data_AYD
#
_chem_comp.id AYD
_chem_comp.name
;4-{[(4'-AMINO-2'-METHYLPYRIMIDIN-5'-YL)METHYL]AMINO}PENT-3-ENYL DIPHOSPHATE
;
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H20 N4 O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-10-31
_chem_comp.pdbx_modified_date 2012-01-05
_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 382.247
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AYD
_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 1N0H
_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
AYD "N1'" "N1'" N 0 1 Y N N 3.781 105.275 52.542 -7.878 0.633 -0.737 "N1'" AYD 1
AYD "C2'" "C2'" C 0 1 Y N N 3.931 106.077 53.701 -8.173 -0.565 -0.273 "C2'" AYD 2
AYD CM2 CM2 C 0 1 N N N 5.039 107.035 53.864 -9.510 -1.172 -0.609 CM2 AYD 3
AYD "N3'" "N3'" N 0 1 Y N N 3.017 105.977 54.737 -7.331 -1.246 0.477 "N3'" AYD 4
AYD "C4'" "C4'" C 0 1 Y N N 1.885 105.065 54.682 -6.142 -0.741 0.793 "C4'" AYD 5
AYD "N4'" "N4'" N 0 1 N N N 1.039 105.032 55.740 -5.258 -1.460 1.582 "N4'" AYD 6
AYD "C5'" "C5'" C 0 1 Y N N 1.682 104.189 53.461 -5.798 0.527 0.317 "C5'" AYD 7
AYD "C6'" "C6'" C 0 1 Y N N 2.693 104.337 52.384 -6.713 1.203 -0.465 "C6'" AYD 8
AYD "C7'" "C7'" C 0 1 N N N 0.483 103.187 53.336 -4.463 1.140 0.650 "C7'" AYD 9
AYD N3 N3 N 0 1 N N N -0.009 102.378 54.563 -3.435 0.580 -0.231 N3 AYD 10
AYD C5 C5 C 0 1 N N N 0.993 101.092 56.636 -1.189 0.491 -0.905 C5 AYD 11
AYD C4 C4 C 0 1 N N N 0.839 101.359 55.096 -2.115 0.996 -0.111 C4 AYD 12
AYD CM4 CM4 C 0 1 N N N 1.609 100.508 54.136 -1.740 2.025 0.924 CM4 AYD 13
AYD C6 C6 C 0 1 N N N 1.842 100.062 57.370 0.218 1.030 -0.859 C6 AYD 14
AYD C7 C7 C 0 1 N N N 2.877 98.880 57.166 1.196 -0.120 -0.609 C7 AYD 15
AYD O7 O7 O 0 1 N N N 4.140 98.065 57.711 2.530 0.391 -0.566 O7 AYD 16
AYD PA PA P 0 1 N N R 5.122 97.978 58.844 3.819 -0.542 -0.320 PA AYD 17
AYD O1A O1A O 0 1 N N N 6.097 96.958 58.702 3.640 -1.309 0.933 O1A AYD 18
AYD O2A O2A O 0 1 N N N 5.827 99.149 58.996 3.986 -1.563 -1.554 O2A AYD 19
AYD O3A O3A O 0 1 N N N 4.358 97.620 60.160 5.134 0.379 -0.203 O3A AYD 20
AYD PB PB P 0 1 N N N 3.419 96.455 60.630 6.633 0.126 0.327 PB AYD 21
AYD O1B O1B O 0 1 N N N 2.090 96.940 60.360 6.590 -0.713 1.546 O1B AYD 22
AYD O2B O2B O 0 1 N N N 3.764 96.295 62.012 7.485 -0.627 -0.813 O2B AYD 23
AYD O3B O3B O 0 1 N N N 3.881 95.329 59.800 7.326 1.538 0.671 O3B AYD 24
AYD HM21 1HM2 H 0 0 N N N 5.157 107.665 54.775 -9.427 -1.745 -1.533 HM21 AYD 25
AYD HM22 2HM2 H 0 0 N N N 5.992 106.475 53.716 -9.824 -1.831 0.200 HM22 AYD 26
AYD HM23 3HM2 H 0 0 N N N 5.026 107.717 52.982 -10.247 -0.379 -0.738 HM23 AYD 27
AYD "H4'1" "1H4'" H 0 0 N N N 0.245 104.392 55.701 -5.505 -2.339 1.908 "H4'1" AYD 28
AYD "H4'2" "2H4'" H 0 0 N N N 0.698 105.975 55.924 -4.393 -1.084 1.808 "H4'2" AYD 29
AYD "H6'" "H6'" H 0 1 N N N 2.635 103.743 51.456 -6.482 2.185 -0.851 "H6'" AYD 30
AYD "H7'1" "1H7'" H 0 0 N N N -0.388 103.739 52.912 -4.513 2.220 0.508 "H7'1" AYD 31
AYD "H7'2" "2H7'" H 0 0 N N N 0.716 102.467 52.516 -4.210 0.922 1.688 "H7'2" AYD 32
AYD HN3 HN3 H 0 1 N N N -0.919 101.971 54.347 -3.676 -0.083 -0.897 HN3 AYD 33
AYD H5 H5 H 0 1 N N N 0.407 101.734 57.314 -1.439 -0.308 -1.587 H5 AYD 34
AYD HM41 1HM4 H 0 0 N N N 2.270 99.712 54.551 -2.611 2.257 1.537 HM41 AYD 35
AYD HM42 2HM4 H 0 0 N N N 0.901 100.048 53.407 -0.945 1.631 1.557 HM42 AYD 36
AYD HM43 3HM4 H 0 0 N N N 2.208 101.166 53.464 -1.394 2.931 0.427 HM43 AYD 37
AYD H61 1H6 H 0 1 N N N 2.415 100.721 58.062 0.455 1.508 -1.810 H61 AYD 38
AYD H62 2H6 H 0 1 N N N 1.063 99.551 57.984 0.301 1.760 -0.054 H62 AYD 39
AYD H71 1H7 H 0 1 N N N 2.161 98.035 57.035 0.959 -0.598 0.341 H71 AYD 40
AYD H72 2H7 H 0 1 N N N 3.260 99.150 56.154 1.112 -0.850 -1.414 H72 AYD 41
AYD H2A H2A H 0 1 N N N 6.448 99.094 59.712 4.107 -1.129 -2.409 H2A AYD 42
AYD H2B H2B H 0 1 N N N 3.195 95.589 62.296 7.555 -0.133 -1.642 H2B AYD 43
AYD H3B H3B H 0 1 N N N 3.312 94.623 60.084 8.233 1.462 0.997 H3B AYD 44
#
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
AYD "N1'" "C2'" DOUB Y N 1
AYD "N1'" "C6'" SING Y N 2
AYD "C2'" CM2 SING N N 3
AYD "C2'" "N3'" SING Y N 4
AYD CM2 HM21 SING N N 5
AYD CM2 HM22 SING N N 6
AYD CM2 HM23 SING N N 7
AYD "N3'" "C4'" DOUB Y N 8
AYD "C4'" "N4'" SING N N 9
AYD "C4'" "C5'" SING Y N 10
AYD "N4'" "H4'1" SING N N 11
AYD "N4'" "H4'2" SING N N 12
AYD "C5'" "C6'" DOUB Y N 13
AYD "C5'" "C7'" SING N N 14
AYD "C6'" "H6'" SING N N 15
AYD "C7'" N3 SING N N 16
AYD "C7'" "H7'1" SING N N 17
AYD "C7'" "H7'2" SING N N 18
AYD N3 C4 SING N N 19
AYD N3 HN3 SING N N 20
AYD C5 C4 DOUB N E 21
AYD C5 C6 SING N N 22
AYD C5 H5 SING N N 23
AYD C4 CM4 SING N N 24
AYD CM4 HM41 SING N N 25
AYD CM4 HM42 SING N N 26
AYD CM4 HM43 SING N N 27
AYD C6 C7 SING N N 28
AYD C6 H61 SING N N 29
AYD C6 H62 SING N N 30
AYD C7 O7 SING N N 31
AYD C7 H71 SING N N 32
AYD C7 H72 SING N N 33
AYD O7 PA SING N N 34
AYD PA O1A DOUB N N 35
AYD PA O2A SING N N 36
AYD PA O3A SING N N 37
AYD O2A H2A SING N N 38
AYD O3A PB SING N N 39
AYD PB O1B DOUB N N 40
AYD PB O2B SING N N 41
AYD PB O3B SING N N 42
AYD O2B H2B SING N N 43
AYD O3B H3B SING N N 44
#
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
AYD SMILES ACDLabs 10.04 "O=P(O)(O)OP(=O)(O)OCC/C=C(/NCc1cnc(nc1N)C)C"
AYD InChI InChI 1.03 "InChI=1S/C11H20N4O7P2/c1-8(13-6-10-7-14-9(2)15-11(10)12)4-3-5-21-24(19,20)22-23(16,17)18/h4,7,13H,3,5-6H2,1-2H3,(H,19,20)(H2,12,14,15)(H2,16,17,18)/b8-4+"
AYD InChIKey InChI 1.03 DPGNBHAKLFOOJK-XBXARRHUSA-N
AYD SMILES_CANONICAL CACTVS 3.385 "CC(\NCc1cnc(C)nc1N)=C/CCO[P](O)(=O)O[P](O)(O)=O"
AYD SMILES CACTVS 3.385 "CC(NCc1cnc(C)nc1N)=CCCO[P](O)(=O)O[P](O)(O)=O"
AYD SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O)/C"
AYD SMILES "OpenEye OEToolkits" 1.7.5 "Cc1ncc(c(n1)N)CNC(=CCCOP(=O)(O)OP(=O)(O)O)C"
#
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
AYD "SYSTEMATIC NAME" ACDLabs 10.04 "(3E)-4-{[(4-amino-2-methylpyrimidin-5-yl)methyl]amino}pent-3-en-1-yl trihydrogen diphosphate"
AYD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(E)-4-[(4-amino-2-methyl-pyrimidin-5-yl)methylamino]pent-3-enyl] phosphono 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
AYD "Create component" 2002-10-31 RCSB
AYD "Modify descriptor" 2011-06-04 RCSB
AYD "Modify descriptor" 2012-01-05 RCSB
AYD "Modify coordinates" 2012-01-05 RCSB
#