data_ADV
#
_chem_comp.id ADV
_chem_comp.name "ALPHA-BETA METHYLENE ADP-RIBOSE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H25 N5 O13 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;AMPCPR; {[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID
MONO-(3,4,5-TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-12-07
_chem_comp.pdbx_modified_date 2020-06-17
_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 557.343
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ADV
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1KHZ
_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.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
ADV PA PA P 0 1 N N R 35.687 33.465 10.905 -1.310 0.404 -0.687 PA ADV 1
ADV "O5'" O5* O 0 1 N N N 34.994 33.533 9.568 -1.129 -0.381 0.705 "O5'" ADV 2
ADV "C5'" C5* C 0 1 N N N 34.531 32.327 8.847 -1.988 0.255 1.653 "C5'" ADV 3
ADV "C4'" C4* C 0 1 N N R 34.090 32.785 7.538 -1.862 -0.446 3.007 "C4'" ADV 4
ADV "O4'" O4* O 0 1 N N N 35.253 32.926 6.676 -0.508 -0.348 3.501 "O4'" ADV 5
ADV "C3'" C3* C 0 1 N N S 33.233 31.758 6.869 -2.723 0.271 4.070 "C3'" ADV 6
ADV "O3'" O3* O 0 1 N N N 31.830 32.084 7.022 -3.972 -0.401 4.241 "O3'" ADV 7
ADV "C2'" C2* C 0 1 N N R 33.672 31.806 5.319 -1.877 0.181 5.362 "C2'" ADV 8
ADV "O2'" O2* O 0 1 N N N 32.914 32.907 4.631 -2.579 -0.547 6.371 "O2'" ADV 9
ADV "C1'" C1* C 0 1 N N R 35.148 32.235 5.361 -0.605 -0.576 4.924 "C1'" ADV 10
ADV N9 N9 N 0 1 Y N N 36.057 30.979 5.373 0.572 -0.036 5.608 N9 ADV 11
ADV C8 C8 C 0 1 Y N N 36.345 30.103 6.386 1.348 0.999 5.180 C8 ADV 12
ADV N7 N7 N 0 1 Y N N 37.088 29.082 5.990 2.309 1.214 6.031 N7 ADV 13
ADV C5 C5 C 0 1 Y N N 37.244 29.271 4.625 2.207 0.338 7.058 C5 ADV 14
ADV C6 C6 C 0 1 Y N N 37.830 28.463 3.568 2.947 0.096 8.228 C6 ADV 15
ADV N6 N6 N 0 1 N N N 38.258 27.217 3.768 4.056 0.864 8.536 N6 ADV 16
ADV N1 N1 N 0 1 Y N N 37.801 28.969 2.245 2.553 -0.883 9.035 N1 ADV 17
ADV C2 C2 C 0 1 Y N N 37.053 30.120 1.975 1.496 -1.621 8.749 C2 ADV 18
ADV N3 N3 N 0 1 Y N N 36.384 30.862 2.868 0.777 -1.435 7.663 N3 ADV 19
ADV C4 C4 C 0 1 Y N N 36.563 30.421 4.204 1.094 -0.479 6.796 C4 ADV 20
ADV CX CX C 0 1 N N N 36.962 32.336 10.807 -0.241 -0.351 -1.956 CX ADV 21
ADV PB PB P 0 1 N N S 37.021 30.703 11.220 -0.447 0.538 -3.533 PB ADV 22
ADV O1B O1B O 0 1 N N N 36.447 29.940 10.090 -0.070 1.958 -3.352 O1B ADV 23
ADV OR5 OR5 O 0 1 N N N 38.596 30.263 11.372 0.496 -0.129 -4.653 OR5 ADV 24
ADV CR5 CR5 C 0 1 N N N 39.225 30.464 12.825 0.291 0.608 -5.860 CR5 ADV 25
ADV CR4 CR4 C 0 1 N N R 39.795 29.092 13.400 1.164 0.021 -6.971 CR4 ADV 26
ADV OR4 OR4 O 0 1 N N N 38.667 27.991 13.428 0.790 -1.339 -7.215 OR4 ADV 27
ADV CR3 CR3 C 0 1 N N S 40.877 28.597 12.375 0.945 0.809 -8.280 CR3 ADV 28
ADV OR3 OR3 O 0 1 N N N 42.003 28.104 13.053 2.005 1.740 -8.505 OR3 ADV 29
ADV CR2 CR2 C 0 1 N N R 40.185 27.455 11.592 0.963 -0.318 -9.349 CR2 ADV 30
ADV OR2 OR2 O 0 1 N N N 41.066 26.477 11.274 2.300 -0.642 -9.733 OR2 ADV 31
ADV CR1 CR1 C 0 1 N N S 39.076 26.888 12.520 0.310 -1.482 -8.562 CR1 ADV 32
ADV OR1 OR1 O 0 1 N N N 39.628 25.825 13.323 0.718 -2.740 -9.103 OR1 ADV 33
ADV O2A O2A O 0 1 N N N 36.197 34.766 11.203 -2.848 0.314 -1.158 O2A ADV 34
ADV O2B O2B O 0 1 N N N 36.241 30.426 12.438 -1.984 0.448 -4.004 O2B ADV 35
ADV O1A O1A O 0 1 N N N 34.764 33.095 11.892 -0.933 1.824 -0.506 O1A ADV 36
ADV "H5'1" 1H5* H 0 0 N N N 35.295 31.516 8.800 -3.019 0.194 1.307 "H5'1" ADV 37
ADV "H5'2" 2H5* H 0 0 N N N 33.754 31.749 9.400 -1.700 1.301 1.759 "H5'2" ADV 38
ADV "H'4" 4H* H 0 1 N N N 33.531 33.738 7.686 -2.160 -1.491 2.920 "H'4" ADV 39
ADV "H'3" 3H* H 0 1 N N N 33.365 30.742 7.309 -2.886 1.311 3.790 "H'3" ADV 40
ADV "HO'3" 3HO* H 0 0 N N N 31.285 31.431 6.597 -4.464 0.089 4.913 "HO'3" ADV 41
ADV "H'2" 2H* H 0 1 N N N 33.491 30.838 4.795 -1.621 1.178 5.721 "H'2" ADV 42
ADV "HO'2" 2HO* H 0 0 N N N 33.172 32.935 3.717 -3.391 -0.055 6.557 "HO'2" ADV 43
ADV "H'1" 1H* H 0 1 N N N 35.453 32.863 4.492 -0.708 -1.641 5.131 "H'1" ADV 44
ADV H8 H8 H 0 1 N N N 36.007 30.210 7.430 1.190 1.557 4.269 H8 ADV 45
ADV H61 1H6 H 0 1 N N N 38.669 26.650 3.026 4.556 0.690 9.349 H61 ADV 46
ADV H62 2H6 H 0 1 N N N 37.483 26.686 4.166 4.336 1.574 7.937 H62 ADV 47
ADV H2 H2 H 0 1 N N N 36.982 30.485 0.936 1.211 -2.407 9.433 H2 ADV 48
ADV HX1 1HX H 0 1 N N N 37.294 32.373 9.743 0.798 -0.290 -1.637 HX1 ADV 49
ADV HX2 2HX H 0 1 N N N 37.800 32.803 11.373 -0.519 -1.396 -2.089 HX2 ADV 50
ADV H5R1 1H5R H 0 0 N N N 40.001 31.264 12.828 -0.757 0.545 -6.150 H5R1 ADV 51
ADV H5R2 2H5R H 0 0 N N N 38.495 30.931 13.526 0.561 1.651 -5.698 H5R2 ADV 52
ADV HR4 4HR H 0 1 N N N 40.192 29.249 14.429 2.213 0.070 -6.681 HR4 ADV 53
ADV HR3 3HR H 0 1 N N N 41.230 29.417 11.707 -0.019 1.318 -8.269 HR3 ADV 54
ADV HOR3 3HOR H 0 0 N N N 42.657 27.804 12.433 1.854 2.131 -9.377 HOR3 ADV 55
ADV HR2 2HR H 0 1 N N N 39.762 27.840 10.634 0.362 -0.047 -10.218 HR2 ADV 56
ADV HOR2 2HOR H 0 0 N N N 40.641 25.776 10.793 2.246 -1.417 -10.309 HOR2 ADV 57
ADV HR1 1HR H 0 1 N N N 38.217 26.501 11.923 -0.775 -1.394 -8.587 HR1 ADV 58
ADV HOR1 1HOR H 0 0 N N N 39.889 25.119 12.742 0.320 -3.425 -8.549 HOR1 ADV 59
ADV HOA2 2HOA H 0 0 N N N 36.633 34.723 12.045 -3.053 -0.624 -1.264 HOA2 ADV 60
ADV HOB2 2HOB H 0 0 N N N 36.274 29.505 12.670 -2.189 -0.491 -4.110 HOB2 ADV 61
# #
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
ADV PA "O5'" SING N N 1
ADV PA CX SING N N 2
ADV PA O2A SING N N 3
ADV PA O1A DOUB N N 4
ADV "O5'" "C5'" SING N N 5
ADV "C5'" "C4'" SING N N 6
ADV "C5'" "H5'1" SING N N 7
ADV "C5'" "H5'2" SING N N 8
ADV "C4'" "O4'" SING N N 9
ADV "C4'" "C3'" SING N N 10
ADV "C4'" "H'4" SING N N 11
ADV "O4'" "C1'" SING N N 12
ADV "C3'" "O3'" SING N N 13
ADV "C3'" "C2'" SING N N 14
ADV "C3'" "H'3" SING N N 15
ADV "O3'" "HO'3" SING N N 16
ADV "C2'" "O2'" SING N N 17
ADV "C2'" "C1'" SING N N 18
ADV "C2'" "H'2" SING N N 19
ADV "O2'" "HO'2" SING N N 20
ADV "C1'" N9 SING N N 21
ADV "C1'" "H'1" SING N N 22
ADV N9 C8 SING Y N 23
ADV N9 C4 SING Y N 24
ADV C8 N7 DOUB Y N 25
ADV C8 H8 SING N N 26
ADV N7 C5 SING Y N 27
ADV C5 C6 DOUB Y N 28
ADV C5 C4 SING Y N 29
ADV C6 N6 SING N N 30
ADV C6 N1 SING Y N 31
ADV N6 H61 SING N N 32
ADV N6 H62 SING N N 33
ADV N1 C2 DOUB Y N 34
ADV C2 N3 SING Y N 35
ADV C2 H2 SING N N 36
ADV N3 C4 DOUB Y N 37
ADV CX PB SING N N 38
ADV CX HX1 SING N N 39
ADV CX HX2 SING N N 40
ADV PB O1B DOUB N N 41
ADV PB OR5 SING N N 42
ADV PB O2B SING N N 43
ADV OR5 CR5 SING N N 44
ADV CR5 CR4 SING N N 45
ADV CR5 H5R1 SING N N 46
ADV CR5 H5R2 SING N N 47
ADV CR4 OR4 SING N N 48
ADV CR4 CR3 SING N N 49
ADV CR4 HR4 SING N N 50
ADV OR4 CR1 SING N N 51
ADV CR3 OR3 SING N N 52
ADV CR3 CR2 SING N N 53
ADV CR3 HR3 SING N N 54
ADV OR3 HOR3 SING N N 55
ADV CR2 OR2 SING N N 56
ADV CR2 CR1 SING N N 57
ADV CR2 HR2 SING N N 58
ADV OR2 HOR2 SING N N 59
ADV CR1 OR1 SING N N 60
ADV CR1 HR1 SING N N 61
ADV OR1 HOR1 SING N N 62
ADV O2A HOA2 SING N N 63
ADV O2B HOB2 SING N N 64
# #
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
ADV SMILES ACDLabs 10.04 "O=P(O)(OCC3OC(n1c2ncnc(N)c2nc1)C(O)C3O)CP(=O)(O)OCC4OC(O)C(O)C4O"
ADV SMILES_CANONICAL CACTVS 3.341 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)C[P@@](O)(=O)OC[C@H]4O[C@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O"
ADV SMILES CACTVS 3.341 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)C[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O"
ADV SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(C[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@H](O4)O)O)O)O)O)O)N"
ADV SMILES "OpenEye OEToolkits" 1.5.0 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(CP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)O)N"
ADV InChI InChI 1.03 "InChI=1S/C16H25N5O13P2/c17-13-8-14(19-3-18-13)21(4-20-8)15-11(24)9(22)6(33-15)1-31-35(27,28)5-36(29,30)32-2-7-10(23)12(25)16(26)34-7/h3-4,6-7,9-12,15-16,22-26H,1-2,5H2,(H,27,28)(H,29,30)(H2,17,18,19)/t6-,7-,9-,10-,11-,12-,15-,16+/m1/s1"
ADV InChIKey InChI 1.03 ZPZRETFSCSWNDT-DBXCYWGHSA-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
ADV "SYSTEMATIC NAME" ACDLabs 10.04 "[(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 methanediylbis[hydrogen (R,S)-phosphonate] (non-preferred name)"
ADV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-[[hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl]methyl]phosphinic 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
ADV "Create component" 2001-12-07 RCSB
ADV "Modify descriptor" 2011-06-04 RCSB
ADV "Modify synonyms" 2020-06-05 PDBE
# #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 ADV AMPCPR ? ?
2 ADV "{[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHOXY]-HYDROXY-PHOSPHORYLMETHYL}-PHOSPHONIC ACID MONO-(3,4,5-TRIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL) ESTER" ? ?
##