data_4SC
#
_chem_comp.id 4SC
_chem_comp.name "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)"
_chem_comp.type "DNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C10 H16 N3 O6 P S"
_chem_comp.mon_nstd_parent_comp_id DC
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2022-04-07
_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 337.289
_chem_comp.one_letter_code C
_chem_comp.three_letter_code 4SC
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6MHT
_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
4SC P P P 0 1 N N N N N N -19.306 45.420 87.739 -3.784 1.166 -0.065 P 4SC 1
4SC OP1 O1P O 0 1 N N N N N N -19.710 45.872 86.370 -4.967 0.544 0.570 OP1 4SC 2
4SC OP2 O2P O 0 1 N N N N N N -17.881 45.200 87.986 -3.352 2.473 0.771 OP2 4SC 3
4SC "O5'" "O5'" O 0 1 N N N N N N -20.057 43.953 87.967 -2.566 0.113 -0.080 "O5'" 4SC 4
4SC "C5'" "C5'" C 0 1 N N N N N N -19.584 42.997 88.988 -2.672 -1.191 -0.654 "C5'" 4SC 5
4SC "C4'" "C4'" C 0 1 N N R N N N -20.227 41.613 88.748 -1.340 -1.927 -0.499 "C4'" 4SC 6
4SC "S4'" "S4'" S 0 1 N N N N N N -19.615 41.206 87.075 -0.001 -1.078 -1.434 "S4'" 4SC 7
4SC "C3'" "C3'" C 0 1 N N S N N N -19.735 40.545 89.724 -0.803 -1.812 0.952 "C3'" 4SC 8
4SC "O3'" "O3'" O 0 1 N N N N N N -20.543 40.545 91.028 -1.461 -2.769 1.785 "O3'" 4SC 9
4SC "C2'" "C2'" C 0 1 N N N N N N -20.000 39.193 88.937 0.702 -2.085 0.948 "C2'" 4SC 10
4SC "C1'" "C1'" C 0 1 N N R N N N -19.633 39.423 87.466 1.372 -1.668 -0.371 "C1'" 4SC 11
4SC N1 N1 N 0 1 N N N N N N -18.565 38.656 86.776 2.333 -0.587 -0.135 N1 4SC 12
4SC C2 C2 C 0 1 N N N N N N -18.515 38.779 85.376 1.949 0.516 0.534 C2 4SC 13
4SC O2 O2 O 0 1 N N N N N N -19.412 39.394 84.818 0.801 0.604 0.936 O2 4SC 14
4SC N3 N3 N 0 1 N N N N N N -17.482 38.177 84.665 2.802 1.513 0.763 N3 4SC 15
4SC C4 C4 C 0 1 N N N N N N -16.486 37.441 85.286 4.056 1.442 0.336 C4 4SC 16
4SC N4 N4 N 0 1 N N N N N N -15.388 36.985 84.562 4.929 2.478 0.578 N4 4SC 17
4SC C5 C5 C 0 1 N N N N N N -16.569 37.288 86.760 4.490 0.300 -0.368 C5 4SC 18
4SC C6 C6 C 0 1 N N N N N N -17.601 37.907 87.431 3.612 -0.707 -0.588 C6 4SC 19
4SC C5M C5M C 0 1 N N N N N N -16.750 35.700 86.690 5.910 0.199 -0.863 C5M 4SC 20
4SC "H5'" "H5'" H 0 1 N N N N N N -18.490 42.907 88.925 -3.457 -1.750 -0.143 "H5'" 4SC 21
4SC "H5''" "H5''" H 0 0 N N N N N N -19.865 43.362 89.987 -2.919 -1.104 -1.712 "H5''" 4SC 22
4SC "H4'" "H4'" H 0 1 N N N N N N -21.325 41.670 88.712 -1.431 -2.969 -0.803 "H4'" 4SC 23
4SC "H3'" "H3'" H 0 1 N N N N N N -18.660 40.662 89.928 -0.988 -0.807 1.332 "H3'" 4SC 24
4SC "HO3'" "HO3'" H 0 0 N Y N N N N -20.209 39.870 91.608 -1.173 -2.752 2.707 "HO3'" 4SC 25
4SC "H2'" "H2'" H 0 1 N N N N N N -19.377 38.389 89.356 1.163 -1.533 1.768 "H2'" 4SC 26
4SC "H2''" "H2''" H 0 0 N N N N N N -21.061 38.915 89.018 0.868 -3.151 1.107 "H2''" 4SC 27
4SC "H1'" "H1'" H 0 1 N N N N N N -20.546 39.109 86.938 1.867 -2.523 -0.831 "H1'" 4SC 28
4SC HN41 HN41 H 0 0 N N N N N N -15.314 37.188 83.586 4.627 3.262 1.063 HN41 4SC 29
4SC HN42 HN42 H 0 0 N N N N N N -14.674 36.454 85.018 5.845 2.424 0.265 HN42 4SC 30
4SC H61 H61 H 0 1 N N N N N N -17.660 37.805 88.505 3.922 -1.595 -1.120 H61 4SC 31
4SC H71 H71 H 0 1 N N N N N N -16.842 35.296 87.709 6.456 1.101 -0.585 H71 4SC 32
4SC H72 H72 H 0 1 N N N N N N -17.658 35.459 86.117 6.391 -0.669 -0.413 H72 4SC 33
4SC H73 H73 H 0 1 N N N N N N -15.875 35.253 86.196 5.910 0.094 -1.947 H73 4SC 34
4SC OP3 OP3 O 0 1 N Y N N N N ? ? ? -4.146 1.590 -1.575 OP3 4SC 35
4SC HOP2 H1 H 0 0 N N N N N N -17.389 45.387 87.195 -4.039 3.152 0.821 HOP2 4SC 36
4SC HOP3 H2 H 0 0 N Y N N N N ? ? ? -3.415 2.006 -2.053 HOP3 4SC 37
#
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
4SC P OP1 DOUB N N 1
4SC P OP2 SING N N 2
4SC P "O5'" SING N N 3
4SC "O5'" "C5'" SING N N 4
4SC "C5'" "C4'" SING N N 5
4SC "C5'" "H5'" SING N N 6
4SC "C5'" "H5''" SING N N 7
4SC "C4'" "S4'" SING N N 8
4SC "C4'" "C3'" SING N N 9
4SC "C4'" "H4'" SING N N 10
4SC "S4'" "C1'" SING N N 11
4SC "C3'" "O3'" SING N N 12
4SC "C3'" "C2'" SING N N 13
4SC "C3'" "H3'" SING N N 14
4SC "O3'" "HO3'" SING N N 15
4SC "C2'" "C1'" SING N N 16
4SC "C2'" "H2'" SING N N 17
4SC "C2'" "H2''" SING N N 18
4SC "C1'" N1 SING N N 19
4SC "C1'" "H1'" SING N N 20
4SC N1 C2 SING N N 21
4SC N1 C6 SING N N 22
4SC C2 O2 DOUB N N 23
4SC C2 N3 SING N N 24
4SC N3 C4 DOUB N N 25
4SC C4 N4 SING N N 26
4SC C4 C5 SING N N 27
4SC N4 HN41 SING N N 28
4SC N4 HN42 SING N N 29
4SC C5 C6 DOUB N N 30
4SC C5 C5M SING N N 31
4SC C6 H61 SING N N 32
4SC C5M H71 SING N N 33
4SC C5M H72 SING N N 34
4SC C5M H73 SING N N 35
4SC P OP3 SING N N 36
4SC OP2 HOP2 SING N N 37
4SC OP3 HOP3 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
4SC SMILES ACDLabs 12.01 O=P(O)(O)OCC1SC(CC1O)N1C=C(C)C(N)=NC1=O
4SC InChI InChI 1.03 InChI=1S/C10H16N3O6PS/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(21-8)4-19-20(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
4SC InChIKey InChI 1.03 GBRJOHLRKRNNCY-XLPZGREQSA-N
4SC SMILES_CANONICAL CACTVS 3.385 CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)S2)C(=O)N=C1N
4SC SMILES CACTVS 3.385 CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)S2)C(=O)N=C1N
4SC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](S2)COP(=O)(O)O)O
4SC SMILES "OpenEye OEToolkits" 2.0.7 CC1=CN(C(=O)N=C1N)C2CC(C(S2)COP(=O)(O)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
4SC "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5-methyl-4'-thiocytidine 5'-(dihydrogen phosphate)"
4SC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-thiolan-2-yl]methyl dihydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
4SC 'Create component' 1999-07-08 RCSB
4SC 'Modify descriptor' 2011-06-04 RCSB
4SC 'Other modification' 2022-04-07 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
4SC P P 9.603 -4.837 1
4SC OP1 O 11.095 -4.680 2
4SC OP2 O 8.993 -6.207 3
4SC "O5'" O 8.722 -3.623 4
4SC "C5'" C 7.230 -3.780 5
4SC "C4'" C 6.348 -2.566 6
4SC "S4'" S 6.812 -1.140 7
4SC "C3'" C 4.848 -2.566 8
4SC "O3'" O 3.966 -3.780 9
4SC "C2'" C 4.385 -1.140 10
4SC "C1'" C 5.598 -0.258 11
4SC N1 N 5.598 1.242 12
4SC C2 C 6.897 1.992 13
4SC O2 O 8.196 1.242 14
4SC N3 N 6.897 3.492 15
4SC C4 C 5.598 4.242 16
4SC N4 N 5.598 5.742 17
4SC C5 C 4.299 3.492 18
4SC C6 C 4.299 1.992 19
4SC C5M C 3.000 4.242 20
4SC OP3 O 10.213 -3.467 21
#
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
4SC P OP1 DOUBLE NONE 1
4SC P OP2 SINGLE NONE 2
4SC P "O5'" SINGLE NONE 3
4SC "O5'" "C5'" SINGLE NONE 4
4SC "C4'" "C5'" SINGLE BEGINDASH 5
4SC "C4'" "S4'" SINGLE NONE 6
4SC "C4'" "C3'" SINGLE NONE 7
4SC "S4'" "C1'" SINGLE NONE 8
4SC "C3'" "O3'" SINGLE BEGINWEDGE 9
4SC "C3'" "C2'" SINGLE NONE 10
4SC "C2'" "C1'" SINGLE NONE 11
4SC "C1'" N1 SINGLE BEGINDASH 12
4SC N1 C2 SINGLE NONE 13
4SC N1 C6 SINGLE NONE 14
4SC C2 O2 DOUBLE NONE 15
4SC C2 N3 SINGLE NONE 16
4SC N3 C4 DOUBLE NONE 17
4SC C4 N4 SINGLE NONE 18
4SC C4 C5 SINGLE NONE 19
4SC C5 C6 DOUBLE NONE 20
4SC C5 C5M SINGLE NONE 21
4SC P OP3 SINGLE NONE 22
#
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
4SC MurckoScaffold S1 scaffold 'O=c1ncccn1[C@H]1CCCS1' InChI=1S/C8H10N2OS/c11-8-9-4-2-5-10(8)7-3-1-6-12-7/h2,4-5,7H,1,3,6H2/t7-/m1/s1 ISXVFGYITXPKLB-SSDOTTSWSA-N
4SC phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
4SC pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
4SC "C4'" S1 1
4SC "S4'" S1 1
4SC "C3'" S1 1
4SC "C2'" S1 1
4SC "C1'" S1 1
4SC N1 S1 1
4SC C2 S1 1
4SC O2 S1 1
4SC N3 S1 1
4SC C4 S1 1
4SC C5 S1 1
4SC C6 S1 1
4SC OP2 F1 1
4SC P F1 1
4SC OP1 F1 1
4SC "O5'" F1 1
4SC "H5'" F1 1
4SC C5 F2 1
4SC C4 F2 1
4SC N3 F2 1
4SC C2 F2 1
4SC N1 F2 1
4SC C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4SC
_pdbe_chem_comp_rdkit_properties.exactmw 337.050
_pdbe_chem_comp_rdkit_properties.amw 337.294
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 10
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 11
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 146.791
_pdbe_chem_comp_rdkit_properties.tpsa 147.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.073
_pdbe_chem_comp_rdkit_properties.CrippenMR 75.700
_pdbe_chem_comp_rdkit_properties.chi0v 11.358
_pdbe_chem_comp_rdkit_properties.chi1v 7.120
_pdbe_chem_comp_rdkit_properties.chi2v 3.184
_pdbe_chem_comp_rdkit_properties.chi3v 3.184
_pdbe_chem_comp_rdkit_properties.chi4v 2.176
_pdbe_chem_comp_rdkit_properties.chi0n 25.647
_pdbe_chem_comp_rdkit_properties.chi1n 12.462
_pdbe_chem_comp_rdkit_properties.chi2n 1.919
_pdbe_chem_comp_rdkit_properties.chi3n 1.919
_pdbe_chem_comp_rdkit_properties.chi4n 1.132
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 5.327
_pdbe_chem_comp_rdkit_properties.kappa2 6.073
_pdbe_chem_comp_rdkit_properties.kappa3 4.058
_pdbe_chem_comp_rdkit_properties.Phi 1.541
#
_pdbe_chem_comp_external_mappings.comp_id 4SC
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id 4SC
#
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
4SC P 4.149 -1.534 1.012 ETKDGv3 1
4SC OP1 3.128 -2.108 1.969 ETKDGv3 2
4SC OP2 5.646 -1.447 1.795 ETKDGv3 3
4SC "O5'" 3.680 0.035 0.534 ETKDGv3 4
4SC "C5'" 2.495 -0.065 -0.221 ETKDGv3 5
4SC "C4'" 2.007 1.341 -0.595 ETKDGv3 6
4SC "S4'" 0.587 1.200 -1.736 ETKDGv3 7
4SC "C3'" 1.563 2.151 0.637 ETKDGv3 8
4SC "O3'" 1.796 3.527 0.452 ETKDGv3 9
4SC "C2'" 0.081 1.877 0.868 ETKDGv3 10
4SC "C1'" -0.603 1.817 -0.495 ETKDGv3 11
4SC N1 -1.812 0.976 -0.448 ETKDGv3 12
4SC C2 -3.126 1.560 -0.414 ETKDGv3 13
4SC O2 -3.286 2.809 -0.457 ETKDGv3 14
4SC N3 -4.269 0.707 -0.328 ETKDGv3 15
4SC C4 -4.157 -0.586 -0.251 ETKDGv3 16
4SC N4 -5.348 -1.375 -0.171 ETKDGv3 17
4SC C5 -2.809 -1.226 -0.239 ETKDGv3 18
4SC C6 -1.710 -0.456 -0.330 ETKDGv3 19
4SC C5M -2.672 -2.720 -0.120 ETKDGv3 20
4SC "H5'" 1.694 -0.584 0.352 ETKDGv3 21
4SC "H5''" 2.691 -0.625 -1.164 ETKDGv3 22
4SC "H4'" 2.832 1.869 -1.122 ETKDGv3 23
4SC "H3'" 2.132 1.840 1.541 ETKDGv3 24
4SC "HO3'" 1.344 3.810 -0.384 ETKDGv3 25
4SC "H2'" -0.377 2.665 1.504 ETKDGv3 26
4SC "H2''" -0.024 0.905 1.398 ETKDGv3 27
4SC "H1'" -0.861 2.852 -0.807 ETKDGv3 28
4SC HN41 -5.320 -2.416 -0.109 ETKDGv3 29
4SC HN42 -6.284 -0.911 -0.175 ETKDGv3 30
4SC H61 -0.730 -0.917 -0.309 ETKDGv3 31
4SC H71 -3.171 -3.209 -0.982 ETKDGv3 32
4SC H72 -1.609 -3.043 -0.110 ETKDGv3 33
4SC H73 -3.143 -3.063 0.824 ETKDGv3 34
4SC OP3 4.288 -2.548 -0.337 ETKDGv3 35
4SC HOP2 6.246 -1.006 1.143 ETKDGv3 36
4SC HOP3 4.954 -2.103 -0.919 ETKDGv3 37
#