data_5DK
#
_chem_comp.id 5DK
_chem_comp.name "(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H22 N5 O7 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms PLP-DArg
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-09-09
_chem_comp.pdbx_modified_date 2021-03-01
_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 403.328
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5DK
_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 5DJ3
_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
5DK C2 C1 C 0 1 Y N N 67.802 8.239 -25.278 1.313 -2.439 2.644 C2 5DK 1
5DK C3 C2 C 0 1 Y N N 67.309 8.601 -26.523 0.446 -2.183 1.591 C3 5DK 2
5DK C4 C3 C 0 1 Y N N 66.002 8.278 -26.884 0.832 -1.261 0.605 C4 5DK 3
5DK C5 C4 C 0 1 Y N N 65.252 7.597 -25.924 2.080 -0.642 0.734 C5 5DK 4
5DK C6 C5 C 0 1 Y N N 65.811 7.260 -24.698 2.876 -0.958 1.816 C6 5DK 5
5DK CB C6 C 0 1 N N N 64.523 8.685 -30.818 -3.405 -0.666 -1.250 CB 5DK 6
5DK O3 O1 O 0 1 N N N 68.166 9.299 -27.371 -0.754 -2.814 1.515 O3 5DK 7
5DK O1P O2 O 0 1 N N N 62.740 4.089 -28.318 5.016 1.288 -2.243 O1P 5DK 8
5DK O2P O3 O 0 1 N N N 61.552 5.261 -26.461 6.009 2.328 -0.042 O2P 5DK 9
5DK O3P O4 O 0 1 N N N 61.832 6.391 -28.604 3.814 3.126 -0.999 O3P 5DK 10
5DK O4P O5 O 0 1 N N N 63.912 6.123 -27.134 3.845 0.838 0.068 O4P 5DK 11
5DK N N1 N 0 1 N N N 66.145 9.143 -29.083 -1.203 -1.538 -0.637 N 5DK 12
5DK P P1 P 0 1 N N N 62.515 5.442 -27.649 4.652 1.922 -0.808 P 5DK 13
5DK C2A C7 C 0 1 N N N 69.242 8.656 -24.946 0.916 -3.426 3.712 C2A 5DK 14
5DK C4A C8 C 0 1 N N N 65.346 8.632 -28.253 -0.054 -0.954 -0.535 C4A 5DK 15
5DK C5A C9 C 0 1 N N N 63.809 7.195 -26.244 2.549 0.356 -0.293 C5A 5DK 16
5DK N1 N2 N 0 1 Y N N 67.051 7.580 -24.403 2.480 -1.835 2.719 N1 5DK 17
5DK CA C10 C 0 1 N N R 65.372 9.774 -30.152 -2.082 -1.233 -1.769 CA 5DK 18
5DK C C11 C 0 1 N N N 66.287 10.414 -31.202 -2.348 -2.493 -2.552 C 5DK 19
5DK O O6 O 0 1 N N N 67.494 10.624 -30.998 -3.133 -2.454 -3.640 O 5DK 20
5DK CG C12 C 0 1 N N N 63.101 9.177 -31.189 -3.149 0.677 -0.562 CG 5DK 21
5DK CD C13 C 0 1 N N N 62.103 7.996 -31.146 -4.472 1.243 -0.043 CD 5DK 22
5DK NE N3 N 0 1 N N N 62.084 7.326 -32.454 -4.228 2.529 0.615 NE 5DK 23
5DK CZ C14 C 0 1 N N N 60.979 6.424 -32.811 -5.276 3.231 1.164 CZ 5DK 24
5DK NH1 N4 N 0 1 N N N 60.154 5.792 -31.771 -6.552 2.726 1.095 NH1 5DK 25
5DK NH2 N5 N 0 1 N N N 60.757 6.177 -34.023 -5.058 4.375 1.750 NH2 5DK 26
5DK OXT O7 O 0 1 N N N 65.875 10.782 -32.330 -1.854 -3.538 -2.200 OXT 5DK 27
5DK H1 H1 H 0 1 N N N 65.215 6.725 -23.973 3.841 -0.485 1.922 H1 5DK 28
5DK H2 H2 H 0 1 N N N 64.432 7.837 -30.124 -4.091 -0.522 -2.084 H2 5DK 29
5DK H3 H3 H 0 1 N N N 65.032 8.355 -31.736 -3.843 -1.363 -0.535 H3 5DK 30
5DK H4 H4 H 0 1 N N N 69.006 9.419 -26.944 -1.474 -2.344 1.959 H4 5DK 31
5DK H5 H5 H 0 1 N N N 62.404 4.115 -29.206 5.565 0.494 -2.194 H5 5DK 32
5DK H6 H6 H 0 1 N N N 60.769 5.779 -26.606 6.547 2.979 -0.513 H6 5DK 33
5DK H9 H9 H 0 1 N N N 69.495 8.325 -23.928 0.392 -2.904 4.512 H9 5DK 34
5DK H10 H10 H 0 1 N N N 69.933 8.191 -25.665 0.260 -4.183 3.282 H10 5DK 35
5DK H11 H11 H 0 1 N N N 69.330 9.751 -25.008 1.809 -3.905 4.114 H11 5DK 36
5DK H12 H12 H 0 1 N N N 64.303 8.456 -28.470 0.259 -0.242 -1.285 H12 5DK 37
5DK H14 H14 H 0 1 N N N 63.271 8.033 -26.711 2.599 -0.124 -1.270 H14 5DK 38
5DK H15 H15 H 0 1 N N N 63.283 6.886 -25.328 1.849 1.191 -0.334 H15 5DK 39
5DK H16 H16 H 0 1 N N N 64.708 10.545 -29.734 -1.601 -0.498 -2.415 H16 5DK 40
5DK H17 H17 H 0 1 N N N 67.878 11.036 -31.763 -3.275 -3.287 -4.109 H17 5DK 41
5DK H18 H18 H 0 1 N N N 63.116 9.604 -32.203 -2.463 0.533 0.272 H18 5DK 42
5DK H19 H19 H 0 1 N N N 62.784 9.948 -30.471 -2.712 1.373 -1.277 H19 5DK 43
5DK H20 H20 H 0 1 N N N 61.097 8.374 -30.912 -5.159 1.387 -0.877 H20 5DK 44
5DK H21 H21 H 0 1 N N N 62.415 7.280 -30.371 -4.910 0.547 0.672 H21 5DK 45
5DK H22 H22 H 0 1 N N N 62.827 7.484 -33.105 -3.327 2.886 0.664 H22 5DK 46
5DK H23 H23 H 0 1 N N N 60.341 5.973 -30.806 -6.714 1.874 0.659 H23 5DK 47
5DK H24 H24 H 0 1 N N N 59.406 5.181 -32.029 -7.291 3.221 1.482 H24 5DK 48
5DK H25 H25 H 0 1 N N N 59.996 5.539 -34.142 -5.797 4.870 2.136 H25 5DK 49
# #
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
5DK NH2 CZ DOUB N N 1
5DK CZ NE SING N N 2
5DK CZ NH1 SING N N 3
5DK NE CD SING N N 4
5DK OXT C DOUB N N 5
5DK C O SING N N 6
5DK C CA SING N N 7
5DK CG CD SING N N 8
5DK CG CB SING N N 9
5DK CB CA SING N N 10
5DK CA N SING N N 11
5DK N C4A DOUB N N 12
5DK O3P P DOUB N N 13
5DK O1P P SING N N 14
5DK C4A C4 SING N N 15
5DK P O4P SING N N 16
5DK P O2P SING N N 17
5DK O3 C3 SING N N 18
5DK O4P C5A SING N N 19
5DK C4 C3 DOUB Y N 20
5DK C4 C5 SING Y N 21
5DK C3 C2 SING Y N 22
5DK C5A C5 SING N N 23
5DK C5 C6 DOUB Y N 24
5DK C2 C2A SING N N 25
5DK C2 N1 DOUB Y N 26
5DK C6 N1 SING Y N 27
5DK C6 H1 SING N N 28
5DK CB H2 SING N N 29
5DK CB H3 SING N N 30
5DK O3 H4 SING N N 31
5DK O1P H5 SING N N 32
5DK O2P H6 SING N N 33
5DK C2A H9 SING N N 34
5DK C2A H10 SING N N 35
5DK C2A H11 SING N N 36
5DK C4A H12 SING N N 37
5DK C5A H14 SING N N 38
5DK C5A H15 SING N N 39
5DK CA H16 SING N N 40
5DK O H17 SING N N 41
5DK CG H18 SING N N 42
5DK CG H19 SING N N 43
5DK CD H20 SING N N 44
5DK CD H21 SING N N 45
5DK NE H22 SING N N 46
5DK NH1 H23 SING N N 47
5DK NH1 H24 SING N N 48
5DK NH2 H25 SING N N 49
# #
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
5DK SMILES ACDLabs 12.01 "c1(C)ncc(c(c1O)/C=N/C(CCCN/C(N)=N)C(O)=O)COP(O)(O)=O"
5DK InChI InChI 1.03 "InChI=1S/C14H22N5O7P/c1-8-12(20)10(9(5-18-8)7-26-27(23,24)25)6-19-11(13(21)22)3-2-4-17-14(15)16/h5-6,11,20H,2-4,7H2,1H3,(H,21,22)(H4,15,16,17)(H2,23,24,25)/b19-6+/t11-/m1/s1"
5DK InChIKey InChI 1.03 PFHOMURYEGODJI-WZZUDYRYSA-N
5DK SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[C@H](CCCNC(N)=N)C(O)=O)c1O"
5DK SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=N[CH](CCCNC(N)=N)C(O)=O)c1O"
5DK SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "[H]/N=C(\N)/NCCC[C@H](C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O"
5DK SMILES "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NC(CCCNC(=N)N)C(=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
5DK "SYSTEMATIC NAME" ACDLabs 12.01 "(E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine"
5DK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2R)-5-carbamimidamido-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]pentanoic 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
5DK "Create component" 2015-09-09 RCSB
5DK "Modify value order" 2015-09-25 RCSB
5DK "Initial release" 2015-11-25 RCSB
5DK "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 5DK
_pdbx_chem_comp_synonyms.name PLP-DArg
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##