data_DBG
#
_chem_comp.id DBG
_chem_comp.name "3-AMINOBENZOPHENONE-4-YL-AMINOHYDROXYPHOSPHINYLAMINOPHOSPHONIC ACID-GUANYLATE ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C23 H27 N8 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms DABP-GPPNHP
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 716.428
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code DBG
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1RVD
_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.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
DBG C22 C22 C 0 1 Y N N ? ? ? 4.799 5.912 -1.602 C22 DBG 1
DBG C21 C21 C 0 1 Y N N ? ? ? 4.973 5.959 -2.985 C21 DBG 2
DBG C20 C20 C 0 1 Y N N ? ? ? 6.253 5.865 -3.531 C20 DBG 3
DBG C19 C19 C 0 1 Y N N ? ? ? 7.359 5.724 -2.694 C19 DBG 4
DBG C18 C18 C 0 1 Y N N ? ? ? 7.186 5.677 -1.310 C18 DBG 5
DBG C17 C17 C 0 1 Y N N ? ? ? 5.910 5.772 -0.804 C17 DBG 6
DBG C16 C16 C 0 1 N N N ? ? ? 5.724 5.722 0.677 C16 DBG 7
DBG O16 O16 O 0 1 N N N ? ? ? 6.742 5.596 1.375 O16 DBG 8
DBG C15 C15 C 0 1 Y N N ? ? ? 2.418 4.746 2.146 C15 DBG 9
DBG N15 N15 N 0 1 N N N ? ? ? 1.685 3.562 2.385 N15 DBG 10
DBG C14 C14 C 0 1 Y N N ? ? ? 3.675 4.657 1.547 C14 DBG 11
DBG C13 C13 C 0 1 Y N N ? ? ? 4.414 5.814 1.302 C13 DBG 12
DBG C12 C12 C 0 1 Y N N ? ? ? 3.897 7.060 1.656 C12 DBG 13
DBG C11 C11 C 0 1 Y N N ? ? ? 2.641 7.150 2.255 C11 DBG 14
DBG C10 C10 C 0 1 Y N N ? ? ? 1.900 5.993 2.500 C10 DBG 15
DBG N3G N3G N 0 1 N N N 5.417 33.254 23.386 0.630 6.106 3.107 N3G DBG 16
DBG PG PG P 0 1 N N R 5.581 32.524 22.061 -0.146 7.514 3.495 PG DBG 17
DBG O1G O1G O 0 1 N N N 5.388 31.087 22.295 0.687 8.113 4.765 O1G DBG 18
DBG O2G O2G O 0 1 N N N 4.560 33.041 21.155 -0.272 8.592 2.442 O2G DBG 19
DBG N3B N3B N 0 1 N N N 7.032 32.780 21.490 -1.577 6.999 4.171 N3B DBG 20
DBG PB PB P 0 1 N N S 7.435 32.245 20.056 -2.692 6.506 3.057 PB DBG 21
DBG O1B O1B O 0 1 N N N 7.471 30.776 20.009 -4.091 6.344 3.865 O1B DBG 22
DBG O2B O2B O 0 1 N N N 6.618 32.841 19.015 -2.856 7.345 1.817 O2B DBG 23
DBG O3A O3A O 0 1 N N N 8.927 32.803 19.873 -2.345 4.958 2.720 O3A DBG 24
DBG PA PA P 0 1 N N S 9.464 34.328 19.614 -3.038 3.894 1.723 PA DBG 25
DBG O1A O1A O 0 1 N N N 9.539 34.634 18.154 -2.055 2.612 1.808 O1A DBG 26
DBG O2A O2A O 0 1 N N N 8.656 35.299 20.404 -4.480 3.600 2.019 O2A DBG 27
DBG "O5'" O5* O 0 1 N N N 10.956 34.236 20.189 -2.733 4.494 0.252 "O5'" DBG 28
DBG "C5'" C5* C 0 1 N N N 11.280 34.210 21.561 -3.088 3.719 -0.880 "C5'" DBG 29
DBG "C4'" C4* C 0 1 N N R 12.690 34.673 21.750 -2.709 4.481 -2.142 "C4'" DBG 30
DBG "O4'" O4* O 0 1 N N N 13.609 33.887 20.949 -1.275 4.674 -2.144 "O4'" DBG 31
DBG "C2'" C2* C 0 1 N N R 13.509 35.986 19.888 -1.771 2.932 -3.670 "C2'" DBG 32
DBG "O2'" O2* O 0 1 N N N 14.303 37.092 19.517 -1.616 2.544 -5.019 "O2'" DBG 33
DBG "C3'" C3* C 0 1 N N S 12.929 36.151 21.305 -3.043 3.719 -3.420 "C3'" DBG 34
DBG "O3'" O3* O 0 1 N N N 13.851 36.797 22.155 -3.237 4.658 -4.478 "O3'" DBG 35
DBG "C1'" C1* C 0 1 N N R 14.365 34.730 20.059 -0.708 3.932 -3.240 "C1'" DBG 36
DBG N9 N9 N 0 1 Y N N 14.565 33.977 18.822 0.551 3.319 -2.822 N9 DBG 37
DBG C4 C4 C 0 1 Y N N 15.723 33.522 18.341 1.655 3.092 -3.591 C4 DBG 38
DBG N3 N3 N 0 1 Y N N 16.918 33.728 18.870 1.789 3.396 -4.901 N3 DBG 39
DBG C2 C2 C 0 1 Y N N 17.944 33.304 18.120 2.964 3.064 -5.389 C2 DBG 40
DBG N2 N2 N 0 1 N N N 19.214 33.561 18.486 3.297 3.290 -6.700 N2 DBG 41
DBG N1 N1 N 0 1 Y N N 17.733 32.577 16.955 3.971 2.453 -4.605 N1 DBG 42
DBG C6 C6 C 0 1 Y N N 16.524 32.516 16.305 3.854 2.129 -3.247 C6 DBG 43
DBG O6 O6 O 0 1 N N N 16.463 31.995 15.201 4.723 1.600 -2.566 O6 DBG 44
DBG C5 C5 C 0 1 Y N N 15.445 32.954 17.151 2.561 2.502 -2.743 C5 DBG 45
DBG N7 N7 N 0 1 Y N N 14.068 32.924 16.938 2.063 2.355 -1.482 N7 DBG 46
DBG C8 C8 C 0 1 Y N N 13.622 33.468 17.989 0.846 2.858 -1.561 C8 DBG 47
DBG H22 H22 H 0 1 N N N ? ? ? 3.797 5.985 -1.188 H22 DBG 48
DBG H21 H21 H 0 1 N N N ? ? ? 4.111 6.068 -3.637 H21 DBG 49
DBG H20 H20 H 0 1 N N N ? ? ? 6.388 5.902 -4.608 H20 DBG 50
DBG H19 H19 H 0 1 N N N ? ? ? 8.356 5.652 -3.118 H19 DBG 51
DBG H18 H18 H 0 1 N N N ? ? ? 8.055 5.567 -0.667 H18 DBG 52
DBG H151 1H15 H 0 0 N N N ? ? ? 2.020 2.913 3.066 H151 DBG 53
DBG H152 2H15 H 0 0 N N N ? ? ? 0.901 3.351 1.803 H152 DBG 54
DBG H14 H14 H 0 1 N N N ? ? ? 4.078 3.685 1.270 H14 DBG 55
DBG H12 H12 H 0 1 N N N ? ? ? 4.465 7.968 1.470 H12 DBG 56
DBG H11 H11 H 0 1 N N N ? ? ? 2.248 8.126 2.527 H11 DBG 57
DBG HNG3 3HNG H 0 0 N N N 5.074 34.009 23.944 0.178 5.204 3.239 HNG3 DBG 58
DBG HOG1 1HOG H 0 0 N N N 5.346 30.633 21.462 0.318 8.887 5.242 HOG1 DBG 59
DBG HNB3 3HNB H 0 0 N N N 7.142 33.773 21.454 -1.482 6.418 5.003 HNB3 DBG 60
DBG HOB1 1HOB H 0 0 N N N 7.479 30.488 19.104 -4.900 6.110 3.363 HOB1 DBG 61
DBG HOA1 1HOA H 0 0 N N N 9.555 35.575 18.028 -2.316 1.783 1.354 HOA1 DBG 62
DBG "H5'1" 1H5* H 0 0 N N N 10.599 34.876 22.111 -2.557 2.764 -0.834 "H5'1" DBG 63
DBG "H5'2" 2H5* H 0 0 N N N 11.177 33.183 21.942 -4.166 3.531 -0.854 "H5'2" DBG 64
DBG "H4'" H4* H 0 1 N N N 12.865 34.567 22.831 -3.175 5.471 -2.121 "H4'" DBG 65
DBG "H2'" H2* H 0 1 N N N 12.745 35.915 19.100 -1.748 2.036 -3.038 "H2'" DBG 66
DBG "HO2'" HO2* H 0 0 N N N 14.481 37.625 20.283 -2.107 1.713 -5.139 "HO2'" DBG 67
DBG "H3'" H3* H 0 1 N N N 12.019 36.769 21.339 -3.941 3.099 -3.357 "H3'" DBG 68
DBG "HO3'" HO3* H 0 0 N N N 14.665 36.942 21.688 -3.700 5.415 -4.090 "HO3'" DBG 69
DBG "H1'" H1* H 0 1 N N N 15.363 35.024 20.417 -0.438 4.629 -4.041 "H1'" DBG 70
DBG HN21 1HN2 H 0 0 N N N 19.853 33.177 17.820 4.183 3.695 -6.897 HN21 DBG 71
DBG HN22 2HN2 H 0 0 N N N 19.480 34.065 19.308 2.641 3.039 -7.402 HN22 DBG 72
DBG HN1 HN1 H 0 1 N N N 18.503 32.070 16.568 4.850 2.230 -5.064 HN1 DBG 73
DBG H8 H8 H 0 1 N N N 12.566 33.524 18.208 0.136 2.918 -0.748 H8 DBG 74
# #
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
DBG C22 C21 SING Y N 1
DBG C22 C17 DOUB Y N 2
DBG C22 H22 SING N N 3
DBG C21 C20 DOUB Y N 4
DBG C21 H21 SING N N 5
DBG C20 C19 SING Y N 6
DBG C20 H20 SING N N 7
DBG C19 C18 DOUB Y N 8
DBG C19 H19 SING N N 9
DBG C18 C17 SING Y N 10
DBG C18 H18 SING N N 11
DBG C17 C16 SING N N 12
DBG C16 O16 DOUB N N 13
DBG C16 C13 SING N N 14
DBG C15 N15 SING N N 15
DBG C15 C14 DOUB Y N 16
DBG C15 C10 SING Y N 17
DBG N15 H151 SING N N 18
DBG N15 H152 SING N N 19
DBG C14 C13 SING Y N 20
DBG C14 H14 SING N N 21
DBG C13 C12 DOUB Y N 22
DBG C12 C11 SING Y N 23
DBG C12 H12 SING N N 24
DBG C11 C10 DOUB Y N 25
DBG C11 H11 SING N N 26
DBG C10 N3G SING N N 27
DBG N3G PG SING N N 28
DBG N3G HNG3 SING N N 29
DBG PG O1G SING N N 30
DBG PG O2G DOUB N N 31
DBG PG N3B SING N N 32
DBG O1G HOG1 SING N N 33
DBG N3B PB SING N N 34
DBG N3B HNB3 SING N N 35
DBG PB O1B SING N N 36
DBG PB O2B DOUB N N 37
DBG PB O3A SING N N 38
DBG O1B HOB1 SING N N 39
DBG O3A PA SING N N 40
DBG PA O1A SING N N 41
DBG PA O2A DOUB N N 42
DBG PA "O5'" SING N N 43
DBG O1A HOA1 SING N N 44
DBG "O5'" "C5'" SING N N 45
DBG "C5'" "C4'" SING N N 46
DBG "C5'" "H5'1" SING N N 47
DBG "C5'" "H5'2" SING N N 48
DBG "C4'" "O4'" SING N N 49
DBG "C4'" "C3'" SING N N 50
DBG "C4'" "H4'" SING N N 51
DBG "O4'" "C1'" SING N N 52
DBG "C2'" "O2'" SING N N 53
DBG "C2'" "C3'" SING N N 54
DBG "C2'" "C1'" SING N N 55
DBG "C2'" "H2'" SING N N 56
DBG "O2'" "HO2'" SING N N 57
DBG "C3'" "O3'" SING N N 58
DBG "C3'" "H3'" SING N N 59
DBG "O3'" "HO3'" SING N N 60
DBG "C1'" N9 SING N N 61
DBG "C1'" "H1'" SING N N 62
DBG N9 C4 SING Y N 63
DBG N9 C8 SING Y N 64
DBG C4 N3 SING Y N 65
DBG C4 C5 DOUB Y N 66
DBG N3 C2 DOUB Y N 67
DBG C2 N2 SING N N 68
DBG C2 N1 SING Y N 69
DBG N2 HN21 SING N N 70
DBG N2 HN22 SING N N 71
DBG N1 C6 SING Y N 72
DBG N1 HN1 SING N N 73
DBG C6 O6 DOUB N N 74
DBG C6 C5 SING Y N 75
DBG C5 N7 SING Y N 76
DBG N7 C8 DOUB Y N 77
DBG C8 H8 SING N N 78
# #
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
DBG SMILES ACDLabs 10.04 "O=C(c1ccccc1)c2ccc(c(N)c2)NP(=O)(O)NP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O"
DBG SMILES_CANONICAL CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)N[P@](O)(=O)Nc4ccc(cc4N)C(=O)c5ccccc5)[C@@H](O)[C@H]3O"
DBG SMILES CACTVS 3.341 "NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(=O)Nc4ccc(cc4N)C(=O)c5ccccc5)[CH](O)[CH]3O"
DBG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)c2ccc(c(c2)N)N[P@@](=O)(N[P@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4N=C(NC5=O)N)O)O)O"
DBG SMILES "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)C(=O)c2ccc(c(c2)N)NP(=O)(NP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4N=C(NC5=O)N)O)O)O"
DBG InChI InChI 1.03 "InChI=1S/C23H27N8O13P3/c24-13-8-12(17(32)11-4-2-1-3-5-11)6-7-14(13)29-45(36,37)30-46(38,39)44-47(40,41)42-9-15-18(33)19(34)22(43-15)31-10-26-16-20(31)27-23(25)28-21(16)35/h1-8,10,15,18-19,22,33-34H,9,24H2,(H,40,41)(H3,25,27,28,35)(H4,29,30,36,37,38,39)/t15-,18-,19-,22-/m1/s1"
DBG InChIKey InChI 1.03 MXYGEAAJPIMEHV-CIVUBGFFSA-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
DBG "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(R)-{[(S)-{[(S)-{[2-amino-4-(phenylcarbonyl)phenyl]amino}(hydroxy)phosphoryl]amino}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine"
DBG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-N-[[[2-amino-4-(phenylcarbonyl)phenyl]amino]-hydroxy-phosphoryl]phosphonamidic 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
DBG "Create component" 1999-07-08 EBI
DBG "Modify descriptor" 2011-06-04 RCSB
DBG "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DBG
_pdbx_chem_comp_synonyms.name DABP-GPPNHP
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##