data_RDF
#
_chem_comp.id RDF
_chem_comp.name "N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)-L-LEUCYL-L-TRYPTOPHAN"
_chem_comp.type peptide-like
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H34 N3 O10 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms PHOSPHORAMIDON
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-12-17
_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 543.504
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RDF
_chem_comp.pdbx_model_coordinates_details "not provided"
_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 1TLP
_chem_comp.pdbx_subcomponent_list "RHA LEU TRP"
_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
RDF C1 C1 C 0 1 N N S 51.183 16.914 -8.254 -2.802 -0.333 0.576 C1 RHA 1
RDF O1 O1 O 0 1 N N N 50.920 18.137 -7.643 -2.887 0.915 -0.114 O1 RHA 2
RDF C2 C2 C 0 1 N N R 50.171 16.113 -7.502 -3.754 -0.319 1.775 C2 RHA 3
RDF O2 O2 O 0 1 N N N 49.976 14.742 -8.034 -3.631 -1.546 2.497 O2 RHA 4
RDF C3 C3 C 0 1 N N R 48.865 16.750 -7.787 -5.193 -0.163 1.272 C3 RHA 5
RDF O3 O3 O 0 1 N N N 48.022 16.009 -6.924 -6.095 -0.223 2.378 O3 RHA 6
RDF C4 C4 C 0 1 N N R 48.610 16.502 -9.263 -5.506 -1.300 0.294 C4 RHA 7
RDF O4 O4 O 0 1 N N N 47.268 16.717 -9.593 -6.821 -1.124 -0.238 O4 RHA 8
RDF C5 C5 C 0 1 N N S 49.572 17.376 -10.084 -4.485 -1.276 -0.848 C5 RHA 9
RDF O5 O5 O 0 1 N N N 50.917 16.967 -9.678 -3.167 -1.393 -0.309 O5 RHA 10
RDF C6 C6 C 0 1 N N N 49.360 17.397 -11.604 -4.755 -2.444 -1.798 C6 RHA 11
RDF P P1 P 0 1 N N S 51.715 18.902 -6.596 -1.626 1.604 -0.840 P RHA 12
RDF O1P O6 O 0 1 N N N 53.231 19.053 -6.870 -0.976 0.623 -1.737 O1P RHA 13
RDF O2P O7 O 0 1 N N N 51.194 20.234 -6.325 -2.127 2.869 -1.701 O2P RHA 14
RDF N N1 N 0 1 N N N 51.667 18.103 -5.418 -0.522 2.119 0.322 N LEU 15
RDF CA C7 C 0 1 N N S 52.688 17.980 -4.388 0.851 1.766 -0.062 CA LEU 16
RDF C C8 C 0 1 N N N 53.504 16.720 -4.374 1.484 0.946 1.032 C LEU 17
RDF O O9 O 0 1 N N N 54.637 16.851 -3.933 0.854 0.683 2.034 O LEU 18
RDF CB C9 C 0 1 N N N 52.144 18.204 -2.986 1.664 3.043 -0.279 CB LEU 19
RDF CG C10 C 0 1 N N N 53.236 18.074 -1.852 1.121 3.793 -1.497 CG LEU 20
RDF CD1 C11 C 0 1 N N N 54.393 19.099 -1.824 1.977 5.035 -1.755 CD1 LEU 21
RDF CD2 C12 C 0 1 N N N 52.637 18.119 -0.440 1.168 2.878 -2.722 CD2 LEU 22
RDF N1 N2 N 0 1 N N N 52.910 15.559 -4.831 2.751 0.507 0.897 N TRP 23
RDF CA1 C13 C 0 1 N N S 53.536 14.231 -4.971 3.367 -0.290 1.962 CA TRP 24
RDF C7 C14 C 0 1 N N N 52.673 13.218 -5.766 3.950 0.630 3.004 C TRP 25
RDF O6 O11 O 0 1 N N N 51.490 13.641 -5.932 3.860 1.827 2.871 O TRP 26
RDF CB1 C15 C 0 1 N N N 54.032 13.779 -3.578 4.478 -1.159 1.370 CB TRP 27
RDF CG1 C16 C 0 1 Y N N 52.938 13.365 -2.684 3.879 -2.161 0.418 CG TRP 28
RDF CD11 C17 C 0 0 Y N N 52.156 14.197 -1.947 3.530 -3.426 0.705 CD1 TRP 29
RDF CD21 C18 C 0 0 Y N N 52.477 12.038 -2.441 3.559 -1.939 -0.995 CD2 TRP 30
RDF NE1 N3 N 0 1 Y N N 51.220 13.492 -1.253 3.019 -4.033 -0.410 NE1 TRP 31
RDF CE2 C19 C 0 1 Y N N 51.394 12.166 -1.521 3.023 -3.151 -1.467 CE2 TRP 32
RDF CE3 C20 C 0 1 Y N N 52.873 10.772 -2.906 3.684 -0.849 -1.858 CE3 TRP 33
RDF CZ2 C21 C 0 1 Y N N 50.676 11.082 -1.052 2.621 -3.246 -2.796 CZ2 TRP 34
RDF CZ3 C22 C 0 1 Y N N 52.145 9.694 -2.444 3.283 -0.965 -3.159 CZ3 TRP 35
RDF CH2 C23 C 0 1 Y N N 51.084 9.848 -1.519 2.752 -2.158 -3.630 CH2 TRP 36
RDF OXT O12 O 0 1 N Y N 53.184 12.087 -6.164 4.569 0.118 4.079 OXT TRP 37
RDF H1 H1 H 0 1 N N N 52.217 16.541 -8.215 -1.781 -0.486 0.925 H1 RHA 38
RDF H2 H2 H 0 1 N N N 50.505 16.071 -6.455 -3.504 0.516 2.430 H2 RHA 39
RDF HO2 H3 H 0 1 N N N 49.934 14.773 -8.983 -2.743 -1.712 2.841 HO2 RHA 40
RDF H3 H4 H 0 1 N N N 48.750 17.832 -7.622 -5.300 0.796 0.765 H3 RHA 41
RDF HO3 H5 H 0 1 N N N 48.474 15.843 -6.105 -5.950 0.465 3.042 HO3 RHA 42
RDF H4 H6 H 0 1 N N N 48.808 15.447 -9.504 -5.448 -2.255 0.815 H4 RHA 43
RDF HO4 H7 H 0 1 N N N 46.750 16.766 -8.798 -7.086 -1.810 -0.866 HO4 RHA 44
RDF H5 H8 H 0 1 N N N 49.375 18.434 -9.857 -4.573 -0.336 -1.393 H5 RHA 45
RDF H61 H9 H 0 1 N N N 48.282 17.402 -11.824 -5.760 -2.355 -2.208 H61 RHA 46
RDF H62 H10 H 0 1 N N N 49.825 18.300 -12.026 -4.028 -2.427 -2.610 H62 RHA 47
RDF H63 H11 H 0 1 N N N 49.821 16.504 -12.051 -4.667 -3.384 -1.252 H63 RHA 48
RDF HOP2 H12 H 0 0 N N N 51.081 20.346 -5.388 -2.563 3.554 -1.177 HOP2 RHA 49
RDF H H14 H 0 1 N N N 51.564 17.171 -5.765 -0.752 1.742 1.230 H LEU 50
RDF HA H16 H 0 1 N N N 53.373 18.787 -4.685 0.832 1.186 -0.985 HA LEU 51
RDF HB2 H17 H 0 1 N N N 51.725 19.220 -2.941 1.585 3.678 0.603 HB2 LEU 52
RDF HB3 H18 H 0 1 N N N 51.392 17.423 -2.802 2.709 2.784 -0.448 HB3 LEU 53
RDF HG H19 H 0 1 N N N 53.657 17.096 -2.130 0.091 4.095 -1.308 HG LEU 54
RDF HD11 H20 H 0 0 N N N 54.693 19.342 -2.854 2.987 4.729 -2.029 HD11 LEU 55
RDF HD12 H21 H 0 0 N N N 54.059 20.014 -1.313 1.540 5.615 -2.568 HD12 LEU 56
RDF HD13 H22 H 0 0 N N N 55.250 18.669 -1.285 2.014 5.645 -0.853 HD13 LEU 57
RDF HD21 H23 H 0 0 N N N 53.448 18.130 0.303 0.480 2.044 -2.579 HD21 LEU 58
RDF HD22 H24 H 0 0 N N N 52.027 19.028 -0.330 0.876 3.442 -3.608 HD22 LEU 59
RDF HD23 H25 H 0 0 N N N 52.006 17.232 -0.281 2.180 2.496 -2.852 HD23 LEU 60
RDF H6 H27 H 0 1 N N N 51.948 15.627 -5.096 3.255 0.718 0.096 H TRP 61
RDF HA1 H29 H 0 1 N N N 54.423 14.292 -5.619 2.612 -0.928 2.421 HA TRP 62
RDF HB21 H30 H 0 0 N N N 54.710 12.923 -3.713 5.187 -0.528 0.834 HB2 TRP 63
RDF HB31 H31 H 0 0 N N N 54.534 14.639 -3.110 4.995 -1.685 2.173 HB3 TRP 64
RDF HD1 H32 H 0 1 N N N 52.262 15.271 -1.916 3.638 -3.894 1.672 HD1 TRP 65
RDF HE1 H33 H 0 1 N N N 50.524 13.880 -0.650 2.700 -4.948 -0.449 HE1 TRP 66
RDF HE3 H34 H 0 1 N N N 53.702 10.649 -3.588 4.095 0.083 -1.498 HE3 TRP 67
RDF HZ2 H35 H 0 1 N N N 49.850 11.193 -0.365 2.208 -4.170 -3.172 HZ2 TRP 68
RDF HZ3 H36 H 0 1 N N N 52.392 8.704 -2.798 3.379 -0.121 -3.826 HZ3 TRP 69
RDF HH2 H37 H 0 1 N N N 50.573 8.965 -1.164 2.440 -2.234 -4.661 HH2 TRP 70
RDF HXT H38 H 0 1 N Y N 52.522 11.584 -6.623 4.927 0.747 4.721 HXT TRP 71
# #
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
RDF C1 O1 SING N N 1
RDF C1 C2 SING N N 2
RDF C1 O5 SING N N 3
RDF C1 H1 SING N N 4
RDF O1 P SING N N 5
RDF C2 O2 SING N N 6
RDF C2 C3 SING N N 7
RDF C2 H2 SING N N 8
RDF O2 HO2 SING N N 9
RDF C3 O3 SING N N 10
RDF C3 C4 SING N N 11
RDF C3 H3 SING N N 12
RDF O3 HO3 SING N N 13
RDF C4 O4 SING N N 14
RDF C4 C5 SING N N 15
RDF C4 H4 SING N N 16
RDF O4 HO4 SING N N 17
RDF C5 O5 SING N N 18
RDF C5 C6 SING N N 19
RDF C5 H5 SING N N 20
RDF C6 H61 SING N N 21
RDF C6 H62 SING N N 22
RDF C6 H63 SING N N 23
RDF P O1P DOUB N N 24
RDF P O2P SING N N 25
RDF O2P HOP2 SING N N 26
RDF N CA SING N N 27
RDF N H SING N N 28
RDF CA C SING N N 29
RDF CA CB SING N N 30
RDF CA HA SING N N 31
RDF C O DOUB N N 32
RDF CB CG SING N N 33
RDF CB HB2 SING N N 34
RDF CB HB3 SING N N 35
RDF CG CD1 SING N N 36
RDF CG CD2 SING N N 37
RDF CG HG SING N N 38
RDF CD1 HD11 SING N N 39
RDF CD1 HD12 SING N N 40
RDF CD1 HD13 SING N N 41
RDF CD2 HD21 SING N N 42
RDF CD2 HD22 SING N N 43
RDF CD2 HD23 SING N N 44
RDF N1 CA1 SING N N 45
RDF N1 H6 SING N N 46
RDF CA1 C7 SING N N 47
RDF CA1 CB1 SING N N 48
RDF CA1 HA1 SING N N 49
RDF C7 O6 DOUB N N 50
RDF C7 OXT SING N N 51
RDF CB1 CG1 SING N N 52
RDF CB1 HB21 SING N N 53
RDF CB1 HB31 SING N N 54
RDF CG1 CD11 DOUB Y N 55
RDF CG1 CD21 SING Y N 56
RDF CD11 NE1 SING Y N 57
RDF CD11 HD1 SING N N 58
RDF CD21 CE2 DOUB Y N 59
RDF CD21 CE3 SING Y N 60
RDF NE1 CE2 SING Y N 61
RDF NE1 HE1 SING N N 62
RDF CE2 CZ2 SING Y N 63
RDF CE3 CZ3 DOUB Y N 64
RDF CE3 HE3 SING N N 65
RDF CZ2 CH2 DOUB Y N 66
RDF CZ2 HZ2 SING N N 67
RDF CZ3 CH2 SING Y N 68
RDF CZ3 HZ3 SING N N 69
RDF CH2 HH2 SING N N 70
RDF OXT HXT SING N N 71
RDF P N SING N N 72
RDF C N1 SING N N 73
# #
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
RDF SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1O)C)(O)NC(C(=O)NC(C(=O)O)Cc3c2ccccc2nc3)CC(C)C"
RDF SMILES_CANONICAL CACTVS 3.341 "CC(C)C[C@H](N[P@@](O)(=O)O[C@@H]1O[C@@H](C)[C@H](O)[C@@H](O)[C@H]1O)C(=O)N[C@@H](Cc2c[nH]c3ccccc23)C(O)=O"
RDF SMILES CACTVS 3.341 "CC(C)C[CH](N[P](O)(=O)O[CH]1O[CH](C)[CH](O)[CH](O)[CH]1O)C(=O)N[CH](Cc2c[nH]c3ccccc23)C(O)=O"
RDF SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)O[P@](=O)(N[C@@H](CC(C)C)C(=O)N[C@@H](Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O"
RDF SMILES "OpenEye OEToolkits" 1.5.0 "CC1C(C(C(C(O1)OP(=O)(NC(CC(C)C)C(=O)NC(Cc2c[nH]c3c2cccc3)C(=O)O)O)O)O)O"
RDF InChI InChI 1.03 "InChI=1S/C23H34N3O10P/c1-11(2)8-16(26-37(33,34)36-23-20(29)19(28)18(27)12(3)35-23)21(30)25-17(22(31)32)9-13-10-24-15-7-5-4-6-14(13)15/h4-7,10-12,16-20,23-24,27-29H,8-9H2,1-3H3,(H,25,30)(H,31,32)(H2,26,33,34)/t12-,16-,17-,18-,19+,20+,23-/m0/s1"
RDF InChIKey InChI 1.03 ZPHBZEQOLSRPAK-XLCYBJAPSA-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
RDF "SYSTEMATIC NAME" ACDLabs 10.04 "(2S)-2-{[(2S)-2-{[(S)-hydroxy{[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}phosphoryl]amino}-4-methylpentanoyl]amino}-3-(1H-indol-3-yl)propanoic acid"
RDF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-[[(2S)-2-[[hydroxy-[(2S,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyl-oxan-2-yl]oxy-phosphoryl]amino]-4-methyl-pentanoyl]amino]-3-(1H-indol-3-yl)propanoic 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
RDF "Create component" 1999-12-17 RCSB
RDF "Modify aromatic_flag" 2011-06-04 RCSB
RDF "Modify descriptor" 2011-06-04 RCSB
RDF "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id RDF
_pdbx_chem_comp_synonyms.name PHOSPHORAMIDON
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##