data_DJJ
#
_chem_comp.id DJJ
_chem_comp.name "5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H17 Cl N3 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 499.629
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DJJ
_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 6BEM
_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
DJJ C4 C1 C 0 1 N N N 9.389 7.658 10.912 -6.904 -2.624 0.483 C4 DJJ 1
DJJ N4 N1 N 0 1 N N N 10.822 7.727 11.100 -7.697 -3.592 1.055 N4 DJJ 2
DJJ C5 C2 C 0 1 N N N 8.575 7.232 11.954 -6.694 -2.612 -0.911 C5 DJJ 3
DJJ C6 C3 C 0 1 N N N 7.199 7.165 11.712 -5.909 -1.648 -1.448 C6 DJJ 4
DJJ N3 N2 N 0 1 N N N 8.864 7.992 9.749 -6.338 -1.693 1.239 N3 DJJ 5
DJJ C2 C4 C 0 1 N N N 7.560 7.909 9.566 -5.569 -0.751 0.697 C2 DJJ 6
DJJ O2 O1 O 0 1 N N N 7.099 8.218 8.512 -5.060 0.095 1.413 O2 DJJ 7
DJJ N1 N3 N 0 1 N N N 6.737 7.525 10.528 -5.345 -0.716 -0.630 N1 DJJ 8
DJJ "C1'" C5 C 0 1 N N R 5.315 7.423 10.226 -4.494 0.333 -1.198 "C1'" DJJ 9
DJJ "C2'" C6 C 0 1 N N N 5.060 6.205 9.822 -5.109 1.725 -0.935 "C2'" DJJ 10
DJJ "C3'" C7 C 0 1 N N S 4.493 5.464 11.043 -3.887 2.629 -0.659 "C3'" DJJ 11
DJJ "O3'" O2 O 0 1 N N N 3.673 4.413 10.694 -3.806 3.673 -1.632 "O3'" DJJ 12
DJJ "O4'" O3 O 0 1 N N N 4.464 7.624 11.555 -3.216 0.361 -0.526 "O4'" DJJ 13
DJJ "C4'" C8 C 0 1 N N R 3.707 6.599 11.715 -2.678 1.676 -0.787 "C4'" DJJ 14
DJJ "C5'" C9 C 0 1 N N N 3.530 6.350 13.242 -1.609 2.030 0.248 "C5'" DJJ 15
DJJ "O5'" O4 O 0 1 N N N 4.798 6.205 13.816 -0.454 1.215 0.038 "O5'" DJJ 16
DJJ PA P1 P 0 1 N N N 5.031 4.957 14.874 0.870 1.318 0.948 PA DJJ 17
DJJ O1A O5 O 0 1 N N N 3.950 4.996 15.939 0.522 0.867 2.454 O1A DJJ 18
DJJ O2A O6 O 0 1 N N N 6.410 5.074 15.455 1.358 2.715 0.952 O2A DJJ 19
DJJ O3A O7 O 0 1 N N N 4.974 3.612 13.959 2.010 0.352 0.349 O3A DJJ 20
DJJ PB P2 P 0 1 N N N 3.801 2.486 13.886 3.598 0.219 0.579 PB DJJ 21
DJJ O2B O8 O 0 1 N N N 3.744 2.181 12.420 3.866 -0.083 2.003 O2B DJJ 22
DJJ O1B O9 O 0 1 N N N 2.466 2.998 14.374 4.316 1.604 0.180 O1B DJJ 23
DJJ C3B C10 C 0 1 N N S 4.359 0.975 14.781 4.253 -1.127 -0.461 C3B DJJ 24
DJJ CL1 CL1 CL 0 0 N N N 6.131 1.084 14.914 3.926 -0.759 -2.196 CL1 DJJ 25
DJJ PG P3 P 0 1 N N N 3.644 0.956 16.484 6.051 -1.277 -0.200 PG DJJ 26
DJJ O1G O10 O 0 1 N N N 3.521 2.393 16.946 6.342 -1.606 1.349 O1G DJJ 27
DJJ O2G O11 O 0 1 N N N 4.588 0.189 17.378 6.629 -2.466 -1.119 O2G DJJ 28
DJJ O3G O12 O 0 1 N N N 2.316 0.286 16.392 6.711 -0.004 -0.567 O3G DJJ 29
DJJ H1 H1 H 0 1 N N N 11.411 8.027 10.350 -8.112 -4.270 0.498 H1 DJJ 30
DJJ H2 H2 H 0 1 N N N 11.224 7.475 11.980 -7.840 -3.598 2.014 H2 DJJ 31
DJJ H3 H3 H 0 1 N N N 8.989 6.963 12.915 -7.151 -3.361 -1.541 H3 DJJ 32
DJJ H4 H4 H 0 1 N N N 6.524 6.824 12.483 -5.733 -1.618 -2.513 H4 DJJ 33
DJJ H5 H5 H 0 1 N N N 5.018 8.190 9.496 -4.357 0.172 -2.267 H5 DJJ 34
DJJ H6 H6 H 0 1 N N N 4.322 6.219 9.007 -5.652 2.075 -1.814 H6 DJJ 35
DJJ H7 H7 H 0 1 N N N 5.982 5.717 9.473 -5.766 1.695 -0.066 H7 DJJ 36
DJJ H8 H8 H 0 1 N N N 5.317 5.145 11.698 -3.940 3.046 0.347 H8 DJJ 37
DJJ H9 H9 H 0 1 N N N 3.766 3.714 11.330 -4.570 4.267 -1.636 H9 DJJ 38
DJJ H10 H10 H 0 1 N N N 2.719 6.698 11.242 -2.263 1.723 -1.794 H10 DJJ 39
DJJ H11 H11 H 0 1 N N N 3.010 7.205 13.700 -1.336 3.080 0.145 H11 DJJ 40
DJJ H12 H12 H 0 1 N N N 2.942 5.434 13.403 -2.000 1.853 1.250 H12 DJJ 41
DJJ H13 H13 H 0 1 N N N 4.351 5.089 16.795 0.195 -0.040 2.527 H13 DJJ 42
DJJ H14 H14 H 0 1 N N N 1.852 3.025 13.649 4.182 1.865 -0.742 H14 DJJ 43
DJJ H15 H15 H 0 1 N N N 4.058 0.071 14.231 3.767 -2.064 -0.191 H15 DJJ 44
DJJ H16 H16 H 0 1 N N N 2.606 2.602 17.093 5.939 -2.428 1.659 H16 DJJ 45
DJJ H17 H17 H 0 1 N N N 4.149 -0.583 17.715 7.582 -2.603 -1.031 H17 DJJ 46
#
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
DJJ O2 C2 DOUB N N 1
DJJ C2 N3 SING N N 2
DJJ C2 N1 SING N N 3
DJJ N3 C4 DOUB N N 4
DJJ "C2'" "C1'" SING N N 5
DJJ "C2'" "C3'" SING N N 6
DJJ "C1'" N1 SING N N 7
DJJ "C1'" "O4'" SING N N 8
DJJ N1 C6 SING N N 9
DJJ "O3'" "C3'" SING N N 10
DJJ C4 N4 SING N N 11
DJJ C4 C5 SING N N 12
DJJ "C3'" "C4'" SING N N 13
DJJ "O4'" "C4'" SING N N 14
DJJ C6 C5 DOUB N N 15
DJJ "C4'" "C5'" SING N N 16
DJJ O2B PB DOUB N N 17
DJJ "C5'" "O5'" SING N N 18
DJJ "O5'" PA SING N N 19
DJJ PB O3A SING N N 20
DJJ PB O1B SING N N 21
DJJ PB C3B SING N N 22
DJJ O3A PA SING N N 23
DJJ C3B CL1 SING N N 24
DJJ C3B PG SING N N 25
DJJ PA O2A DOUB N N 26
DJJ PA O1A SING N N 27
DJJ O3G PG DOUB N N 28
DJJ PG O1G SING N N 29
DJJ PG O2G SING N N 30
DJJ N4 H1 SING N N 31
DJJ N4 H2 SING N N 32
DJJ C5 H3 SING N N 33
DJJ C6 H4 SING N N 34
DJJ "C1'" H5 SING N N 35
DJJ "C2'" H6 SING N N 36
DJJ "C2'" H7 SING N N 37
DJJ "C3'" H8 SING N N 38
DJJ "O3'" H9 SING N N 39
DJJ "C4'" H10 SING N N 40
DJJ "C5'" H11 SING N N 41
DJJ "C5'" H12 SING N N 42
DJJ O1A H13 SING N N 43
DJJ O1B H14 SING N N 44
DJJ C3B H15 SING N N 45
DJJ O1G H16 SING N N 46
DJJ O2G H17 SING N N 47
#
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
DJJ SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)P(O)(O)=O)=O"
DJJ InChI InChI 1.03 "InChI=1S/C10H17ClN3O12P3/c11-9(27(17,18)19)28(20,21)26-29(22,23)24-4-6-5(15)3-8(25-6)14-2-1-7(12)13-10(14)16/h1-2,5-6,8-9,15H,3-4H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t5-,6+,8+,9-/m0/s1"
DJJ InChIKey InChI 1.03 DDLGFLMLTFUPNR-LWIVVEGESA-N
DJJ SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@@H](Cl)[P](O)(O)=O)O2"
DJJ SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O2"
DJJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)([C@H](P(=O)(O)O)Cl)O)O"
DJJ SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)Cl)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
DJJ "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine"
DJJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-chloranyl-methyl]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
DJJ "Create component" 2017-10-26 RCSB
DJJ "Initial release" 2018-06-20 RCSB
#