data_HDB
#
_chem_comp.id HDB
_chem_comp.name "(R)-1-(4-(4-(HYDROXYMETHYL)-1,3,2-DIOXABOROLAN-2-YL)BENZYL)GUANIDINE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H16 B N3 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-06-02
_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 249.074
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HDB
_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 1ZMJ
_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
HDB C01 C01 C 0 1 Y N N N N N 9.701 71.977 81.750 -2.015 -0.260 -0.610 C01 HDB 1
HDB C02 C02 C 0 1 Y N N N N N 8.619 72.909 82.349 -1.208 0.833 -0.871 C02 HDB 2
HDB C03 C03 C 0 1 Y N N N N N 8.399 72.886 83.753 0.158 0.743 -0.694 C03 HDB 3
HDB C04 C04 C 0 1 Y N N N N N 9.158 72.019 84.603 0.724 -0.454 -0.261 C04 HDB 4
HDB C05 C05 C 0 1 Y N N N N N 10.151 71.165 84.025 -0.093 -1.554 -0.004 C05 HDB 5
HDB C06 C06 C 0 1 Y N N N N N 10.411 71.148 82.641 -1.458 -1.451 -0.180 C06 HDB 6
HDB C07 C07 C 0 1 N N N N N N 10.002 71.954 80.269 -3.506 -0.154 -0.801 C07 HDB 7
HDB B B B 0 1 N N N N N N 8.956 71.985 86.102 2.278 -0.564 -0.061 B HDB 8
HDB N09 N09 N 0 1 N N N N N N 11.447 72.121 80.117 -4.128 0.289 0.450 N09 HDB 9
HDB C10 C10 C 0 1 N N N N N N 12.131 71.852 78.900 -5.491 0.458 0.517 C10 HDB 10
HDB N11 N11 N 0 1 N N N N N N 13.407 72.003 78.814 -6.270 0.212 -0.588 N11 HDB 11
HDB N12 N12 N 0 1 N N N N N N 11.430 71.411 77.770 -6.044 0.852 1.630 N12 HDB 12
HDB O13 O13 O 0 1 N N N N N N 7.905 72.812 86.613 3.219 0.484 -0.295 O13 HDB 13
HDB O14 O14 O 0 1 N N N N N N 8.720 70.648 86.570 2.974 -1.727 0.375 O14 HDB 14
HDB C15 C15 C 0 1 N N R N N N 7.059 71.975 87.366 4.352 0.157 0.549 C15 HDB 15
HDB C16 C16 C 0 1 N N N N N N 7.936 70.789 87.737 4.374 -1.389 0.449 C16 HDB 16
HDB C17 C17 C 0 1 N N N N N N 6.499 72.698 88.615 5.642 0.761 -0.010 C17 HDB 17
HDB O18 O18 O 0 1 N N N N N N 6.358 74.082 88.395 5.638 2.174 0.204 O18 HDB 18
HDB H02 H02 H 0 1 N N N N N N 8.043 73.564 81.712 -1.648 1.760 -1.207 H02 HDB 19
HDB H03 H03 H 0 1 N N N N N N 7.649 73.532 84.185 0.787 1.598 -0.894 H03 HDB 20
HDB H05 H05 H 0 1 N N N N N N 10.719 70.513 84.671 0.340 -2.484 0.332 H05 HDB 21
HDB H06 H06 H 0 1 N N N N N N 11.171 70.485 82.254 -2.092 -2.302 0.018 H06 HDB 22
HDB H071 1H07 H 0 0 N N N N N N 9.461 72.759 79.750 -3.907 -1.128 -1.081 H071 HDB 23
HDB H072 2H07 H 0 0 N N N N N N 9.682 70.997 79.831 -3.722 0.567 -1.589 H072 HDB 24
HDB H09 H09 H 0 1 N N N N N N 11.977 72.438 80.903 -3.579 0.463 1.230 H09 HDB 25
HDB H111 1H11 H 0 0 N N N N N N 13.999 72.308 79.560 -5.858 -0.082 -1.416 H111 HDB 26
HDB H112 2H11 H 0 0 N N N N N N 13.720 71.771 77.893 -7.232 0.327 -0.539 H112 HDB 27
HDB H12 H12 H 0 1 N N N N N N 10.455 71.336 77.977 -7.006 0.971 1.677 H12 HDB 28
HDB H15 H15 H 0 1 N N N N N N 6.167 71.667 86.801 4.185 0.480 1.576 H15 HDB 29
HDB H161 1H16 H 0 0 N N N N N N 8.523 70.937 88.655 4.830 -1.827 1.338 H161 HDB 30
HDB H162 2H16 H 0 0 N N N N N N 7.346 69.886 87.955 4.897 -1.710 -0.452 H162 HDB 31
HDB H171 1H17 H 0 0 N N N N N N 7.207 72.551 89.444 6.500 0.319 0.498 H171 HDB 32
HDB H172 2H17 H 0 0 N N N N N N 5.512 72.276 88.855 5.707 0.555 -1.078 H172 HDB 33
HDB H18 H18 H 0 1 N N N N N N 6.326 74.534 89.230 6.466 2.514 -0.162 H18 HDB 34
#
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
HDB C01 C02 SING Y N 1
HDB C01 C06 DOUB Y N 2
HDB C01 C07 SING N N 3
HDB C02 C03 DOUB Y N 4
HDB C02 H02 SING N N 5
HDB C03 C04 SING Y N 6
HDB C03 H03 SING N N 7
HDB C04 C05 DOUB Y N 8
HDB C04 B SING N N 9
HDB C05 C06 SING Y N 10
HDB C05 H05 SING N N 11
HDB C06 H06 SING N N 12
HDB C07 N09 SING N N 13
HDB C07 H071 SING N N 14
HDB C07 H072 SING N N 15
HDB B O13 SING N N 16
HDB B O14 SING N N 17
HDB N09 C10 SING N N 18
HDB N09 H09 SING N N 19
HDB C10 N11 SING N N 20
HDB C10 N12 DOUB N N 21
HDB N11 H111 SING N N 22
HDB N11 H112 SING N N 23
HDB N12 H12 SING N N 24
HDB O13 C15 SING N N 25
HDB O14 C16 SING N N 26
HDB C15 C16 SING N N 27
HDB C15 C17 SING N N 28
HDB C15 H15 SING N N 29
HDB C16 H161 SING N N 30
HDB C16 H162 SING N N 31
HDB C17 O18 SING N N 32
HDB C17 H171 SING N N 33
HDB C17 H172 SING N N 34
HDB O18 H18 SING N N 35
#
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
HDB SMILES ACDLabs 10.04 "OCC1OB(OC1)c2ccc(cc2)CNC(=[N@H])N"
HDB SMILES_CANONICAL CACTVS 3.341 "NC(=N)NCc1ccc(cc1)B2OC[C@@H](CO)O2"
HDB SMILES CACTVS 3.341 "NC(=N)NCc1ccc(cc1)B2OC[CH](CO)O2"
HDB SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "[H]/N=C(/N)\NCc1ccc(cc1)B2OC[C@H](O2)CO"
HDB SMILES "OpenEye OEToolkits" 1.5.0 "[H]N=C(N)NCc1ccc(cc1)B2OCC(O2)CO"
HDB InChI InChI 1.03 "InChI=1S/C11H16BN3O3/c13-11(14)15-5-8-1-3-9(4-2-8)12-17-7-10(6-16)18-12/h1-4,10,16H,5-7H2,(H4,13,14,15)/t10-/m1/s1"
HDB InChIKey InChI 1.03 IIZOWFNBOXPJES-SNVBAGLBSA-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
HDB "SYSTEMATIC NAME" ACDLabs 10.04 "1-{4-[(4R)-4-(hydroxymethyl)-1,3,2-dioxaborolan-2-yl]benzyl}guanidine"
HDB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[[4-[(4R)-4-(hydroxymethyl)-1,3,2-dioxaborolan-2-yl]phenyl]methyl]guanidine"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HDB "Create component" 2005-06-02 RCSB
HDB "Modify descriptor" 2011-06-04 RCSB
HDB "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id HDB
_pdbx_chem_comp_pcm.modified_residue_id SER
_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 B
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#