data_4ZN
#
_chem_comp.id 4ZN
_chem_comp.name "(2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H22 N O4 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-07-02
_chem_comp.pdbx_modified_date 2020-06-01
_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 299.303
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4ZN
_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 5CBM
_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.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
4ZN N12 N1 N 0 1 N N N N N N 187.791 50.078 96.243 -1.313 2.058 1.207 N12 4ZN 1
4ZN C13 C1 C 0 1 Y N N N N N 187.778 48.022 97.380 -2.944 0.408 0.485 C13 4ZN 2
4ZN C15 C2 C 0 1 Y N N N N N 186.169 46.368 98.003 -4.652 1.077 -1.053 C15 4ZN 3
4ZN C17 C3 C 0 1 Y N N N N N 187.378 47.538 99.717 -4.976 -0.849 0.332 C17 4ZN 4
4ZN C02 C4 C 0 1 N N N N N N 189.286 42.663 92.968 5.165 2.149 0.526 C02 4ZN 5
4ZN C03 C5 C 0 1 N N N N N N 188.655 43.848 92.259 3.820 1.605 0.040 C03 4ZN 6
4ZN C04 C6 C 0 1 N N N N N N 189.679 44.518 91.376 3.655 1.912 -1.449 C04 4ZN 7
4ZN C05 C7 C 0 1 N N N N N N 187.882 44.854 93.122 3.774 0.091 0.257 C05 4ZN 8
4ZN C06 C8 C 0 1 N N S N N N 188.364 45.429 94.475 2.405 -0.444 -0.166 C06 4ZN 9
4ZN C07 C9 C 0 1 N N N N N N 189.403 46.577 94.461 1.331 0.097 0.780 C07 4ZN 10
4ZN P08 P1 P 0 1 N N N N N N 188.634 48.207 94.652 -0.315 -0.157 0.041 P08 4ZN 11
4ZN O09 O1 O 0 1 N N N N N N 187.183 48.160 94.048 -0.611 -1.735 -0.081 O09 4ZN 12
4ZN O10 O2 O 0 1 N N N N N N 189.410 49.216 93.906 -0.352 0.456 -1.306 O10 4ZN 13
4ZN C11 C10 C 0 1 N N R N N N 188.517 48.848 96.352 -1.583 0.618 1.097 C11 4ZN 14
4ZN C14 C11 C 0 1 Y N N N N N 186.828 47.091 97.016 -3.406 1.274 -0.488 C14 4ZN 15
4ZN C16 C12 C 0 1 Y N N N N N 186.438 46.595 99.346 -5.436 0.014 -0.645 C16 4ZN 16
4ZN C18 C13 C 0 1 Y N N N N N 188.038 48.249 98.727 -3.728 -0.655 0.893 C18 4ZN 17
4ZN C19 C14 C 0 1 N N N N N N 188.746 44.410 95.530 2.413 -1.949 -0.108 C19 4ZN 18
4ZN O20 O3 O 0 1 N N N N N N 189.800 44.582 96.189 1.791 -2.662 -1.060 O20 4ZN 19
4ZN O21 O4 O 0 1 N N N N N N 188.007 43.416 95.756 2.980 -2.516 0.797 O21 4ZN 20
4ZN H1 H1 H 0 1 N N N N N N 187.690 50.487 97.150 -1.333 2.500 0.301 H1 4ZN 21
4ZN H2 H2 H 0 1 N N N N N N 188.290 50.708 95.647 -1.964 2.500 1.839 H2 4ZN 22
4ZN H4 H4 H 0 1 N N N N N N 185.440 45.622 97.722 -5.012 1.752 -1.816 H4 4ZN 23
4ZN H5 H5 H 0 1 N N N N N N 187.594 47.718 100.760 -5.589 -1.679 0.651 H5 4ZN 24
4ZN H6 H6 H 0 1 N N N N N N 188.536 42.178 93.610 5.972 1.677 -0.034 H6 4ZN 25
4ZN H7 H7 H 0 1 N N N N N N 189.652 41.942 92.222 5.198 3.227 0.372 H7 4ZN 26
4ZN H8 H8 H 0 1 N N N N N N 190.128 43.011 93.585 5.283 1.930 1.588 H8 4ZN 27
4ZN H9 H9 H 0 1 N N N N N N 187.909 43.418 91.574 3.013 2.077 0.601 H9 4ZN 28
4ZN H10 H10 H 0 1 N N N N N N 189.218 45.376 90.864 2.657 1.613 -1.773 H10 4ZN 29
4ZN H11 H11 H 0 1 N N N N N N 190.521 44.868 91.991 3.786 2.980 -1.617 H11 4ZN 30
4ZN H12 H12 H 0 1 N N N N N N 190.045 43.799 90.628 4.402 1.360 -2.019 H12 4ZN 31
4ZN H13 H13 H 0 1 N N N N N N 187.719 45.729 92.475 4.551 -0.386 -0.340 H13 4ZN 32
4ZN H14 H14 H 0 1 N N N N N N 186.917 44.372 93.337 3.941 -0.130 1.312 H14 4ZN 33
4ZN H15 H15 H 0 1 N N N N N N 187.462 45.905 94.886 2.188 -0.121 -1.184 H15 4ZN 34
4ZN H16 H16 H 0 1 N N N N N N 190.112 46.422 95.288 1.387 -0.430 1.733 H16 4ZN 35
4ZN H17 H17 H 0 1 N N N N N N 189.944 46.552 93.504 1.495 1.163 0.944 H17 4ZN 36
4ZN H18 H18 H 0 1 N N N N N N 187.115 48.786 93.337 -0.603 -2.203 0.766 H18 4ZN 37
4ZN H19 H19 H 0 1 N N N N N N 189.549 49.027 96.688 -1.556 0.167 2.088 H19 4ZN 38
4ZN H20 H20 H 0 1 N N N N N N 186.598 46.925 95.974 -2.794 2.105 -0.806 H20 4ZN 39
4ZN H21 H21 H 0 1 N N N N N N 185.911 46.033 100.103 -6.408 -0.142 -1.090 H21 4ZN 40
4ZN H22 H22 H 0 1 N N N N N N 188.768 48.994 99.007 -3.365 -1.335 1.650 H22 4ZN 41
4ZN H23 H23 H 0 1 N N N N N N 189.899 43.877 96.819 1.824 -3.625 -0.980 H23 4ZN 42
#
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
4ZN C04 C03 SING N N 1
4ZN C03 C02 SING N N 2
4ZN C03 C05 SING N N 3
4ZN C05 C06 SING N N 4
4ZN O10 P08 DOUB N N 5
4ZN O09 P08 SING N N 6
4ZN C07 C06 SING N N 7
4ZN C07 P08 SING N N 8
4ZN C06 C19 SING N N 9
4ZN P08 C11 SING N N 10
4ZN C19 O21 DOUB N N 11
4ZN C19 O20 SING N N 12
4ZN N12 C11 SING N N 13
4ZN C11 C13 SING N N 14
4ZN C14 C13 DOUB Y N 15
4ZN C14 C15 SING Y N 16
4ZN C13 C18 SING Y N 17
4ZN C15 C16 DOUB Y N 18
4ZN C18 C17 DOUB Y N 19
4ZN C16 C17 SING Y N 20
4ZN N12 H1 SING N N 21
4ZN N12 H2 SING N N 22
4ZN C15 H4 SING N N 23
4ZN C17 H5 SING N N 24
4ZN C02 H6 SING N N 25
4ZN C02 H7 SING N N 26
4ZN C02 H8 SING N N 27
4ZN C03 H9 SING N N 28
4ZN C04 H10 SING N N 29
4ZN C04 H11 SING N N 30
4ZN C04 H12 SING N N 31
4ZN C05 H13 SING N N 32
4ZN C05 H14 SING N N 33
4ZN C06 H15 SING N N 34
4ZN C07 H16 SING N N 35
4ZN C07 H17 SING N N 36
4ZN O09 H18 SING N N 37
4ZN C11 H19 SING N N 38
4ZN C14 H20 SING N N 39
4ZN C16 H21 SING N N 40
4ZN C18 H22 SING N N 41
4ZN O20 H23 SING N N 42
#
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
4ZN SMILES ACDLabs 12.01 NC(c1ccccc1)P(CC(CC(C)C)C(=O)O)(O)=O
4ZN InChI InChI 1.03 InChI=1S/C14H22NO4P/c1-10(2)8-12(14(16)17)9-20(18,19)13(15)11-6-4-3-5-7-11/h3-7,10,12-13H,8-9,15H2,1-2H3,(H,16,17)(H,18,19)/t12-,13-/m1/s1
4ZN InChIKey InChI 1.03 RUYPIGFYJMPICK-CHWSQXEVSA-N
4ZN SMILES_CANONICAL CACTVS 3.385 CC(C)C[C@H](C[P](O)(=O)[C@@H](N)c1ccccc1)C(O)=O
4ZN SMILES CACTVS 3.385 CC(C)C[CH](C[P](O)(=O)[CH](N)c1ccccc1)C(O)=O
4ZN SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 CC(C)C[C@H](CP(=O)([C@H](c1ccccc1)N)O)C(=O)O
4ZN SMILES "OpenEye OEToolkits" 1.9.2 CC(C)CC(CP(=O)(C(c1ccccc1)N)O)C(=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
4ZN "SYSTEMATIC NAME" ACDLabs 12.01 "(2S)-2-{[(R)-[(R)-amino(phenyl)methyl](hydroxy)phosphoryl]methyl}-4-methylpentanoic acid"
4ZN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S)-2-[[[(R)-azanyl(phenyl)methyl]-oxidanyl-phosphoryl]methyl]-4-methyl-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
4ZN 'Create component' 2015-07-02 RCSB
4ZN 'Initial release' 2015-10-07 RCSB
4ZN 'Other modification' 2020-06-01 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
4ZN N12 N 3.805 0.000 1
4ZN C13 C 5.104 -2.250 2
4ZN C15 C 3.805 -4.500 3
4ZN C17 C 6.404 -4.500 4
4ZN C02 C 7.702 5.250 5
4ZN C03 C 6.404 4.500 6
4ZN C04 C 5.104 5.250 7
4ZN C05 C 6.404 3.000 8
4ZN C06 C 7.702 2.250 9
4ZN C07 C 7.702 0.750 10
4ZN P08 P 6.404 0.000 11
4ZN O09 O 7.154 -1.299 12
4ZN O10 O 5.654 1.299 13
4ZN C11 C 5.104 -0.750 14
4ZN C14 C 3.805 -3.000 15
4ZN C16 C 5.104 -5.250 16
4ZN C18 C 6.404 -3.000 17
4ZN C19 C 9.002 3.000 18
4ZN O20 O 10.301 2.250 19
4ZN O21 O 9.002 4.500 20
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
4ZN C04 C03 SINGLE NONE 1
4ZN C03 C02 SINGLE NONE 2
4ZN C03 C05 SINGLE NONE 3
4ZN C06 C05 SINGLE BEGINWEDGE 4
4ZN O10 P08 DOUBLE NONE 5
4ZN P08 O09 SINGLE BEGINDASH 6
4ZN C07 C06 SINGLE NONE 7
4ZN C07 P08 SINGLE NONE 8
4ZN C06 C19 SINGLE NONE 9
4ZN P08 C11 SINGLE NONE 10
4ZN C19 O21 DOUBLE NONE 11
4ZN C19 O20 SINGLE NONE 12
4ZN C11 N12 SINGLE BEGINDASH 13
4ZN C11 C13 SINGLE NONE 14
4ZN C14 C13 DOUBLE NONE 15
4ZN C14 C15 SINGLE NONE 16
4ZN C13 C18 SINGLE NONE 17
4ZN C15 C16 DOUBLE NONE 18
4ZN C18 C17 DOUBLE NONE 19
4ZN C16 C17 SINGLE NONE 20
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
4ZN MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
4ZN phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
4ZN C13 S1 1
4ZN C15 S1 1
4ZN C17 S1 1
4ZN C14 S1 1
4ZN C16 S1 1
4ZN C18 S1 1
4ZN C13 F1 1
4ZN C14 F1 1
4ZN C15 F1 1
4ZN C16 F1 1
4ZN C17 F1 1
4ZN C18 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4ZN
_pdbe_chem_comp_rdkit_properties.exactmw 299.129
_pdbe_chem_comp_rdkit_properties.amw 299.307
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 42
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 150.016
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.606
_pdbe_chem_comp_rdkit_properties.CrippenMR 78.378
_pdbe_chem_comp_rdkit_properties.chi0v 10.422
_pdbe_chem_comp_rdkit_properties.chi1v 6.319
_pdbe_chem_comp_rdkit_properties.chi2v 3.015
_pdbe_chem_comp_rdkit_properties.chi3v 3.015
_pdbe_chem_comp_rdkit_properties.chi4v 1.912
_pdbe_chem_comp_rdkit_properties.chi0n 31.527
_pdbe_chem_comp_rdkit_properties.chi1n 15.405
_pdbe_chem_comp_rdkit_properties.chi2n 1.716
_pdbe_chem_comp_rdkit_properties.chi3n 1.716
_pdbe_chem_comp_rdkit_properties.chi4n 0.959
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.160
_pdbe_chem_comp_rdkit_properties.kappa1 3.595
_pdbe_chem_comp_rdkit_properties.kappa2 7.023
_pdbe_chem_comp_rdkit_properties.kappa3 4.745
_pdbe_chem_comp_rdkit_properties.Phi 1.262
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
4ZN UniChem PDBe 4ZN
4ZN UniChem ZINC ZINC000012888865
4ZN UniChem Mcule MCULE-1988460111
4ZN UniChem PubChem 25579284
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
4ZN N12 2.528 2.030 1.420 ETKDGv3 1
4ZN C13 3.464 0.126 0.208 ETKDGv3 2
4ZN C15 5.079 -1.190 -1.085 ETKDGv3 3
4ZN C17 4.979 -1.439 1.338 ETKDGv3 4
4ZN C02 -4.417 0.957 -1.679 ETKDGv3 5
4ZN C03 -3.838 -0.341 -1.097 ETKDGv3 6
4ZN C04 -4.719 -0.873 0.039 ETKDGv3 7
4ZN C05 -2.345 -0.202 -0.698 ETKDGv3 8
4ZN C06 -2.053 0.737 0.507 ETKDGv3 9
4ZN C07 -0.648 1.378 0.431 ETKDGv3 10
4ZN P08 0.750 0.196 0.530 ETKDGv3 11
4ZN O09 0.620 -0.967 -0.693 ETKDGv3 12
4ZN O10 0.757 -0.483 1.881 ETKDGv3 13
4ZN C11 2.318 1.107 0.305 ETKDGv3 14
4ZN C14 3.985 -0.201 -0.990 ETKDGv3 15
4ZN C16 5.552 -1.777 0.020 ETKDGv3 16
4ZN C18 3.990 -0.541 1.430 ETKDGv3 17
4ZN C19 -2.268 0.066 1.842 ETKDGv3 18
4ZN O20 -2.008 -1.292 2.010 ETKDGv3 19
4ZN O21 -2.651 0.751 2.828 ETKDGv3 20
4ZN H1 3.431 2.534 1.262 ETKDGv3 21
4ZN H2 1.784 2.764 1.385 ETKDGv3 22
4ZN H4 5.495 -1.440 -2.052 ETKDGv3 23
4ZN H5 5.358 -1.922 2.230 ETKDGv3 24
4ZN H6 -3.749 1.361 -2.469 ETKDGv3 25
4ZN H7 -4.559 1.729 -0.894 ETKDGv3 26
4ZN H8 -5.407 0.753 -2.139 ETKDGv3 27
4ZN H9 -3.874 -1.098 -1.913 ETKDGv3 28
4ZN H10 -5.732 -1.112 -0.349 ETKDGv3 29
4ZN H11 -4.284 -1.804 0.460 ETKDGv3 30
4ZN H12 -4.827 -0.119 0.847 ETKDGv3 31
4ZN H13 -1.799 0.171 -1.593 ETKDGv3 32
4ZN H14 -1.939 -1.216 -0.501 ETKDGv3 33
4ZN H15 -2.761 1.589 0.457 ETKDGv3 34
4ZN H16 -0.543 2.112 1.258 ETKDGv3 35
4ZN H17 -0.555 1.946 -0.520 ETKDGv3 36
4ZN H18 1.252 -1.685 -0.435 ETKDGv3 37
4ZN H19 2.237 1.696 -0.637 ETKDGv3 38
4ZN H20 3.607 0.248 -1.900 ETKDGv3 39
4ZN H21 6.352 -2.503 -0.049 ETKDGv3 40
4ZN H22 3.574 -0.305 2.401 ETKDGv3 41
4ZN H23 -2.138 -1.739 2.909 ETKDGv3 42
#