4'" H3 SING N N 33
2TM "C3'" H4 SING N N 34
2TM "O3'" H5 SING N N 35
2TM "C2'" H6 SING N N 36
2TM "O2'" H7 SING N N 37
2TM "C1'" H8 SING N N 38
2TM C5 H9 SING N N 39
2TM C6 H10 SING N N 40
2TM O3G H11 SING N N 41
2TM O2G H12 SING N N 42
2TM O1B H13 SING N N 43
2TM O2A H14 SING N N 44
2TM N4 H15 SING N N 45
2TM N4 H16 SING N N 46
2TM C1 H17 SING N N 47
2TM C1 H18 SING N N 48
# #
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
2TM SMILES ACDLabs 12.01 "O=P(O)(O)OP(=O)(O)CP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O"
2TM InChI InChI 1.03 "InChI=1S/C10H18N3O13P3/c11-6-1-2-13(10(16)12-6)9-8(15)7(14)5(25-9)3-24-27(17,18)4-28(19,20)26-29(21,22)23/h1-2,5,7-9,14-15H,3-4H2,(H,17,18)(H,19,20)(H2,11,12,16)(H2,21,22,23)/t5-,7-,8-,9-/m1/s1"
2TM InChIKey InChI 1.03 STGUOVSTMBLHFT-ZOQUXTDFSA-N
2TM SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O"
2TM SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)C[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O"
2TM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O"
2TM SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(CP(=O)(O)OP(=O)(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
2TM "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine"
2TM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,4R,5R)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-[[oxidanyl(phosphonooxy)phosphoryl]methyl]phosphinic 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
2TM "Create component" 2014-01-30 RCSB
2TM "Initial release" 2014-05-07 RCSB
2TM "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 2TM
_pdbx_chem_comp_synonyms.name CMPcPP
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##