data_6YT
#
_chem_comp.id 6YT
_chem_comp.name N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H15 N3 O4 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2013-10-01
_chem_comp.pdbx_modified_date 2014-09-05
_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 333.362
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 6YT
_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 4C8R
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
6YT CAK CAK C 0 1 Y N N N N N -98.270 21.614 19.347 -4.380 -1.295 0.985 CAK 6YT 1
6YT CAF CAF C 0 1 Y N N N N N -99.100 21.165 20.330 -5.248 -2.306 0.603 CAF 6YT 2
6YT CAE CAE C 0 1 Y N N N N N -100.434 21.004 20.100 -6.007 -2.125 -0.544 CAE 6YT 3
6YT CAH CAH C 0 1 Y N N N N N -100.951 21.301 18.852 -5.873 -0.952 -1.262 CAH 6YT 4
6YT NAN NAN N 0 1 Y N N N N N -100.128 21.756 17.865 -5.036 -0.012 -0.869 NAN 6YT 5
6YT CAU CAU C 0 1 Y N N N N N -98.788 21.913 18.096 -4.299 -0.149 0.216 CAU 6YT 6
6YT CAL CAL C 0 1 N N N N N N -97.877 22.413 16.987 -3.358 0.955 0.622 CAL 6YT 7
6YT SAQ SAQ S 0 1 N N N N N N -96.285 21.633 17.032 -1.739 0.685 -0.149 SAQ 6YT 8
6YT CB CB C 0 1 N N N N N N -96.844 20.012 16.581 -0.762 2.091 0.448 CB 6YT 9
6YT CA CA C 0 1 N N R N N N -96.259 19.554 15.266 0.655 2.008 -0.123 CA 6YT 10
6YT C C C 0 1 N N N N N N -97.002 20.268 14.155 1.466 3.176 0.373 C 6YT 11
6YT O O O 0 1 N N N N N N -96.730 21.489 13.988 1.078 4.431 0.094 O 6YT 12
6YT OXT OXT O 0 1 N N N N N N -97.841 19.596 13.495 2.467 2.985 1.022 OXT 6YT 13
6YT N N N 0 1 N N N N N N -94.861 19.834 15.208 1.283 0.757 0.310 N 6YT 14
6YT CAS CAS C 0 1 N N N N N N -94.022 19.177 16.029 2.276 0.213 -0.421 CAS 6YT 15
6YT OAB OAB O 0 1 N N N N N N -94.446 18.524 17.118 2.649 0.759 -1.441 OAB 6YT 16
6YT CAV CAV C 0 1 Y N N N N N -92.665 19.145 15.752 2.910 -1.049 0.017 CAV 6YT 17
6YT NAO NAO N 0 1 Y N N N N N -91.810 18.805 16.759 2.498 -1.642 1.132 NAO 6YT 18
6YT CAI CAI C 0 1 Y N N N N N -90.468 18.755 16.527 3.035 -2.764 1.556 CAI 6YT 19
6YT CAG CAG C 0 1 Y N N N N N -89.967 19.042 15.266 4.060 -3.378 0.851 CAG 6YT 20
6YT CAJ CAJ C 0 1 Y N N N N N -90.824 19.375 14.255 4.524 -2.800 -0.317 CAJ 6YT 21
6YT CAT CAT C 0 1 Y N N N N N -92.173 19.426 14.486 3.935 -1.613 -0.749 CAT 6YT 22
6YT OAD OAD O 0 1 N N N N N N -93.064 19.766 13.447 4.354 -1.012 -1.891 OAD 6YT 23
6YT HAK HAK H 0 1 N N N N N N -97.215 21.736 19.541 -3.777 -1.400 1.875 HAK 6YT 24
6YT HAF HAF H 0 1 N N N N N N -98.696 20.934 21.304 -5.332 -3.212 1.184 HAF 6YT 25
6YT HAE HAE H 0 1 N N N N N N -101.082 20.647 20.887 -6.694 -2.891 -0.871 HAE 6YT 26
6YT HAH HAH H 0 1 N N N N N N -102.006 21.173 18.660 -6.461 -0.804 -2.156 HAH 6YT 27
6YT HAL1 HAL1 H 0 0 N N N N N N -98.349 22.200 16.017 -3.761 1.914 0.295 HAL1 6YT 28
6YT HAL2 HAL2 H 0 0 N N N N N N -97.744 23.499 17.100 -3.248 0.959 1.707 HAL2 6YT 29
6YT HB1C HB1C H 0 0 N N N N N N -96.547 19.303 17.368 -1.230 3.022 0.125 HB1C 6YT 30
6YT HB2C HB2C H 0 0 N N N N N N -97.941 20.026 16.495 -0.717 2.066 1.537 HB2C 6YT 31
6YT HA HA H 0 1 N N N N N N -96.428 18.472 15.163 0.609 2.033 -1.212 HA 6YT 32
6YT H H H 0 1 N N N N N N -94.508 20.512 14.563 0.985 0.322 1.124 H 6YT 33
6YT HB HB H 0 1 N N N N N N -97.258 21.838 13.279 1.630 5.147 0.433 HB 6YT 34
6YT HAI HAI H 0 1 N N N N N N -89.793 18.491 17.327 2.672 -3.215 2.467 HAI 6YT 35
6YT HAG HAG H 0 1 N N N N N N -88.903 19.002 15.084 4.492 -4.300 1.211 HAG 6YT 36
6YT HAJ HAJ H 0 1 N N N N N N -90.437 19.598 13.272 5.321 -3.259 -0.882 HAJ 6YT 37
6YT HAD HAD H 0 1 N N N N N N -92.574 19.928 12.649 5.072 -0.378 -1.761 HAD 6YT 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
6YT CAK CAF DOUB Y N 1
6YT CAK CAU SING Y N 2
6YT CAF CAE SING Y N 3
6YT CAE CAH DOUB Y N 4
6YT CAH NAN SING Y N 5
6YT NAN CAU DOUB Y N 6
6YT CAU CAL SING N N 7
6YT CAL SAQ SING N N 8
6YT SAQ CB SING N N 9
6YT CB CA SING N N 10
6YT CA C SING N N 11
6YT CA N SING N N 12
6YT C O SING N N 13
6YT C OXT DOUB N N 14
6YT N CAS SING N N 15
6YT CAS OAB DOUB N N 16
6YT CAS CAV SING N N 17
6YT CAV NAO SING Y N 18
6YT CAV CAT DOUB Y N 19
6YT NAO CAI DOUB Y N 20
6YT CAI CAG SING Y N 21
6YT CAG CAJ DOUB Y N 22
6YT CAJ CAT SING Y N 23
6YT CAT OAD SING N N 24
6YT CAK HAK SING N N 25
6YT CAF HAF SING N N 26
6YT CAE HAE SING N N 27
6YT CAH HAH SING N N 28
6YT CAL HAL1 SING N N 29
6YT CAL HAL2 SING N N 30
6YT CB HB1C SING N N 31
6YT CB HB2C SING N N 32
6YT CA HA SING N N 33
6YT N H SING N N 34
6YT O HB SING N N 35
6YT CAI HAI SING N N 36
6YT CAG HAG SING N N 37
6YT CAJ HAJ SING N N 38
6YT OAD HAD SING N N 39
#
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
6YT SMILES ACDLabs 12.01 O=C(c1ncccc1O)NC(C(=O)O)CSCc2ncccc2
6YT InChI InChI 1.03 InChI=1S/C15H15N3O4S/c19-12-5-3-7-17-13(12)14(20)18-11(15(21)22)9-23-8-10-4-1-2-6-16-10/h1-7,11,19H,8-9H2,(H,18,20)(H,21,22)/t11-/m0/s1
6YT InChIKey InChI 1.03 KMBXCWNZAPWGKZ-NSHDSACASA-N
6YT SMILES_CANONICAL CACTVS 3.385 OC(=O)[C@H](CSCc1ccccn1)NC(=O)c2ncccc2O
6YT SMILES CACTVS 3.385 OC(=O)[CH](CSCc1ccccn1)NC(=O)c2ncccc2O
6YT SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1ccnc(c1)CSC[C@@H](C(=O)O)NC(=O)c2c(cccn2)O
6YT SMILES "OpenEye OEToolkits" 1.9.2 c1ccnc(c1)CSCC(C(=O)O)NC(=O)c2c(cccn2)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
6YT "SYSTEMATIC NAME" ACDLabs 12.01 N-[(3-hydroxypyridin-2-yl)carbonyl]-S-(pyridin-2-ylmethyl)-L-cysteine
6YT "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2R)-2-[(3-oxidanylpyridin-2-yl)carbonylamino]-3-(pyridin-2-ylmethylsulfanyl)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
6YT 'Create component' 2013-10-01 EBI
6YT 'Initial release' 2014-05-14 RCSB
6YT 'Modify descriptor' 2014-09-05 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
6YT CAK C 6.404 -4.875 1
6YT CAF C 6.404 -6.375 2
6YT CAE C 5.104 -7.125 3
6YT CAH C 3.805 -6.375 4
6YT NAN N 3.805 -4.875 5
6YT CAU C 5.104 -4.125 6
6YT CAL C 5.104 -2.625 7
6YT SAQ S 6.404 -1.875 8
6YT CB C 6.404 -0.375 9
6YT CA C 7.702 0.375 10
6YT C C 9.002 -0.375 11
6YT O O 9.002 -1.875 12
6YT OXT O 10.301 0.375 13
6YT N N 7.702 1.875 14
6YT CAS C 6.404 2.625 15
6YT OAB O 5.104 1.875 16
6YT CAV C 6.404 4.125 17
6YT NAO N 7.702 4.875 18
6YT CAI C 7.702 6.375 19
6YT CAG C 6.404 7.125 20
6YT CAJ C 5.104 6.375 21
6YT CAT C 5.104 4.875 22
6YT OAD O 3.805 4.125 23
#
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
6YT CAK CAF DOUBLE NONE 1
6YT CAK CAU SINGLE NONE 2
6YT CAF CAE SINGLE NONE 3
6YT CAE CAH DOUBLE NONE 4
6YT CAH NAN SINGLE NONE 5
6YT NAN CAU DOUBLE NONE 6
6YT CAU CAL SINGLE NONE 7
6YT CAL SAQ SINGLE NONE 8
6YT SAQ CB SINGLE NONE 9
6YT CA CB SINGLE BEGINDASH 10
6YT CA C SINGLE NONE 11
6YT CA N SINGLE NONE 12
6YT C O SINGLE NONE 13
6YT C OXT DOUBLE NONE 14
6YT N CAS SINGLE NONE 15
6YT CAS OAB DOUBLE NONE 16
6YT CAS CAV SINGLE NONE 17
6YT CAV NAO DOUBLE NONE 18
6YT CAV CAT SINGLE NONE 19
6YT NAO CAI SINGLE NONE 20
6YT CAI CAG DOUBLE NONE 21
6YT CAG CAJ SINGLE NONE 22
6YT CAJ CAT DOUBLE NONE 23
6YT CAT OAD SINGLE NONE 24
#
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
6YT MurckoScaffold S1 scaffold O=C(NCCSCc1ccccn1)c1ccccn1 InChI=1S/C14H15N3OS/c18-14(13-6-2-4-8-16-13)17-9-10-19-11-12-5-1-3-7-15-12/h1-8H,9-11H2,(H,17,18) QUGOOFNDCOZWRP-UHFFFAOYSA-N
6YT amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
6YT peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
6YT pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
6YT CAK S1 1
6YT CAF S1 1
6YT CAE S1 1
6YT CAH S1 1
6YT NAN S1 1
6YT CAU S1 1
6YT CAL S1 1
6YT SAQ S1 1
6YT CB S1 1
6YT CA S1 1
6YT N S1 1
6YT CAS S1 1
6YT OAB S1 1
6YT CAV S1 1
6YT NAO S1 1
6YT CAI S1 1
6YT CAG S1 1
6YT CAJ S1 1
6YT CAT S1 1
6YT N F1 1
6YT CAS F1 1
6YT OAB F1 1
6YT CAV F1 1
6YT OXT F2 1
6YT C F2 1
6YT CA F2 1
6YT N F2 1
6YT CAH F3 1
6YT CAE F3 1
6YT CAF F3 1
6YT CAK F3 1
6YT CAU F3 1
6YT NAN F3 1
6YT CAV F3 2
6YT CAT F3 2
6YT CAJ F3 2
6YT CAG F3 2
6YT CAI F3 2
6YT NAO F3 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 6YT
_pdbe_chem_comp_rdkit_properties.exactmw 333.078
_pdbe_chem_comp_rdkit_properties.amw 333.369
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.200
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 157.643
_pdbe_chem_comp_rdkit_properties.tpsa 112.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.727
_pdbe_chem_comp_rdkit_properties.CrippenMR 84.049
_pdbe_chem_comp_rdkit_properties.chi0v 11.699
_pdbe_chem_comp_rdkit_properties.chi1v 6.383
_pdbe_chem_comp_rdkit_properties.chi2v 2.577
_pdbe_chem_comp_rdkit_properties.chi3v 2.577
_pdbe_chem_comp_rdkit_properties.chi4v 1.559
_pdbe_chem_comp_rdkit_properties.chi0n 25.883
_pdbe_chem_comp_rdkit_properties.chi1n 12.830
_pdbe_chem_comp_rdkit_properties.chi2n 1.986
_pdbe_chem_comp_rdkit_properties.chi3n 1.986
_pdbe_chem_comp_rdkit_properties.chi4n 1.089
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.610
_pdbe_chem_comp_rdkit_properties.kappa1 5.789
_pdbe_chem_comp_rdkit_properties.kappa2 8.136
_pdbe_chem_comp_rdkit_properties.kappa3 4.958
_pdbe_chem_comp_rdkit_properties.Phi 2.048
#
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
6YT UniChem ZINC ZINC000098208557
6YT UniChem SureChEMBL SCHEMBL16834576
6YT UniChem PubChem 73659100
6YT UniChem BRENDA 223688
#
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
6YT CAK 4.724 -1.755 0.079 ETKDGv3 1
6YT CAF 5.881 -1.677 -0.587 ETKDGv3 2
6YT CAE 6.385 -0.364 -1.032 ETKDGv3 3
6YT CAH 5.673 0.737 -0.762 ETKDGv3 4
6YT NAN 4.430 0.634 -0.047 ETKDGv3 5
6YT CAU 3.964 -0.514 0.360 ETKDGv3 6
6YT CAL 2.656 -0.576 1.088 ETKDGv3 7
6YT SAQ 1.367 -1.322 0.027 ETKDGv3 8
6YT CB 0.983 0.180 -0.950 ETKDGv3 9
6YT CA -0.100 1.027 -0.262 ETKDGv3 10
6YT C -0.324 2.290 -1.043 ETKDGv3 11
6YT O -1.017 2.249 -2.250 ETKDGv3 12
6YT OXT 0.140 3.383 -0.622 ETKDGv3 13
6YT N -1.359 0.283 -0.157 ETKDGv3 14
6YT CAS -2.413 0.691 0.732 ETKDGv3 15
6YT OAB -2.256 1.715 1.452 ETKDGv3 16
6YT CAV -3.677 -0.079 0.808 ETKDGv3 17
6YT NAO -3.820 -1.144 0.067 ETKDGv3 18
6YT CAI -5.014 -1.942 0.086 ETKDGv3 19
6YT CAG -6.031 -1.605 0.883 ETKDGv3 20
6YT CAJ -5.913 -0.410 1.738 ETKDGv3 21
6YT CAT -4.793 0.329 1.711 ETKDGv3 22
6YT OAD -4.680 1.460 2.519 ETKDGv3 23
6YT HAK 4.348 -2.716 0.407 ETKDGv3 24
6YT HAF 6.448 -2.574 -0.801 ETKDGv3 25
6YT HAE 7.321 -0.294 -1.570 ETKDGv3 26
6YT HAH 6.029 1.707 -1.082 ETKDGv3 27
6YT HAL1 2.349 0.434 1.433 ETKDGv3 28
6YT HAL2 2.776 -1.212 1.990 ETKDGv3 29
6YT HB1C 1.901 0.785 -1.108 ETKDGv3 30
6YT HB2C 0.625 -0.143 -1.951 ETKDGv3 31
6YT HA 0.255 1.288 0.759 ETKDGv3 32
6YT H -1.504 -0.554 -0.767 ETKDGv3 33
6YT HB -1.166 3.092 -2.792 ETKDGv3 34
6YT HAI -5.086 -2.816 -0.547 ETKDGv3 35
6YT HAG -6.934 -2.202 0.903 ETKDGv3 36
6YT HAJ -6.738 -0.137 2.383 ETKDGv3 37
6YT HAD -5.428 1.753 3.139 ETKDGv3 38
#