data_PDD
#
_chem_comp.id PDD
_chem_comp.name "N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE"
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C11 H17 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-03-18
_chem_comp.pdbx_modified_date 2024-09-27
_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 320.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PDD
_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 1L6G
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm Y
#
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.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_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
PDD N N N 0 1 N N N N N N 24.688 15.923 69.190 0.731 -0.122 1.963 N PDD 1
PDD N1 N1 N 0 1 Y N N N N N 23.966 10.714 69.264 -3.550 -0.520 -0.450 N1 PDD 2
PDD C2 C2 C 0 1 Y N N N N N 25.093 11.460 69.401 -3.594 -0.174 0.821 C2 PDD 3
PDD C2A C2A C 0 1 N N N N N N 26.340 10.727 69.790 -4.882 -0.321 1.590 C2A PDD 4
PDD C3 C3 C 0 1 Y N N N N N 25.100 12.856 69.192 -2.467 0.323 1.458 C3 PDD 5
PDD O3A O3A O 0 1 N N N N N N 26.268 13.564 69.388 -2.517 0.679 2.769 O3A PDD 6
PDD C4 C4 C 0 1 Y N N N N N 23.898 13.510 68.743 -1.285 0.453 0.736 C4 PDD 7
PDD C4A C4A C 0 1 N N N N N N 24.040 14.974 68.287 -0.037 0.989 1.388 C4A PDD 8
PDD C5 C5 C 0 1 Y N N N N N 22.676 12.725 68.644 -1.284 0.082 -0.598 C5 PDD 9
PDD C5A C5A C 0 1 N N N N N N 21.334 13.298 68.246 -0.029 0.204 -1.423 C5A PDD 10
PDD OP4 OP4 O 0 1 N N N N N N 21.454 13.928 66.978 -0.287 -0.250 -2.753 OP4 PDD 11
PDD P P P 0 1 N N N N N N 20.296 14.769 66.406 1.089 -0.092 -3.573 P PDD 12
PDD OP1 OP1 O 0 1 N N N N N N 19.098 13.895 66.278 2.141 -0.912 -2.933 OP1 PDD 13
PDD OP2 OP2 O 0 1 N N N N N N 20.723 15.304 65.068 0.870 -0.589 -5.089 OP2 PDD 14
PDD OP3 OP3 O 0 1 N N N N N N 19.988 15.915 67.296 1.539 1.452 -3.575 OP3 PDD 15
PDD C6 C6 C 0 1 Y N N N N N 22.784 11.338 68.905 -2.446 -0.410 -1.162 C6 PDD 16
PDD CA CA C 0 1 N N R N N N 24.892 17.350 68.809 1.927 0.465 2.580 CA PDD 17
PDD CB CB C 0 1 N N N N N N 23.766 17.929 67.928 3.058 0.520 1.550 CB PDD 18
PDD C C C 0 1 N N N N N N 26.258 17.582 68.097 2.356 -0.379 3.752 C PDD 19
PDD O O O 0 1 N N N N N N 26.422 18.844 67.664 1.729 -1.370 4.043 O PDD 20
PDD OXT OXT O 0 1 N Y N N N N 27.097 16.766 67.948 3.434 -0.032 4.471 OXT PDD 21
PDD H HN H 0 1 N N N N N N 25.595 15.536 69.453 1.051 -0.685 1.189 H PDD 22
PDD H2A1 1H2A H 0 0 N N N N N N 26.526 9.896 69.070 -5.462 0.597 1.506 H2A1 PDD 23
PDD H2A2 2H2A H 0 0 N N N N N N 27.265 11.339 69.903 -5.457 -1.152 1.181 H2A2 PDD 24
PDD H2A3 3H2A H 0 0 N N N N N N 26.158 10.149 70.726 -4.658 -0.515 2.639 H2A3 PDD 25
PDD HO3 HO3 H 0 1 N N N N N N 26.273 14.504 69.247 -2.770 1.612 2.795 HO3 PDD 26
PDD H4A1 1H4A H 0 0 N N N N N N 24.560 14.998 67.301 -0.311 1.688 2.179 H4A1 PDD 27
PDD H4A2 2H4A H 0 0 N N N N N N 23.034 15.367 68.009 0.569 1.504 0.644 H4A2 PDD 28
PDD H5A1 1H5A H 0 0 N N N N N N 20.919 13.983 69.022 0.287 1.246 -1.450 H5A1 PDD 29
PDD H5A2 2H5A H 0 0 N N N N N N 20.524 12.532 68.263 0.758 -0.403 -0.977 H5A2 PDD 30
PDD HOP2 2HOP H 0 0 N N N N N N 20.009 15.822 64.715 1.716 -0.479 -5.544 HOP2 PDD 31
PDD HOP3 3HOP H 0 0 N N N N N N 19.274 16.433 66.943 0.827 1.950 -4.000 HOP3 PDD 32
PDD H6 H6 H 0 1 N N N N N N 21.887 10.701 68.823 -2.451 -0.704 -2.201 H6 PDD 33
PDD HA HA H 0 1 N N N N N N 24.879 17.895 69.782 1.700 1.474 2.924 HA PDD 34
PDD HB1 1HB H 0 1 N N N N N N 22.774 17.792 68.419 3.285 -0.488 1.206 HB1 PDD 35
PDD HB2 2HB H 0 1 N N N N N N 23.919 18.996 67.643 2.747 1.132 0.703 HB2 PDD 36
PDD HB3 3HB H 0 1 N N N N N N 23.615 17.299 67.021 3.945 0.957 2.008 HB3 PDD 37
PDD HXT HXT H 0 1 N Y N N N N 27.930 16.908 67.514 3.709 -0.574 5.223 HXT PDD 38
#
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
PDD N C4A SING N N 1
PDD N CA SING N N 2
PDD N H SING N N 3
PDD N1 C2 DOUB Y N 4
PDD N1 C6 SING Y N 5
PDD C2 C2A SING N N 6
PDD C2 C3 SING Y N 7
PDD C2A H2A1 SING N N 8
PDD C2A H2A2 SING N N 9
PDD C2A H2A3 SING N N 10
PDD C3 O3A SING N N 11
PDD C3 C4 DOUB Y N 12
PDD O3A HO3 SING N N 13
PDD C4 C4A SING N N 14
PDD C4 C5 SING Y N 15
PDD C4A H4A1 SING N N 16
PDD C4A H4A2 SING N N 17
PDD C5 C5A SING N N 18
PDD C5 C6 DOUB Y N 19
PDD C5A OP4 SING N N 20
PDD C5A H5A1 SING N N 21
PDD C5A H5A2 SING N N 22
PDD OP4 P SING N N 23
PDD P OP1 DOUB N N 24
PDD P OP2 SING N N 25
PDD P OP3 SING N N 26
PDD OP2 HOP2 SING N N 27
PDD OP3 HOP3 SING N N 28
PDD C6 H6 SING N N 29
PDD CA CB SING N N 30
PDD CA C SING N N 31
PDD CA HA SING N N 32
PDD CB HB1 SING N N 33
PDD CB HB2 SING N N 34
PDD CB HB3 SING N N 35
PDD C O DOUB N N 36
PDD C OXT SING N N 37
PDD OXT HXT SING N N 38
#
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
PDD SMILES ACDLabs 10.04 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)C"
PDD SMILES_CANONICAL CACTVS 3.341 "C[C@@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PDD SMILES CACTVS 3.341 "C[CH](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)C(O)=O"
PDD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](C)C(=O)O)O"
PDD SMILES "OpenEye OEToolkits" 1.5.0 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)C(=O)O)O"
PDD InChI InChI 1.03 "InChI=1S/C11H17N2O7P/c1-6-10(14)9(4-13-7(2)11(15)16)8(3-12-6)5-20-21(17,18)19/h3,7,13-14H,4-5H2,1-2H3,(H,15,16)(H2,17,18,19)/t7-/m1/s1"
PDD InChIKey InChI 1.03 WACJCHFWJNNBPR-SSDOTTSWSA-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
PDD "SYSTEMATIC NAME" ACDLabs 10.04 "N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-D-alanine"
PDD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]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
PDD "Create component" 2002-03-18 RCSB
PDD "Modify descriptor" 2011-06-04 RCSB
PDD "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PDD
_pdbx_chem_comp_pcm.modified_residue_id LYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category "Covalent chemical modification"
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom CB
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#