data_9LO
#
_chem_comp.id 9LO
_chem_comp.name "4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]benzoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H12 N6 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-08-13
_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 304.261
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9LO
_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 4B4W
_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
9LO N2A N2A N 0 1 N N N N N N 7.282 8.658 60.361 6.150 -1.726 -0.399 N2A 9LO 1
9LO N1 N1 N 0 1 N N N N N N 5.225 9.701 60.723 4.790 0.053 -1.000 N1 9LO 2
9LO C2 C2 C 0 1 N N N N N N 5.983 8.583 60.664 5.024 -0.968 -0.204 C2 9LO 3
9LO N3 N3 N 0 1 N N N N N N 5.437 7.373 60.910 4.174 -1.289 0.809 N3 9LO 4
9LO C4 C4 C 0 1 N N N N N N 4.131 7.265 61.217 3.060 -0.556 1.018 C4 9LO 5
9LO O4A O4A O 0 1 N N N N N N 3.607 6.030 61.470 2.291 -0.837 1.924 O4A 9LO 6
9LO N5A N5A N 0 1 N N N N N N 2.037 8.253 61.597 1.649 1.328 0.357 N5A 9LO 7
9LO C5 C5 C 0 1 N N N N N N 3.331 8.412 61.303 2.801 0.535 0.175 C5 9LO 8
9LO C6 C6 C 0 1 N N N N N N 3.912 9.650 61.030 3.703 0.819 -0.844 C6 9LO 9
9LO N7 N7 N 0 1 N N N N N N 3.182 10.765 61.089 3.478 1.887 -1.694 N7 9LO 10
9LO O8A O8A O 0 1 N N N N N N 2.310 7.956 63.840 0.318 -0.442 0.180 O8A 9LO 11
9LO N9 N9 N 0 1 N N N N N N 0.247 7.839 62.898 -0.676 1.535 0.376 N9 9LO 12
9LO C1B C1B C 0 1 Y N N N N N -0.484 7.433 63.945 -1.938 0.966 0.209 C1B 9LO 13
9LO C2B C2B C 0 1 Y N N N N N -1.852 7.718 63.966 -3.027 1.474 0.910 C2B 9LO 14
9LO C3B C3B C 0 1 Y N N N N N -2.652 7.243 65.004 -4.274 0.915 0.748 C3B 9LO 15
9LO C4B C4B C 0 1 Y N N N N N -2.109 6.463 66.020 -4.445 -0.166 -0.123 C4B 9LO 16
9LO C5B C5B C 0 1 Y N N N N N -0.754 6.137 65.978 -3.349 -0.674 -0.826 C5B 9LO 17
9LO C6B C6B C 0 1 Y N N N N N 0.050 6.610 64.943 -2.106 -0.106 -0.663 C6B 9LO 18
9LO C7B C7B C 0 1 N N N N N N -2.984 5.900 67.157 -5.780 -0.768 -0.299 C7B 9LO 19
9LO O7B O7B O 0 1 N N N N N N -2.575 4.951 67.832 -6.732 -0.325 0.313 O7B 9LO 20
9LO CAW CAW C 0 1 N N N N N N 1.581 7.993 62.840 0.426 0.763 0.300 CAW 9LO 21
9LO H2A1 H2A1 H 0 0 N N N N N N 7.702 9.547 60.175 6.764 -1.507 -1.118 H2A1 9LO 22
9LO H2A2 H2A2 H 0 0 N N N N N N 7.835 7.826 60.320 6.336 -2.478 0.184 H2A2 9LO 23
9LO H71N H71N H 0 0 N N N N N N 3.760 11.554 60.879 4.109 2.082 -2.404 H71N 9LO 24
9LO H72N H72N H 0 0 N N N N N N 2.437 10.711 60.424 2.690 2.440 -1.579 H72N 9LO 25
9LO H9 H9 H 0 1 N N N N N N -0.259 8.052 62.062 -0.592 2.486 0.547 H9 9LO 26
9LO H2B H2B H 0 1 N N N N N N -2.291 8.308 63.175 -2.894 2.309 1.582 H2B 9LO 27
9LO H6B H6B H 0 1 N N N N N N 1.095 6.339 64.911 -1.259 -0.495 -1.209 H6B 9LO 28
9LO H3B H3B H 0 1 N N N N N N -3.705 7.483 65.020 -5.119 1.310 1.292 H3B 9LO 29
9LO H5B H5B H 0 1 N N N N N N -0.326 5.516 66.751 -3.478 -1.508 -1.499 H5B 9LO 30
9LO H5A H5A H 0 1 N N N N N N 1.371 8.331 60.856 1.737 2.279 0.524 H5A 9LO 31
9LO HN3 HN3 H 0 1 N N N N N N 6.006 6.552 60.864 4.368 -2.046 1.383 HN3 9LO 32
9LO OXT OXT O 0 1 N Y N N N N ? ? ? -5.943 -1.809 -1.139 OXT 9LO 33
9LO HXT HXT H 0 1 N Y N N N N ? ? ? -6.836 -2.171 -1.221 HXT 9LO 34
#
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
9LO N2A C2 SING N N 1
9LO N1 C2 DOUB N N 2
9LO N1 C6 SING N N 3
9LO C2 N3 SING N N 4
9LO N3 C4 SING N N 5
9LO C4 O4A DOUB N N 6
9LO C4 C5 SING N N 7
9LO N5A C5 SING N N 8
9LO N5A CAW SING N N 9
9LO C5 C6 DOUB N N 10
9LO C6 N7 SING N N 11
9LO O8A CAW DOUB N N 12
9LO N9 C1B SING N N 13
9LO N9 CAW SING N N 14
9LO C1B C2B SING Y N 15
9LO C1B C6B DOUB Y N 16
9LO C2B C3B DOUB Y N 17
9LO C3B C4B SING Y N 18
9LO C4B C5B DOUB Y N 19
9LO C4B C7B SING N N 20
9LO C5B C6B SING Y N 21
9LO C7B O7B DOUB N N 22
9LO N2A H2A1 SING N N 23
9LO N2A H2A2 SING N N 24
9LO N7 H71N SING N N 25
9LO N7 H72N SING N N 26
9LO N9 H9 SING N N 27
9LO C2B H2B SING N N 28
9LO C6B H6B SING N N 29
9LO C3B H3B SING N N 30
9LO C5B H5B SING N N 31
9LO N5A H5A SING N N 32
9LO N3 HN3 SING N N 33
9LO C7B OXT SING N N 34
9LO OXT HXT 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
9LO SMILES ACDLabs 12.01 O=C2C(NC(=O)Nc1ccc(C(=O)O)cc1)=C(N=C(N)N2)N
9LO InChI InChI 1.03 InChI=1S/C12H12N6O4/c13-8-7(9(19)18-11(14)17-8)16-12(22)15-6-3-1-5(2-4-6)10(20)21/h1-4H,(H,20,21)(H2,15,16,22)(H5,13,14,17,18,19)
9LO InChIKey InChI 1.03 PYZLZAMQAFSOFT-UHFFFAOYSA-N
9LO SMILES_CANONICAL CACTVS 3.385 NC1=NC(=C(NC(=O)Nc2ccc(cc2)C(O)=O)C(=O)N1)N
9LO SMILES CACTVS 3.385 NC1=NC(=C(NC(=O)Nc2ccc(cc2)C(O)=O)C(=O)N1)N
9LO SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1cc(ccc1C(=O)O)NC(=O)NC2=C(N=C(NC2=O)N)N
9LO SMILES "OpenEye OEToolkits" 1.9.2 c1cc(ccc1C(=O)O)NC(=O)NC2=C(N=C(NC2=O)N)N
#
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
9LO "SYSTEMATIC NAME" ACDLabs 12.01 "4-{[(2,4-diamino-6-oxo-1,6-dihydropyrimidin-5-yl)carbamoyl]amino}benzoic acid"
9LO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "4-[[2,4-bis(azanyl)-6-oxidanylidene-1H-pyrimidin-5-yl]carbamoylamino]benzoic 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
9LO 'Create component' 2012-08-13 EBI
9LO 'Modify descriptor' 2014-09-05 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
9LO N2A N 10.794 -6.000 1
9LO N1 N 9.495 -3.750 2
9LO C2 C 9.495 -5.250 3
9LO N3 N 8.196 -6.000 4
9LO C4 C 6.897 -5.250 5
9LO O4A O 5.598 -6.000 6
9LO N5A N 5.598 -3.000 7
9LO C5 C 6.897 -3.750 8
9LO C6 C 8.196 -3.000 9
9LO N7 N 8.196 -1.500 10
9LO O8A O 6.897 -0.750 11
9LO N9 N 4.299 -0.750 12
9LO C1B C 4.299 0.750 13
9LO C2B C 5.598 1.500 14
9LO C3B C 5.598 3.000 15
9LO C4B C 4.299 3.750 16
9LO C5B C 3.000 3.000 17
9LO C6B C 3.000 1.500 18
9LO C7B C 4.299 5.250 19
9LO O7B O 3.000 6.000 20
9LO CAW C 5.598 -1.500 21
9LO OXT O 5.598 6.000 22
#
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
9LO N2A C2 SINGLE NONE 1
9LO N1 C2 DOUBLE NONE 2
9LO N1 C6 SINGLE NONE 3
9LO C2 N3 SINGLE NONE 4
9LO N3 C4 SINGLE NONE 5
9LO C4 O4A DOUBLE NONE 6
9LO C4 C5 SINGLE NONE 7
9LO N5A C5 SINGLE NONE 8
9LO N5A CAW SINGLE NONE 9
9LO C5 C6 DOUBLE NONE 10
9LO C6 N7 SINGLE NONE 11
9LO O8A CAW DOUBLE NONE 12
9LO N9 C1B SINGLE NONE 13
9LO N9 CAW SINGLE NONE 14
9LO C1B C2B DOUBLE NONE 15
9LO C1B C6B SINGLE NONE 16
9LO C2B C3B SINGLE NONE 17
9LO C3B C4B DOUBLE NONE 18
9LO C4B C5B SINGLE NONE 19
9LO C4B C7B SINGLE NONE 20
9LO C5B C6B DOUBLE NONE 21
9LO C7B O7B DOUBLE NONE 22
9LO C7B OXT 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
9LO MurckoScaffold S1 scaffold 'O=C(Nc1ccccc1)Nc1cnc[nH]c1=O' InChI=1S/C11H10N4O2/c16-10-9(6-12-7-13-10)15-11(17)14-8-4-2-1-3-5-8/h1-7H,(H,12,13,16)(H2,14,15,17) ILOBSNVUHYTGQY-UHFFFAOYSA-N
9LO phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
9LO 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
9LO N1 S1 1
9LO C2 S1 1
9LO N3 S1 1
9LO C4 S1 1
9LO O4A S1 1
9LO N5A S1 1
9LO C5 S1 1
9LO C6 S1 1
9LO O8A S1 1
9LO N9 S1 1
9LO C1B S1 1
9LO C2B S1 1
9LO C3B S1 1
9LO C4B S1 1
9LO C5B S1 1
9LO C6B S1 1
9LO CAW S1 1
9LO C1B F1 1
9LO C2B F1 1
9LO C3B F1 1
9LO C4B F1 1
9LO C5B F1 1
9LO C6B F1 1
9LO C5 F2 1
9LO C4 F2 1
9LO N3 F2 1
9LO C2 F2 1
9LO N1 F2 1
9LO C6 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 9LO
_pdbe_chem_comp_rdkit_properties.exactmw 304.092
_pdbe_chem_comp_rdkit_properties.amw 304.266
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 10
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 6
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 140.069
_pdbe_chem_comp_rdkit_properties.tpsa 176.220
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.401
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.271
_pdbe_chem_comp_rdkit_properties.chi0v 10.316
_pdbe_chem_comp_rdkit_properties.chi1v 5.303
_pdbe_chem_comp_rdkit_properties.chi2v 2.053
_pdbe_chem_comp_rdkit_properties.chi3v 2.053
_pdbe_chem_comp_rdkit_properties.chi4v 1.190
_pdbe_chem_comp_rdkit_properties.chi0n 22.316
_pdbe_chem_comp_rdkit_properties.chi1n 10.841
_pdbe_chem_comp_rdkit_properties.chi2n 2.053
_pdbe_chem_comp_rdkit_properties.chi3n 2.053
_pdbe_chem_comp_rdkit_properties.chi4n 1.190
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -3.560
_pdbe_chem_comp_rdkit_properties.kappa1 5.674
_pdbe_chem_comp_rdkit_properties.kappa2 5.828
_pdbe_chem_comp_rdkit_properties.kappa3 3.304
_pdbe_chem_comp_rdkit_properties.Phi 1.503
#
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
9LO UniChem ChEMBL CHEMBL3622700
9LO UniChem PDBe 9LO
9LO UniChem ZINC ZINC000098208619
9LO UniChem PubChem 137028343
#
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
9LO N2A 6.666 -0.046 -1.270 ETKDGv3 1
9LO N1 4.962 -1.094 -0.016 ETKDGv3 2
9LO C2 5.362 -0.056 -0.691 ETKDGv3 3
9LO N3 4.497 1.073 -0.848 ETKDGv3 4
9LO C4 3.204 1.047 -0.241 ETKDGv3 5
9LO O4A 2.455 2.058 -0.311 ETKDGv3 6
9LO N5A 1.497 -0.217 1.132 ETKDGv3 7
9LO C5 2.784 -0.164 0.493 ETKDGv3 8
9LO C6 3.661 -1.185 0.598 ETKDGv3 9
9LO N7 3.319 -2.394 1.285 ETKDGv3 10
9LO O8A 0.283 0.232 -0.813 ETKDGv3 11
9LO N9 -0.959 0.121 1.170 ETKDGv3 12
9LO C1B -2.262 0.182 0.567 ETKDGv3 13
9LO C2B -2.556 -0.502 -0.554 ETKDGv3 14
9LO C3B -3.915 -0.444 -1.132 ETKDGv3 15
9LO C4B -4.882 0.277 -0.533 ETKDGv3 16
9LO C5B -4.563 1.008 0.719 ETKDGv3 17
9LO C6B -3.330 0.958 1.238 ETKDGv3 18
9LO C7B -6.248 0.344 -1.098 ETKDGv3 19
9LO O7B -6.536 -0.272 -2.159 ETKDGv3 20
9LO CAW 0.273 0.049 0.435 ETKDGv3 21
9LO H2A1 6.998 0.781 -1.813 ETKDGv3 22
9LO H2A2 7.303 -0.867 -1.158 ETKDGv3 23
9LO H71N 2.364 -2.574 1.663 ETKDGv3 24
9LO H72N 4.029 -3.155 1.372 ETKDGv3 25
9LO H9 -0.896 0.238 2.206 ETKDGv3 26
9LO H2B -1.817 -1.129 -1.035 ETKDGv3 27
9LO H6B -3.112 1.495 2.152 ETKDGv3 28
9LO H3B -4.112 -0.997 -2.042 ETKDGv3 29
9LO H5B -5.326 1.586 1.225 ETKDGv3 30
9LO H5A 1.444 -0.514 2.132 ETKDGv3 31
9LO HN3 4.813 1.914 -1.381 ETKDGv3 32
9LO OXT -7.230 1.095 -0.457 ETKDGv3 33
9LO HXT -8.170 1.150 -0.832 ETKDGv3 34
#