data_AR6
#
_chem_comp.id AR6
_chem_comp.name
"[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H23 N5 O14 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2009-08-10
_chem_comp.pdbx_modified_date 2025-01-29
_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 559.316
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AR6
_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 2WPS
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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
AR6 N1 N1 N 0 1 Y N N N N N -27.227 -0.488 -34.579 -8.232 3.116 0.345 N1 AR6 1
AR6 C2 C2 C 0 1 Y N N N N N -26.982 -1.058 -33.385 -8.022 2.281 1.347 C2 AR6 2
AR6 N3 N3 N 0 1 Y N N N N N -27.418 -0.522 -32.234 -7.005 1.445 1.368 N3 AR6 3
AR6 C4 C4 C 0 1 Y N N N N N -28.139 0.624 -32.218 -6.135 1.410 0.364 C4 AR6 4
AR6 C5 C5 C 0 1 Y N N N N N -28.451 1.306 -33.473 -6.315 2.279 -0.725 C5 AR6 5
AR6 C6 C6 C 0 1 Y N N N N N -27.935 0.661 -34.701 -7.415 3.153 -0.702 C6 AR6 6
AR6 N6 N6 N 0 1 N N N N N N -28.167 1.191 -35.920 -7.643 4.031 -1.747 N6 AR6 7
AR6 N7 N7 N 0 1 Y N N N N N -29.180 2.399 -33.151 -5.304 2.042 -1.596 N7 AR6 8
AR6 C8 C8 C 0 1 Y N N N N N -29.308 2.419 -31.802 -4.535 1.105 -1.122 C8 AR6 9
AR6 N9 N9 N 0 1 Y N N N N N -28.677 1.361 -31.260 -5.006 0.683 0.086 N9 AR6 10
AR6 PA PA P 0 1 N N N N N N -30.937 5.146 -26.734 0.814 -2.273 -0.782 PA AR6 11
AR6 PB PB P 0 1 N N N N N N -33.759 5.142 -26.881 3.292 -0.786 -1.442 PB AR6 12
AR6 "C1'" "C1'" C 0 1 N N R N N N -28.595 1.000 -29.827 -4.414 -0.357 0.931 "C1'" AR6 13
AR6 O1A O1A O 0 1 N N N N N N -30.966 5.333 -25.232 1.339 -3.723 -0.319 O1A AR6 14
AR6 O1B O1B O 0 1 N N N N N N -34.561 4.556 -28.010 2.859 0.174 -2.659 O1B AR6 15
AR6 C1D C1D C 0 1 N N S N N N -34.026 3.465 -21.791 7.806 0.743 1.993 C1D AR6 16
AR6 O1D O1D O 0 1 N Y N N N N -33.895 2.242 -21.057 7.282 1.453 3.117 O1D AR6 17
AR6 "C2'" "C2'" C 0 1 N N R N N N -27.710 1.946 -29.048 -5.091 -1.726 0.668 "C2'" AR6 18
AR6 "O2'" "O2'" O 0 1 N N N N N N -26.333 1.550 -29.145 -6.262 -1.878 1.472 "O2'" AR6 19
AR6 O2A O2A O 0 1 N N N N N N -30.644 6.243 -27.719 0.420 -2.322 -2.208 O2A AR6 20
AR6 O2B O2B O 0 1 N N N N N N -33.741 6.610 -26.586 3.926 -2.010 -1.980 O2B AR6 21
AR6 C2D C2D C 0 1 N N R N N N -35.433 3.591 -22.339 8.538 1.718 1.051 C2D AR6 22
AR6 O2D O2D O 0 1 N N N N N N -36.402 2.982 -21.482 8.509 3.044 1.583 O2D AR6 23
AR6 "C3'" "C3'" C 0 1 N N S N N N -28.298 1.842 -27.654 -3.989 -2.722 1.104 "C3'" AR6 24
AR6 "O3'" "O3'" O 0 1 N N N N N N -27.778 0.716 -26.948 -4.227 -3.180 2.437 "O3'" AR6 25
AR6 O3A O3A O 0 1 N N N N N N -32.329 4.565 -27.218 1.988 -1.189 -0.587 O3A AR6 26
AR6 C3D C3D C 0 1 N N S N N N -35.377 2.898 -23.687 7.732 1.646 -0.269 C3D AR6 27
AR6 O3D O3D O 0 1 N N N N N N -36.029 1.640 -23.707 7.582 2.945 -0.846 O3D AR6 28
AR6 "C4'" "C4'" C 0 1 N N R N N N -29.779 1.615 -27.916 -2.688 -1.898 1.041 "C4'" AR6 29
AR6 "O4'" "O4'" O 0 1 N N N N N N -29.889 1.066 -29.228 -3.036 -0.587 0.565 "O4'" AR6 30
AR6 C4D C4D C 0 1 N N R N N N -33.900 2.647 -23.920 6.367 1.093 0.213 C4D AR6 31
AR6 O4D O4D O 0 1 N N N N N N -33.181 3.390 -22.935 6.731 0.151 1.245 O4D AR6 32
AR6 "C5'" "C5'" C 0 1 N N N N N N -30.606 2.885 -27.930 -1.701 -2.557 0.076 "C5'" AR6 33
AR6 "O5'" "O5'" O 0 1 N N N N N N -30.037 3.896 -27.105 -0.458 -1.853 0.112 "O5'" AR6 34
AR6 C5D C5D C 0 1 N N N N N N -33.511 3.083 -25.306 5.638 0.385 -0.931 C5D AR6 35
AR6 O5D O5D O 0 1 N N N N N N -34.124 4.345 -25.551 4.337 -0.012 -0.493 O5D AR6 36
AR6 H2 H2 H 0 1 N N N N N N -26.416 -1.977 -33.352 -8.710 2.284 2.179 H2 AR6 37
AR6 HN6 HN6 H 0 1 N N N N N N -27.749 0.613 -36.621 -8.407 4.629 -1.720 HN6 AR6 38
AR6 HN6A HN6A H 0 0 N N N N N N -29.153 1.245 -36.078 -7.040 4.048 -2.507 HN6A AR6 39
AR6 H8 H8 H 0 1 N N N N N N -29.840 3.175 -31.243 -3.654 0.720 -1.613 H8 AR6 40
AR6 "H1'" "H1'" H 0 1 N N N N N N -28.191 -0.019 -29.734 -4.493 -0.085 1.984 "H1'" AR6 41
AR6 H1D H1D H 0 1 N N N N N N -33.783 4.337 -21.166 8.494 -0.032 2.333 H1D AR6 42
AR6 "H2'" "H2'" H 0 1 N N N N N N -27.845 2.970 -29.426 -5.329 -1.846 -0.389 "H2'" AR6 43
AR6 "HO2'" "HO2'" H 0 0 N N N N N N -25.793 2.155 -28.650 -6.722 -2.719 1.343 "HO2'" AR6 44
AR6 H2D H2D H 0 1 N N N N N N -35.669 4.655 -22.489 9.566 1.394 0.891 H2D AR6 45
AR6 HO2D HO2D H 0 0 N N N N N N -37.268 3.083 -21.860 8.949 3.133 2.440 HO2D AR6 46
AR6 "H3'" "H3'" H 0 1 N N N N N N -28.145 2.780 -27.100 -3.943 -3.565 0.414 "H3'" AR6 47
AR6 "HO3'" "HO3'" H 0 0 N N N N N N -28.165 0.679 -26.081 -5.062 -3.655 2.546 "HO3'" AR6 48
AR6 H3D H3D H 0 1 N N N N N N -35.771 3.566 -24.468 8.203 0.962 -0.975 H3D AR6 49
AR6 HO3D HO3D H 0 0 N N N N N N -35.958 1.260 -24.575 8.418 3.370 -1.081 HO3D AR6 50
AR6 "H4'" "H4'" H 0 1 N N N N N N -30.183 0.920 -27.165 -2.247 -1.826 2.035 "H4'" AR6 51
AR6 H4D H4D H 0 1 N N N N N N -33.697 1.572 -23.809 5.752 1.894 0.624 H4D AR6 52
AR6 "H5'" "H5'" H 0 1 N N N N N N -30.665 3.260 -28.962 -1.540 -3.593 0.372 "H5'" AR6 53
AR6 "H5'A" "H5'A" H 0 0 N N N N N N -31.618 2.655 -27.565 -2.107 -2.527 -0.936 "H5'A" AR6 54
AR6 H5D H5D H 0 1 N N N N N N -32.417 3.178 -25.376 5.545 1.064 -1.778 H5D AR6 55
AR6 H5DA H5DA H 0 0 N N N N N N -33.863 2.346 -26.043 6.205 -0.496 -1.232 H5DA AR6 56
AR6 H1A H1A H 0 1 N N N N N N -30.772 6.239 -25.021 1.615 -3.764 0.607 H1A AR6 57
AR6 H1B H1B H 0 1 N N N N N N -35.021 5.251 -28.466 2.435 0.998 -2.379 H1B AR6 58
AR6 HD1 HD1 H 0 1 N N N N N N -33.011 2.170 -20.717 6.809 0.896 3.749 HD1 AR6 59
#
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
AR6 N1 C2 DOUB Y N 1
AR6 N1 C6 SING Y N 2
AR6 C2 N3 SING Y N 3
AR6 N3 C4 DOUB Y N 4
AR6 C4 C5 SING Y N 5
AR6 C4 N9 SING Y N 6
AR6 C5 C6 DOUB Y N 7
AR6 C5 N7 SING Y N 8
AR6 C6 N6 SING N N 9
AR6 N7 C8 DOUB Y N 10
AR6 C8 N9 SING Y N 11
AR6 N9 "C1'" SING N N 12
AR6 PA O1A SING N N 13
AR6 PA O2A DOUB N N 14
AR6 PA O3A SING N N 15
AR6 PA "O5'" SING N N 16
AR6 PB O1B SING N N 17
AR6 PB O2B DOUB N N 18
AR6 PB O3A SING N N 19
AR6 PB O5D SING N N 20
AR6 "C1'" "C2'" SING N N 21
AR6 "C1'" "O4'" SING N N 22
AR6 C1D O1D SING N N 23
AR6 C1D C2D SING N N 24
AR6 C1D O4D SING N N 25
AR6 "C2'" "O2'" SING N N 26
AR6 "C2'" "C3'" SING N N 27
AR6 C2D O2D SING N N 28
AR6 C2D C3D SING N N 29
AR6 "C3'" "O3'" SING N N 30
AR6 "C3'" "C4'" SING N N 31
AR6 C3D O3D SING N N 32
AR6 C3D C4D SING N N 33
AR6 "C4'" "O4'" SING N N 34
AR6 "C4'" "C5'" SING N N 35
AR6 C4D O4D SING N N 36
AR6 C4D C5D SING N N 37
AR6 "C5'" "O5'" SING N N 38
AR6 C5D O5D SING N N 39
AR6 C2 H2 SING N N 40
AR6 N6 HN6 SING N N 41
AR6 N6 HN6A SING N N 42
AR6 C8 H8 SING N N 43
AR6 "C1'" "H1'" SING N N 44
AR6 C1D H1D SING N N 45
AR6 "C2'" "H2'" SING N N 46
AR6 "O2'" "HO2'" SING N N 47
AR6 C2D H2D SING N N 48
AR6 O2D HO2D SING N N 49
AR6 "C3'" "H3'" SING N N 50
AR6 "O3'" "HO3'" SING N N 51
AR6 C3D H3D SING N N 52
AR6 O3D HO3D SING N N 53
AR6 "C4'" "H4'" SING N N 54
AR6 C4D H4D SING N N 55
AR6 "C5'" "H5'" SING N N 56
AR6 "C5'" "H5'A" SING N N 57
AR6 C5D H5D SING N N 58
AR6 C5D H5DA SING N N 59
AR6 O1A H1A SING N N 60
AR6 O1B H1B SING N N 61
AR6 O1D HD1 SING N N 62
#
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
AR6 SMILES ACDLabs 12.01 O=P(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)(O)OP(=O)(O)OCC4OC(O)C(O)C4O
AR6 InChI InChI 1.03 InChI=1S/C15H23N5O14P2/c16-12-7-13(18-3-17-12)20(4-19-7)14-10(23)8(21)5(32-14)1-30-35(26,27)34-36(28,29)31-2-6-9(22)11(24)15(25)33-6/h3-6,8-11,14-15,21-25H,1-2H2,(H,26,27)(H,28,29)(H2,16,17,18)/t5-,6-,8-,9-,10-,11-,14-,15+/m1/s1
AR6 InChIKey InChI 1.03 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
AR6 SMILES_CANONICAL CACTVS 3.370 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
AR6 SMILES CACTVS 3.370 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O
AR6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)N
AR6 SMILES "OpenEye OEToolkits" 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)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
AR6 "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4R,5S)-3,4,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"
AR6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen 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
AR6 'Create component' 2009-08-10 EBI
AR6 'Modify aromatic_flag' 2011-06-04 RCSB
AR6 'Modify descriptor' 2011-06-04 RCSB
AR6 'Modify leaving atom flag' 2013-06-20 RCSB
AR6 'Other modification' 2019-09-05 EBI
AR6 'Modify synonyms' 2020-06-05 PDBE
AR6 'Modify PCM' 2024-09-27 PDBE
AR6 'Modify PCM' 2025-01-29 PDBJ
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id AR6
_pdbx_chem_comp_synonyms.name Adenosine-5-Diphosphoribose
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_position
_pdbx_chem_comp_pcm.comp_id_linking_atom
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 AR6 ARG ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D NH1 PTM-0709 PTM-0053
2 AR6 ASN ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D ND2 ? PTM-0054
3 AR6 ASP ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OD2 ? PTM-0497
4 AR6 CYS ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D SG ? PTM-0055
5 AR6 DDE ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D NE2 ? PTM-0672
6 AR6 GLU ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OE2 ? PTM-0646
7 AR6 GLY ADP-ribosylation ADP-ribose 'Amino-acid backbone' C-terminal C1D OXT ? PTM-0671
8 AR6 HIS ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D NE2 ? PTM-0720
9 AR6 SER ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OG ? PTM-0056
10 AR6 THR ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OG1 ? PTM-0721
11 AR6 TYR ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OH ? PTM-0670
12 AR6 LYS ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D NZ ? PTM-0355
13 AR6 GLU ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' C1D OE1 ? ?
14 AR6 ARG ADP-ribosylation ADP-ribose 'Amino-acid side chain' 'Any position' O1D NH1 ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id AR6
_pdbe_chem_comp_drugbank_details.drugbank_id DB02059
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Adenosine-5-Diphosphoribose
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
AR6 Adenosine-5-Diphosphoribose wwPDB ?
AR6 Adenosine-5-Diphosphoribose DrugBank ?
AR6 ADPR DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id AR6
_pdbe_chem_comp_drugbank_classification.drugbank_id DB02059
_pdbe_chem_comp_drugbank_classification.parent 'Purine nucleotide sugars'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Purine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as purine nucleotide sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
AR6 DB02059 'NAD-dependent protein deacylase sirtuin-5, mitochondrial' Humans Q9NXA8 unknown 1
AR6 DB02059 'p-hydroxybenzoate hydroxylase' 'Pseudomonas fluorescens' P00438 unknown 2
AR6 DB02059 'ADP-ribose pyrophosphatase' 'Shigella flexneri' P83844 unknown 3
AR6 DB02059 'CDP-glucose 4,6-dehydratase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P26397 unknown 4
AR6 DB02059 'Elongation factor 2' Humans P13639 unknown 5
AR6 DB02059 'Glyceraldehyde-3-phosphate dehydrogenase' Humans P04406 unknown 6
AR6 DB02059 'Lactaldehyde reductase' 'Escherichia coli (strain K12)' P0A9S1 unknown 7
AR6 DB02059 'MutT/nudix family protein' 'Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)' O33199 unknown 8
AR6 DB02059 'ADP compounds hydrolase NudE' 'Escherichia coli (strain K12)' P45799 unknown 9
AR6 DB02059 'ADP-ribose pyrophosphatase' 'Thermus thermophilus' Q84CU3 unknown 10
AR6 DB02059 'NAD-dependent protein deacetylase sirtuin-3, mitochondrial' Humans Q9NTG7 unknown 11
#
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
AR6 N1 N 6.335 9.068 1
AR6 C2 C 7.706 8.460 2
AR6 N3 N 7.865 6.968 3
AR6 C4 C 6.654 6.085 4
AR6 C5 C 5.282 6.692 5
AR6 C6 C 5.123 8.184 6
AR6 N6 N 3.752 8.792 7
AR6 N7 N 4.289 5.580 8
AR6 C8 C 5.038 4.291 9
AR6 N9 N 6.496 4.602 10
AR6 PA P 10.875 -1.902 11
AR6 PB P 12.614 -3.833 12
AR6 "C1'" C 7.611 3.598 13
AR6 O1A O 9.408 -2.214 14
AR6 O1B O 13.077 -2.406 15
AR6 C1D C 18.206 -6.227 16
AR6 O1D O 19.632 -5.763 17
AR6 "C2'" C 9.078 3.910 18
AR6 "O2'" O 9.688 5.280 19
AR6 O2A O 12.342 -1.590 20
AR6 O2B O 12.150 -5.259 21
AR6 C2D C 17.742 -7.653 22
AR6 O2D O 18.624 -8.867 23
AR6 "C3'" C 9.828 2.611 24
AR6 "O3'" O 11.320 2.454 25
AR6 O3A O 11.187 -3.369 26
AR6 C3D C 16.242 -7.653 27
AR6 O3D O 15.360 -8.867 28
AR6 "C4'" C 8.825 1.496 29
AR6 "O4'" O 7.454 2.107 30
AR6 C4D C 15.778 -6.227 31
AR6 O4D O 16.992 -5.345 32
AR6 "C5'" C 9.136 0.029 33
AR6 "O5'" O 10.563 -0.434 34
AR6 C5D C 14.352 -5.763 35
AR6 O5D O 14.040 -4.296 36
#
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
AR6 N1 C2 DOUBLE NONE 1
AR6 N1 C6 SINGLE NONE 2
AR6 C2 N3 SINGLE NONE 3
AR6 N3 C4 DOUBLE NONE 4
AR6 C4 C5 SINGLE NONE 5
AR6 C4 N9 SINGLE NONE 6
AR6 C5 C6 DOUBLE NONE 7
AR6 C5 N7 SINGLE NONE 8
AR6 C6 N6 SINGLE NONE 9
AR6 N7 C8 DOUBLE NONE 10
AR6 C8 N9 SINGLE NONE 11
AR6 "C1'" N9 SINGLE BEGINWEDGE 12
AR6 PA O1A SINGLE BEGINDASH 13
AR6 PA O2A DOUBLE NONE 14
AR6 PA O3A SINGLE NONE 15
AR6 PA "O5'" SINGLE NONE 16
AR6 PB O1B SINGLE BEGINDASH 17
AR6 PB O2B DOUBLE NONE 18
AR6 PB O3A SINGLE NONE 19
AR6 PB O5D SINGLE NONE 20
AR6 "C1'" "C2'" SINGLE NONE 21
AR6 "C1'" "O4'" SINGLE NONE 22
AR6 C1D O1D SINGLE BEGINDASH 23
AR6 C1D C2D SINGLE NONE 24
AR6 C1D O4D SINGLE NONE 25
AR6 "C2'" "O2'" SINGLE BEGINDASH 26
AR6 "C2'" "C3'" SINGLE NONE 27
AR6 C2D O2D SINGLE BEGINDASH 28
AR6 C2D C3D SINGLE NONE 29
AR6 "C3'" "O3'" SINGLE BEGINDASH 30
AR6 "C3'" "C4'" SINGLE NONE 31
AR6 C3D O3D SINGLE BEGINDASH 32
AR6 C3D C4D SINGLE NONE 33
AR6 "C4'" "O4'" SINGLE NONE 34
AR6 "C4'" "C5'" SINGLE BEGINWEDGE 35
AR6 C4D O4D SINGLE NONE 36
AR6 C4D C5D SINGLE BEGINWEDGE 37
AR6 "C5'" "O5'" SINGLE NONE 38
AR6 C5D O5D SINGLE NONE 39
#
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
AR6 MurckoScaffold S1 scaffold 'O=[PH](OC[C@@H]1CCCO1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C15H22N4O7P2/c20-27(23-7-11-2-1-5-22-11)26-28(21)24-8-12-3-4-14(25-12)19-10-18-13-6-16-9-17-15(13)19/h6,9-12,14,27-28H,1-5,7-8H2/t11-,12-,14+/m0/s1 UJUHCPFOMLEXIT-SGMGOOAPSA-N
AR6 adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
AR6 furanose F2 fragment OC1CCCO1 InChI=1S/C4H8O2/c5-4-2-1-3-6-4/h4-5H,1-3H2 JNODDICFTDYODH-UHFFFAOYSA-N
AR6 imidazole F3 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
AR6 phosphate F4 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
AR6 purine F5 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
AR6 pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
AR6 ribose F7 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-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
AR6 N1 S1 1
AR6 C2 S1 1
AR6 N3 S1 1
AR6 C4 S1 1
AR6 C5 S1 1
AR6 C6 S1 1
AR6 N7 S1 1
AR6 C8 S1 1
AR6 N9 S1 1
AR6 PA S1 1
AR6 PB S1 1
AR6 "C1'" S1 1
AR6 C1D S1 1
AR6 "C2'" S1 1
AR6 O2A S1 1
AR6 O2B S1 1
AR6 C2D S1 1
AR6 "C3'" S1 1
AR6 O3A S1 1
AR6 C3D S1 1
AR6 "C4'" S1 1
AR6 "O4'" S1 1
AR6 C4D S1 1
AR6 O4D S1 1
AR6 "C5'" S1 1
AR6 "O5'" S1 1
AR6 C5D S1 1
AR6 O5D S1 1
AR6 N1 F1 1
AR6 C6 F1 1
AR6 C5 F1 1
AR6 C4 F1 1
AR6 N3 F1 1
AR6 C2 F1 1
AR6 N9 F1 1
AR6 C8 F1 1
AR6 N7 F1 1
AR6 N6 F1 1
AR6 C3D F2 1
AR6 C4D F2 1
AR6 O4D F2 1
AR6 C1D F2 1
AR6 C2D F2 1
AR6 O1D F2 1
AR6 C4 F3 1
AR6 C5 F3 1
AR6 N7 F3 1
AR6 C8 F3 1
AR6 N9 F3 1
AR6 O1A F4 1
AR6 PA F4 1
AR6 O2A F4 1
AR6 O3A F4 1
AR6 "O5'" F4 1
AR6 O1B F4 2
AR6 PB F4 2
AR6 O2B F4 2
AR6 O3A F4 2
AR6 O5D F4 2
AR6 N7 F5 1
AR6 C8 F5 1
AR6 N9 F5 1
AR6 C4 F5 1
AR6 C5 F5 1
AR6 C6 F5 1
AR6 N1 F5 1
AR6 C2 F5 1
AR6 N3 F5 1
AR6 C5 F6 1
AR6 C4 F6 1
AR6 N3 F6 1
AR6 C2 F6 1
AR6 N1 F6 1
AR6 C6 F6 1
AR6 "C2'" F7 1
AR6 "C3'" F7 1
AR6 "C4'" F7 1
AR6 "O4'" F7 1
AR6 "C1'" F7 1
AR6 "C5'" F7 1
AR6 "O5'" F7 1
AR6 "O3'" F7 1
AR6 "O2'" F7 1
AR6 C2D F7 2
AR6 C3D F7 2
AR6 C4D F7 2
AR6 O4D F7 2
AR6 C1D F7 2
AR6 C5D F7 2
AR6 O5D F7 2
AR6 O3D F7 2
AR6 O2D F7 2
#
_pdbe_chem_comp_rdkit_properties.comp_id AR6
_pdbe_chem_comp_rdkit_properties.exactmw 559.072
_pdbe_chem_comp_rdkit_properties.amw 559.318
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 8
_pdbe_chem_comp_rdkit_properties.NumHBA 19
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 59
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.667
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 10
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 233.433
_pdbe_chem_comp_rdkit_properties.tpsa 291.520
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.092
_pdbe_chem_comp_rdkit_properties.CrippenMR 108.162
_pdbe_chem_comp_rdkit_properties.chi0v 18.135
_pdbe_chem_comp_rdkit_properties.chi1v 11.363
_pdbe_chem_comp_rdkit_properties.chi2v 5.940
_pdbe_chem_comp_rdkit_properties.chi3v 5.940
_pdbe_chem_comp_rdkit_properties.chi4v 3.909
_pdbe_chem_comp_rdkit_properties.chi0n 39.346
_pdbe_chem_comp_rdkit_properties.chi1n 19.194
_pdbe_chem_comp_rdkit_properties.chi2n 3.710
_pdbe_chem_comp_rdkit_properties.chi3n 3.710
_pdbe_chem_comp_rdkit_properties.chi4n 2.273
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.670
_pdbe_chem_comp_rdkit_properties.kappa1 10.478
_pdbe_chem_comp_rdkit_properties.kappa2 10.239
_pdbe_chem_comp_rdkit_properties.kappa3 5.592
_pdbe_chem_comp_rdkit_properties.Phi 2.980
#
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
AR6 UniChem DrugBank DB02059
AR6 UniChem ChEBI 191408
AR6 UniChem ZINC ZINC000014880207
AR6 UniChem PubChem 447048
AR6 UniChem MetaboLights MTBLC191408
AR6 UniChem BRENDA 248627
AR6 UniChem 'Probes And Drugs' PD008183
#
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
AR6 N1 8.033 -2.022 -0.710 ETKDGv3 1
AR6 C2 7.643 -1.286 -1.726 ETKDGv3 2
AR6 N3 6.551 -0.349 -1.576 ETKDGv3 3
AR6 C4 5.948 -0.310 -0.428 ETKDGv3 4
AR6 C5 6.357 -1.085 0.685 ETKDGv3 5
AR6 C6 7.388 -1.922 0.581 ETKDGv3 6
AR6 N6 7.868 -2.672 1.696 ETKDGv3 7
AR6 N7 5.622 -0.675 1.829 ETKDGv3 8
AR6 C8 4.828 0.275 1.405 ETKDGv3 9
AR6 N9 4.928 0.576 -0.005 ETKDGv3 10
AR6 PA -1.053 0.811 -0.582 ETKDGv3 11
AR6 PB -2.219 -0.608 1.472 ETKDGv3 12
AR6 "C1'" 4.529 1.825 -0.658 ETKDGv3 13
AR6 O1A -2.528 1.274 -1.271 ETKDGv3 14
AR6 O1B -2.612 -0.541 3.117 ETKDGv3 15
AR6 C1D -7.711 -2.363 1.014 ETKDGv3 16
AR6 O1D -8.823 -2.606 0.188 ETKDGv3 17
AR6 "C2'" 3.988 1.558 -2.062 ETKDGv3 18
AR6 "O2'" 4.963 1.820 -3.039 ETKDGv3 19
AR6 O2A -0.630 -0.521 -1.164 ETKDGv3 20
AR6 O2B -1.476 -1.898 1.200 ETKDGv3 21
AR6 C2D -7.615 -0.894 1.421 ETKDGv3 22
AR6 O2D -8.850 -0.228 1.341 ETKDGv3 23
AR6 "C3'" 2.811 2.500 -2.163 ETKDGv3 24
AR6 "O3'" 3.167 3.734 -2.745 ETKDGv3 25
AR6 O3A -1.210 0.716 1.113 ETKDGv3 26
AR6 C3D -6.611 -0.336 0.449 ETKDGv3 27
AR6 O3D -7.256 0.159 -0.698 ETKDGv3 28
AR6 "C4'" 2.400 2.679 -0.701 ETKDGv3 29
AR6 "O4'" 3.535 2.475 0.112 ETKDGv3 30
AR6 C4D -5.771 -1.569 0.092 ETKDGv3 31
AR6 O4D -6.525 -2.738 0.346 ETKDGv3 32
AR6 "C5'" 1.298 1.697 -0.279 ETKDGv3 33
AR6 "O5'" 0.112 1.990 -0.980 ETKDGv3 34
AR6 C5D -4.467 -1.630 0.897 ETKDGv3 35
AR6 O5D -3.648 -0.540 0.541 ETKDGv3 36
AR6 H2 8.148 -1.375 -2.678 ETKDGv3 37
AR6 HN6 8.687 -3.309 1.582 ETKDGv3 38
AR6 HN6A 7.412 -2.600 2.633 ETKDGv3 39
AR6 H8 4.160 0.801 2.073 ETKDGv3 40
AR6 "H1'" 5.413 2.499 -0.710 ETKDGv3 41
AR6 H1D -7.818 -2.986 1.927 ETKDGv3 42
AR6 "H2'" 3.629 0.504 -2.144 ETKDGv3 43
AR6 "HO2'" 4.602 1.471 -3.896 ETKDGv3 44
AR6 H2D -7.201 -0.817 2.454 ETKDGv3 45
AR6 HO2D -9.392 -0.553 2.107 ETKDGv3 46
AR6 "H3'" 2.002 2.045 -2.777 ETKDGv3 47
AR6 "HO3'" 3.876 4.149 -2.185 ETKDGv3 48
AR6 H3D -6.017 0.476 0.932 ETKDGv3 49
AR6 HO3D -6.578 0.684 -1.198 ETKDGv3 50
AR6 "H4'" 2.024 3.713 -0.534 ETKDGv3 51
AR6 H4D -5.505 -1.551 -0.989 ETKDGv3 52
AR6 "H5'" 1.134 1.817 0.816 ETKDGv3 53
AR6 "H5'A" 1.647 0.658 -0.483 ETKDGv3 54
AR6 H5D -3.958 -2.590 0.655 ETKDGv3 55
AR6 H5DA -4.715 -1.610 1.983 ETKDGv3 56
AR6 H1A -2.767 2.117 -0.810 ETKDGv3 57
AR6 H1B -3.110 0.309 3.221 ETKDGv3 58
AR6 HD1 -8.637 -2.183 -0.691 ETKDGv3 59
#