data_S3E
#
_chem_comp.id S3E
_chem_comp.name "[(2S)-4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)morpholin-2-yl]acetic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H14 N4 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-06-23
_chem_comp.pdbx_modified_date 2022-07-08
_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 262.265
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S3E
_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 5SP2
_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
S3E C02 C1 C 0 1 N N N N N N -43.947 -31.994 3.026 4.192 -0.197 -0.775 C02 S3E 1
S3E C03 C2 C 0 1 N N N N N N -43.955 -31.376 1.630 2.726 0.142 -0.861 C03 S3E 2
S3E C04 C3 C 0 1 N N S N N N -45.235 -30.630 1.228 2.306 0.910 0.393 C04 S3E 3
S3E C05 C4 C 0 1 N N N N N N -46.108 -30.253 2.424 0.850 1.363 0.251 C05 S3E 4
S3E C07 C5 C 0 1 Y N N N N N -48.167 -29.047 2.970 -1.339 0.550 -0.023 C07 S3E 5
S3E C08 C6 C 0 1 Y N N N N N -48.015 -29.104 4.368 -2.349 -0.419 -0.131 C08 S3E 6
S3E C09 C7 C 0 1 Y N N N N N -46.957 -29.298 5.280 -2.389 -1.880 -0.099 C09 S3E 7
S3E C10 C8 C 0 1 Y N N N N N -47.506 -29.249 6.554 -3.674 -2.236 -0.259 C10 S3E 8
S3E C12 C9 C 0 1 Y N N N N N -49.148 -28.945 5.142 -3.677 0.007 -0.316 C12 S3E 9
S3E C14 C10 C 0 1 Y N N N N N -50.429 -28.685 3.228 -2.945 2.188 -0.277 C14 S3E 10
S3E C16 C11 C 0 1 N N N N N N -47.303 -29.088 0.702 0.131 -0.669 1.350 C16 S3E 11
S3E C17 C12 C 0 1 N N N N N N -46.010 -28.789 -0.055 1.594 -1.102 1.480 C17 S3E 12
S3E N06 N1 N 0 1 N N N N N N -47.008 -29.192 2.096 -0.019 0.181 0.160 N06 S3E 13
S3E N11 N2 N 0 1 Y N N N N N -48.802 -29.038 6.433 -4.454 -1.116 -0.390 N11 S3E 14
S3E N13 N3 N 0 1 Y N N N N N -50.329 -28.740 4.541 -3.922 1.315 -0.382 N13 S3E 15
S3E N15 N4 N 0 1 Y N N N N N -49.369 -28.832 2.446 -1.684 1.832 -0.107 N15 S3E 16
S3E O01 O1 O 0 1 N N N N N N -43.600 -31.311 4.024 4.785 -0.870 -1.774 O01 S3E 17
S3E O18 O2 O 0 1 N N N N N N -44.878 -29.448 0.513 2.426 0.060 1.537 O18 S3E 18
S3E O19 O3 O 0 1 N N N N N N -44.271 -33.201 3.171 4.834 0.141 0.190 O19 S3E 19
S3E H031 H1 H 0 0 N N N N N N -43.796 -32.186 0.903 2.547 0.758 -1.742 H031 S3E 20
S3E H032 H2 H 0 0 N N N N N N -43.119 -30.663 1.573 2.144 -0.777 -0.937 H032 S3E 21
S3E H041 H3 H 0 0 N N N N N N -45.821 -31.291 0.572 2.948 1.782 0.518 H041 S3E 22
S3E H051 H4 H 0 0 N N N N N N -46.690 -31.133 2.735 0.567 1.957 1.121 H051 S3E 23
S3E H052 H5 H 0 0 N N N N N N -45.461 -29.930 3.253 0.743 1.966 -0.650 H052 S3E 24
S3E H091 H6 H 0 0 N N N N N N -45.917 -29.455 5.034 -1.548 -2.545 0.028 H091 S3E 25
S3E H101 H7 H 0 0 N N N N N N -46.966 -29.364 7.482 -4.039 -3.253 -0.281 H101 S3E 26
S3E H141 H8 H 0 0 N N N N N N -51.397 -28.516 2.779 -3.182 3.240 -0.335 H141 S3E 27
S3E H161 H9 H 0 0 N N N N N N -48.025 -28.274 0.537 -0.502 -1.551 1.249 H161 S3E 28
S3E H162 H10 H 0 0 N N N N N N -47.731 -30.036 0.343 -0.164 -0.109 2.237 H162 S3E 29
S3E H172 H11 H 0 0 N N N N N N -45.833 -27.704 -0.035 1.720 -1.685 2.392 H172 S3E 30
S3E H171 H12 H 0 0 N N N N N N -46.126 -29.123 -1.097 1.872 -1.708 0.618 H171 S3E 31
S3E H111 H13 H 0 0 N N N N N N -49.439 -28.958 7.200 -5.416 -1.119 -0.516 H111 S3E 32
S3E H1 H14 H 0 1 N N N N N N -43.636 -31.850 4.805 5.727 -1.061 -1.676 H1 S3E 33
#
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
S3E C17 O18 SING N N 1
S3E C17 C16 SING N N 2
S3E O18 C04 SING N N 3
S3E C16 N06 SING N N 4
S3E C04 C03 SING N N 5
S3E C04 C05 SING N N 6
S3E C03 C02 SING N N 7
S3E N06 C05 SING N N 8
S3E N06 C07 SING N N 9
S3E N15 C07 DOUB Y N 10
S3E N15 C14 SING Y N 11
S3E C07 C08 SING Y N 12
S3E C02 O19 DOUB N N 13
S3E C02 O01 SING N N 14
S3E C14 N13 DOUB Y N 15
S3E C08 C12 DOUB Y N 16
S3E C08 C09 SING Y N 17
S3E N13 C12 SING Y N 18
S3E C12 N11 SING Y N 19
S3E C09 C10 DOUB Y N 20
S3E N11 C10 SING Y N 21
S3E C03 H031 SING N N 22
S3E C03 H032 SING N N 23
S3E C04 H041 SING N N 24
S3E C05 H051 SING N N 25
S3E C05 H052 SING N N 26
S3E C09 H091 SING N N 27
S3E C10 H101 SING N N 28
S3E C14 H141 SING N N 29
S3E C16 H161 SING N N 30
S3E C16 H162 SING N N 31
S3E C17 H172 SING N N 32
S3E C17 H171 SING N N 33
S3E N11 H111 SING N N 34
S3E O01 H1 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
S3E SMILES ACDLabs 12.01 O=C(O)CC1CN(CCO1)c1ncnc2[NH]ccc12
S3E InChI InChI 1.06 InChI=1S/C12H14N4O3/c17-10(18)5-8-6-16(3-4-19-8)12-9-1-2-13-11(9)14-7-15-12/h1-2,7-8H,3-6H2,(H,17,18)(H,13,14,15)/t8-/m0/s1
S3E InChIKey InChI 1.06 PRFABXNJKOXNTN-QMMMGPOBSA-N
S3E SMILES_CANONICAL CACTVS 3.385 OC(=O)C[C@H]1CN(CCO1)c2ncnc3[nH]ccc23
S3E SMILES CACTVS 3.385 OC(=O)C[CH]1CN(CCO1)c2ncnc3[nH]ccc23
S3E SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCO[C@H](C3)CC(=O)O
S3E SMILES "OpenEye OEToolkits" 2.0.7 c1c[nH]c2c1c(ncn2)N3CCOC(C3)CC(=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
S3E "SYSTEMATIC NAME" ACDLabs 12.01 "[(2S)-4-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)morpholin-2-yl]acetic acid"
S3E "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[(2~{S})-4-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl)morpholin-2-yl]ethanoic 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
S3E 'Create component' 2022-06-23 RCSB
S3E 'Initial release' 2022-07-13 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
S3E C02 C 6.897 3.955 1
S3E C03 C 6.897 2.455 2
S3E C04 C 5.598 1.706 3
S3E C05 C 5.598 0.205 4
S3E C07 C 4.299 -2.045 5
S3E C08 C 5.598 -2.795 6
S3E C09 C 7.018 -2.337 7
S3E C10 C 7.893 -3.545 8
S3E C12 C 5.598 -4.295 9
S3E C14 C 3.000 -4.295 10
S3E C16 C 3.000 0.205 11
S3E C17 C 3.000 1.706 12
S3E N06 N 4.299 -0.544 13
S3E N11 N 7.018 -4.752 14
S3E N13 N 4.299 -5.045 15
S3E N15 N 3.000 -2.795 16
S3E O01 O 5.598 4.705 17
S3E O18 O 4.299 2.455 18
S3E O19 O 8.196 4.705 19
#
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
S3E C17 O18 SINGLE NONE 1
S3E C17 C16 SINGLE NONE 2
S3E O18 C04 SINGLE NONE 3
S3E C16 N06 SINGLE NONE 4
S3E C04 C03 SINGLE BEGINWEDGE 5
S3E C04 C05 SINGLE NONE 6
S3E C03 C02 SINGLE NONE 7
S3E N06 C05 SINGLE NONE 8
S3E N06 C07 SINGLE NONE 9
S3E N15 C07 SINGLE NONE 10
S3E N15 C14 DOUBLE NONE 11
S3E C07 C08 DOUBLE NONE 12
S3E C02 O19 DOUBLE NONE 13
S3E C02 O01 SINGLE NONE 14
S3E C14 N13 SINGLE NONE 15
S3E C08 C12 SINGLE NONE 16
S3E C08 C09 SINGLE NONE 17
S3E N13 C12 DOUBLE NONE 18
S3E C12 N11 SINGLE NONE 19
S3E C09 C10 DOUBLE NONE 20
S3E N11 C10 SINGLE NONE 21
#
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
S3E MurckoScaffold S1 scaffold 'c1nc(N2CCOCC2)c2cc[nH]c2n1' InChI=1S/C10H12N4O/c1-2-11-9-8(1)10(13-7-12-9)14-3-5-15-6-4-14/h1-2,7H,3-6H2,(H,11,12,13) GIAZHSRKWYDANE-UHFFFAOYSA-N
S3E pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
S3E pyrrole F2 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
S3E C04 S1 1
S3E C05 S1 1
S3E C07 S1 1
S3E C08 S1 1
S3E C09 S1 1
S3E C10 S1 1
S3E C12 S1 1
S3E C14 S1 1
S3E C16 S1 1
S3E C17 S1 1
S3E N06 S1 1
S3E N11 S1 1
S3E N13 S1 1
S3E N15 S1 1
S3E O18 S1 1
S3E C08 F1 1
S3E C07 F1 1
S3E N15 F1 1
S3E C14 F1 1
S3E N13 F1 1
S3E C12 F1 1
S3E C10 F2 1
S3E C09 F2 1
S3E C08 F2 1
S3E C12 F2 1
S3E N11 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S3E
_pdbe_chem_comp_rdkit_properties.exactmw 262.107
_pdbe_chem_comp_rdkit_properties.amw 262.269
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.417
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 128.589
_pdbe_chem_comp_rdkit_properties.tpsa 91.340
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.171
_pdbe_chem_comp_rdkit_properties.CrippenMR 65.065
_pdbe_chem_comp_rdkit_properties.chi0v 9.014
_pdbe_chem_comp_rdkit_properties.chi1v 4.829
_pdbe_chem_comp_rdkit_properties.chi2v 2.053
_pdbe_chem_comp_rdkit_properties.chi3v 2.053
_pdbe_chem_comp_rdkit_properties.chi4v 1.347
_pdbe_chem_comp_rdkit_properties.chi0n 23.014
_pdbe_chem_comp_rdkit_properties.chi1n 11.684
_pdbe_chem_comp_rdkit_properties.chi2n 2.053
_pdbe_chem_comp_rdkit_properties.chi3n 2.053
_pdbe_chem_comp_rdkit_properties.chi4n 1.347
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.150
_pdbe_chem_comp_rdkit_properties.kappa1 3.923
_pdbe_chem_comp_rdkit_properties.kappa2 4.848
_pdbe_chem_comp_rdkit_properties.kappa3 2.366
_pdbe_chem_comp_rdkit_properties.Phi 1.001
#
_pdbe_chem_comp_external_mappings.comp_id S3E
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 164513207
#
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
S3E C02 -3.397 1.638 0.054 ETKDGv3 1
S3E C03 -3.446 0.141 0.060 ETKDGv3 2
S3E C04 -2.198 -0.478 -0.589 ETKDGv3 3
S3E C05 -0.931 -0.184 0.241 ETKDGv3 4
S3E C07 1.511 -0.346 -0.444 ETKDGv3 5
S3E C08 2.052 0.443 0.493 ETKDGv3 6
S3E C09 1.645 0.879 1.828 ETKDGv3 7
S3E C10 2.646 1.610 2.338 ETKDGv3 8
S3E C12 3.366 0.979 0.309 ETKDGv3 9
S3E C14 3.515 -0.116 -1.764 ETKDGv3 10
S3E C16 -0.015 -2.334 -0.671 ETKDGv3 11
S3E C17 -1.339 -2.470 -1.426 ETKDGv3 12
S3E N06 0.201 -0.931 -0.314 ETKDGv3 13
S3E N11 3.761 1.723 1.444 ETKDGv3 14
S3E N13 4.088 0.724 -0.738 ETKDGv3 15
S3E N15 2.312 -0.617 -1.619 ETKDGv3 16
S3E O01 -2.995 2.324 1.196 ETKDGv3 17
S3E O18 -2.397 -1.879 -0.694 ETKDGv3 18
S3E O19 -3.689 2.275 -0.993 ETKDGv3 19
S3E H031 -4.349 -0.187 -0.501 ETKDGv3 20
S3E H032 -3.555 -0.225 1.104 ETKDGv3 21
S3E H041 -2.086 -0.030 -1.605 ETKDGv3 22
S3E H051 -1.091 -0.501 1.294 ETKDGv3 23
S3E H052 -0.722 0.908 0.216 ETKDGv3 24
S3E H091 0.725 0.646 2.345 ETKDGv3 25
S3E H101 2.629 2.053 3.325 ETKDGv3 26
S3E H141 4.086 -0.341 -2.654 ETKDGv3 27
S3E H161 -0.055 -2.942 0.259 ETKDGv3 28
S3E H162 0.809 -2.723 -1.306 ETKDGv3 29
S3E H172 -1.563 -3.549 -1.562 ETKDGv3 30
S3E H171 -1.255 -2.024 -2.444 ETKDGv3 31
S3E H111 4.675 2.197 1.616 ETKDGv3 32
S3E H1 -2.942 3.335 1.203 ETKDGv3 33
#