data_A1AJL
#
_chem_comp.id A1AJL
_chem_comp.name "(3R)-3-methoxy-1-(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)pyrrolidine-3-carboxylic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H14 N4 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2024-04-03
_chem_comp.pdbx_modified_date 2024-05-10
_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 290.275
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A1AJL
_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 7GZ6
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
A1AJL N1 N1 N 0 1 Y N N N N N -3.889 15.431 -3.854 1.686 -1.437 -0.254 N1 A1AJL 1
A1AJL N3 N2 N 0 1 Y N N N N N -5.344 15.407 -0.077 5.334 0.273 0.214 N3 A1AJL 2
A1AJL C4 C1 C 0 1 N N N N N N -1.808 13.427 -4.405 -0.910 -1.184 -0.465 C4 A1AJL 3
A1AJL C5 C2 C 0 1 N N N N N N -1.587 15.510 -3.050 0.632 0.771 -0.166 C5 A1AJL 4
A1AJL C6 C3 C 0 1 Y N N N N N -3.071 15.473 -2.783 1.817 -0.117 -0.133 C6 A1AJL 5
A1AJL C7 C4 C 0 1 Y N N N N N -5.201 15.364 -3.612 2.737 -2.230 -0.224 C7 A1AJL 6
A1AJL C8 C5 C 0 1 Y N N N N N -4.991 15.386 -1.395 4.205 -0.484 0.051 C8 A1AJL 7
A1AJL C10 C6 C 0 1 Y N N N N N -3.107 15.528 -0.142 3.670 1.746 0.185 C10 A1AJL 8
A1AJL O3 O1 O 0 1 N N N N N N -0.912 16.381 -2.508 0.770 1.974 -0.055 O3 A1AJL 9
A1AJL N N3 N 0 1 N N N N N N -1.036 14.538 -3.812 -0.600 0.246 -0.320 N A1AJL 10
A1AJL C3 C7 C 0 1 N N N N N N -0.741 12.500 -4.974 -2.443 -1.310 -0.586 C3 A1AJL 11
A1AJL C12 C8 C 0 1 N N N N N N 0.393 14.356 -4.069 -1.860 1.010 -0.370 C12 A1AJL 12
A1AJL C1 C9 C 0 1 N N R N N N 0.495 12.825 -4.152 -2.952 0.003 0.065 C1 A1AJL 13
A1AJL C2 C10 C 0 1 N N N N N N 0.540 12.147 -2.786 -4.299 0.393 -0.488 C2 A1AJL 14
A1AJL O2 O2 O 0 1 N N N N N N 0.927 12.841 -1.758 -5.121 1.171 0.234 O2 A1AJL 15
A1AJL O1 O3 O 0 1 N N N N N N 0.282 10.964 -2.723 -4.638 0.007 -1.581 O1 A1AJL 16
A1AJL O O4 O 0 1 N N N N N N 1.667 12.426 -4.863 -3.001 -0.117 1.489 O A1AJL 17
A1AJL C C11 C 0 1 N N N N N N 2.918 12.756 -4.253 -3.914 -1.112 1.957 C A1AJL 18
A1AJL C11 C12 C 0 1 Y N N N N N -3.593 15.465 -1.478 3.108 0.410 0.026 C11 A1AJL 19
A1AJL C9 C13 C 0 1 Y N N N N N -4.194 15.492 0.670 5.003 1.599 0.292 C9 A1AJL 20
A1AJL N2 N4 N 0 1 Y N N N N N -5.830 15.323 -2.439 3.967 -1.782 -0.077 N2 A1AJL 21
A1AJL H H1 H 0 1 N N N N N N -6.276 15.367 0.282 6.237 -0.079 0.266 H A1AJL 22
A1AJL H7 H2 H 0 1 N N N N N N -2.472 13.794 -5.201 -0.433 -1.576 -1.364 H7 A1AJL 23
A1AJL H8 H3 H 0 1 N N N N N N -2.405 12.912 -3.638 -0.558 -1.730 0.410 H8 A1AJL 24
A1AJL H9 H4 H 0 1 N N N N N N -5.837 15.340 -4.485 2.584 -3.294 -0.326 H9 A1AJL 25
A1AJL H11 H5 H 0 1 N N N N N N -2.074 15.592 0.166 3.121 2.676 0.212 H11 A1AJL 26
A1AJL H5 H6 H 0 1 N N N N N N -0.569 12.708 -6.040 -2.744 -1.363 -1.633 H5 A1AJL 27
A1AJL H6 H7 H 0 1 N N N N N N -1.030 11.446 -4.848 -2.802 -2.181 -0.038 H6 A1AJL 28
A1AJL H12 H8 H 0 1 N N N N N N 0.695 14.831 -5.014 -1.821 1.851 0.323 H12 A1AJL 29
A1AJL H13 H9 H 0 1 N N N N N N 1.004 14.756 -3.246 -2.049 1.364 -1.383 H13 A1AJL 30
A1AJL H4 H10 H 0 1 N N N N N N 0.967 12.279 -0.993 -5.974 1.395 -0.162 H4 A1AJL 31
A1AJL H2 H11 H 0 1 N N N N N N 3.742 12.400 -4.889 -4.900 -0.929 1.532 H2 A1AJL 32
A1AJL H1 H12 H 0 1 N N N N N N 2.991 13.847 -4.134 -3.564 -2.099 1.653 H1 A1AJL 33
A1AJL H3 H13 H 0 1 N N N N N N 2.983 12.275 -3.266 -3.973 -1.068 3.045 H3 A1AJL 34
A1AJL H10 H14 H 0 1 N N N N N N -4.160 15.525 1.749 5.707 2.407 0.421 H10 A1AJL 35
#
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
A1AJL C O SING N N 1
A1AJL O C1 SING N N 2
A1AJL C2 C1 SING N N 3
A1AJL O1 C2 DOUB N N 4
A1AJL O2 C2 SING N N 5
A1AJL C1 C3 SING N N 6
A1AJL C3 C4 SING N N 7
A1AJL C4 N SING N N 8
A1AJL N C5 SING N N 9
A1AJL C5 O3 DOUB N N 10
A1AJL C6 C5 SING N N 11
A1AJL C6 N1 DOUB Y N 12
A1AJL N1 C7 SING Y N 13
A1AJL C7 N2 DOUB Y N 14
A1AJL N2 C8 SING Y N 15
A1AJL C8 N3 SING Y N 16
A1AJL N3 C9 SING Y N 17
A1AJL C9 C10 DOUB Y N 18
A1AJL C10 C11 SING Y N 19
A1AJL C11 C6 SING Y N 20
A1AJL C8 C11 DOUB Y N 21
A1AJL C12 N SING N N 22
A1AJL C1 C12 SING N N 23
A1AJL N3 H SING N N 24
A1AJL C4 H7 SING N N 25
A1AJL C4 H8 SING N N 26
A1AJL C7 H9 SING N N 27
A1AJL C10 H11 SING N N 28
A1AJL C3 H5 SING N N 29
A1AJL C3 H6 SING N N 30
A1AJL C12 H12 SING N N 31
A1AJL C12 H13 SING N N 32
A1AJL O2 H4 SING N N 33
A1AJL C H2 SING N N 34
A1AJL C H1 SING N N 35
A1AJL C H3 SING N N 36
A1AJL C9 H10 SING N N 37
#
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
A1AJL SMILES ACDLabs 12.01 "COC1(CCN(C1)C(=O)c1ncnc2[NH]ccc21)C(=O)O"
A1AJL InChI InChI 1.06 "InChI=1S/C13H14N4O4/c1-21-13(12(19)20)3-5-17(6-13)11(18)9-8-2-4-14-10(8)16-7-15-9/h2,4,7H,3,5-6H2,1H3,(H,19,20)(H,14,15,16)/t13-/m1/s1"
A1AJL InChIKey InChI 1.06 YEFYXGDSKBIWST-CYBMUJFWSA-N
A1AJL SMILES_CANONICAL CACTVS 3.385 "CO[C@@]1(CCN(C1)C(=O)c2ncnc3[nH]ccc23)C(O)=O"
A1AJL SMILES CACTVS 3.385 "CO[C]1(CCN(C1)C(=O)c2ncnc3[nH]ccc23)C(O)=O"
A1AJL SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CO[C@@]1(CCN(C1)C(=O)c2c3cc[nH]c3ncn2)C(=O)O"
A1AJL SMILES "OpenEye OEToolkits" 2.0.7 "COC1(CCN(C1)C(=O)c2c3cc[nH]c3ncn2)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
A1AJL "SYSTEMATIC NAME" ACDLabs 12.01 "(3R)-3-methoxy-1-(7H-pyrrolo[2,3-d]pyrimidine-4-carbonyl)pyrrolidine-3-carboxylic acid"
A1AJL "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(3~{R})-3-methoxy-1-(7~{H}-pyrrolo[2,3-d]pyrimidin-4-ylcarbonyl)pyrrolidine-3-carboxylic 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
A1AJL 'Create component' 2024-04-03 RCSB
A1AJL 'Initial release' 2024-05-15 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
A1AJL N1 N 8.027 -2.106 1
A1AJL N3 N 12.045 -4.063 2
A1AJL C4 C 6.657 0.284 3
A1AJL C5 C 9.326 0.144 4
A1AJL C6 C 9.326 -1.356 5
A1AJL C7 C 8.027 -3.606 6
A1AJL C8 C 10.626 -3.606 7
A1AJL C10 C 12.045 -1.649 8
A1AJL O3 O 10.626 0.894 9
A1AJL N N 8.027 0.894 10
A1AJL C3 C 5.654 1.398 11
A1AJL C12 C 7.871 2.385 12
A1AJL C1 C 6.404 2.697 13
A1AJL C2 C 5.104 3.447 14
A1AJL O2 O 5.104 4.947 15
A1AJL O1 O 3.805 2.697 16
A1AJL O O 6.715 4.165 17
A1AJL C C 8.142 4.628 18
A1AJL C11 C 10.626 -2.106 19
A1AJL C9 C 12.920 -2.856 20
A1AJL N2 N 9.326 -4.356 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
A1AJL C O SINGLE NONE 1
A1AJL C1 O SINGLE BEGINWEDGE 2
A1AJL C2 C1 SINGLE NONE 3
A1AJL O1 C2 DOUBLE NONE 4
A1AJL O2 C2 SINGLE NONE 5
A1AJL C1 C3 SINGLE NONE 6
A1AJL C3 C4 SINGLE NONE 7
A1AJL C4 N SINGLE NONE 8
A1AJL N C5 SINGLE NONE 9
A1AJL C5 O3 DOUBLE NONE 10
A1AJL C6 C5 SINGLE NONE 11
A1AJL C6 N1 DOUBLE NONE 12
A1AJL N1 C7 SINGLE NONE 13
A1AJL C7 N2 DOUBLE NONE 14
A1AJL N2 C8 SINGLE NONE 15
A1AJL C8 N3 SINGLE NONE 16
A1AJL N3 C9 SINGLE NONE 17
A1AJL C9 C10 DOUBLE NONE 18
A1AJL C10 C11 SINGLE NONE 19
A1AJL C11 C6 SINGLE NONE 20
A1AJL C8 C11 DOUBLE NONE 21
A1AJL C12 N SINGLE NONE 22
A1AJL C1 C12 SINGLE NONE 23
#
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
A1AJL MurckoScaffold S1 scaffold 'O=C(c1ncnc2[nH]ccc12)N1CCCC1' InChI=1S/C11H12N4O/c16-11(15-5-1-2-6-15)9-8-3-4-12-10(8)14-7-13-9/h3-4,7H,1-2,5-6H2,(H,12,13,14) ZSNIICIIFJKZSI-UHFFFAOYSA-N
A1AJL amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
A1AJL pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
A1AJL pyrrole F3 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
A1AJL N1 S1 1
A1AJL N3 S1 1
A1AJL C4 S1 1
A1AJL C5 S1 1
A1AJL C6 S1 1
A1AJL C7 S1 1
A1AJL C8 S1 1
A1AJL C10 S1 1
A1AJL O3 S1 1
A1AJL N S1 1
A1AJL C3 S1 1
A1AJL C12 S1 1
A1AJL C1 S1 1
A1AJL C11 S1 1
A1AJL C9 S1 1
A1AJL N2 S1 1
A1AJL N F1 1
A1AJL C5 F1 1
A1AJL O3 F1 1
A1AJL C6 F1 1
A1AJL C11 F2 1
A1AJL C6 F2 1
A1AJL N1 F2 1
A1AJL C7 F2 1
A1AJL N2 F2 1
A1AJL C8 F2 1
A1AJL C8 F3 1
A1AJL C11 F3 1
A1AJL C10 F3 1
A1AJL C9 F3 1
A1AJL N3 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id A1AJL
_pdbe_chem_comp_rdkit_properties.exactmw 290.102
_pdbe_chem_comp_rdkit_properties.amw 290.279
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 8
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 6
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 35
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_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 139.115
_pdbe_chem_comp_rdkit_properties.tpsa 108.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.210
_pdbe_chem_comp_rdkit_properties.CrippenMR 69.313
_pdbe_chem_comp_rdkit_properties.chi0v 9.922
_pdbe_chem_comp_rdkit_properties.chi1v 5.283
_pdbe_chem_comp_rdkit_properties.chi2v 2.580
_pdbe_chem_comp_rdkit_properties.chi3v 2.580
_pdbe_chem_comp_rdkit_properties.chi4v 1.570
_pdbe_chem_comp_rdkit_properties.chi0n 23.922
_pdbe_chem_comp_rdkit_properties.chi1n 12.139
_pdbe_chem_comp_rdkit_properties.chi2n 2.580
_pdbe_chem_comp_rdkit_properties.chi3n 2.580
_pdbe_chem_comp_rdkit_properties.chi4n 1.570
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.480
_pdbe_chem_comp_rdkit_properties.kappa1 4.771
_pdbe_chem_comp_rdkit_properties.kappa2 4.813
_pdbe_chem_comp_rdkit_properties.kappa3 2.037
_pdbe_chem_comp_rdkit_properties.Phi 1.093
#
#
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
A1AJL N1 1.634 -0.920 1.354 ETKDGv3 1
A1AJL N3 5.516 -0.433 0.018 ETKDGv3 2
A1AJL C4 -1.682 -0.904 -1.484 ETKDGv3 3
A1AJL C5 0.789 -0.925 -0.919 ETKDGv3 4
A1AJL C6 1.885 -0.832 0.073 ETKDGv3 5
A1AJL C7 2.686 -0.860 2.346 ETKDGv3 6
A1AJL C8 4.235 -0.641 0.585 ETKDGv3 7
A1AJL C10 3.944 -0.491 -1.629 ETKDGv3 8
A1AJL O3 1.061 -1.291 -2.094 ETKDGv3 9
A1AJL N -0.580 -0.625 -0.580 ETKDGv3 10
A1AJL C3 -2.934 -0.457 -0.742 ETKDGv3 11
A1AJL C12 -1.005 0.113 0.601 ETKDGv3 12
A1AJL C1 -2.451 0.558 0.323 ETKDGv3 13
A1AJL C2 -2.419 1.984 -0.206 ETKDGv3 14
A1AJL O2 -2.466 3.050 0.688 ETKDGv3 15
A1AJL O1 -2.284 2.214 -1.439 ETKDGv3 16
A1AJL O -3.190 0.481 1.539 ETKDGv3 17
A1AJL C -4.580 0.682 1.348 ETKDGv3 18
A1AJL C11 3.297 -0.687 -0.333 ETKDGv3 19
A1AJL C9 5.246 -0.347 -1.382 ETKDGv3 20
A1AJL N2 3.933 -0.725 1.982 ETKDGv3 21
A1AJL H 6.431 -0.323 0.508 ETKDGv3 22
A1AJL H7 -1.557 -0.319 -2.421 ETKDGv3 23
A1AJL H8 -1.728 -1.989 -1.718 ETKDGv3 24
A1AJL H9 2.438 -0.928 3.396 ETKDGv3 25
A1AJL H11 3.478 -0.449 -2.604 ETKDGv3 26
A1AJL H5 -3.692 -0.029 -1.434 ETKDGv3 27
A1AJL H6 -3.373 -1.348 -0.240 ETKDGv3 28
A1AJL H12 -0.328 0.977 0.790 ETKDGv3 29
A1AJL H13 -0.974 -0.567 1.480 ETKDGv3 30
A1AJL H4 -2.421 4.007 0.359 ETKDGv3 31
A1AJL H2 -5.037 0.921 2.330 ETKDGv3 32
A1AJL H1 -5.062 -0.247 0.978 ETKDGv3 33
A1AJL H3 -4.810 1.527 0.664 ETKDGv3 34
A1AJL H10 6.003 -0.173 -2.135 ETKDGv3 35
#