data_IM5
#
_chem_comp.id IM5
_chem_comp.name "2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H17 N5 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms DADMe-ImmG
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-11-05
_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 279.295
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code IM5
_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 3PHB
_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
IM5 N1 N1 N 0 1 N N N -41.449 3.900 -2.332 4.063 0.977 -0.482 N1 IM5 1
IM5 C2 C2 C 0 1 N N N -41.313 2.858 -3.191 3.032 1.794 -0.123 C2 IM5 2
IM5 N2 N2 N 0 1 N N N -40.109 2.579 -3.716 3.175 3.153 -0.268 N2 IM5 3
IM5 N3 N3 N 0 1 N N N -42.334 2.073 -3.547 1.906 1.320 0.355 N3 IM5 4
IM5 C4 C4 C 0 1 Y N N -43.553 2.352 -3.038 1.724 -0.006 0.511 C4 IM5 5
IM5 C5 C5 C 0 1 Y N N -43.800 3.445 -2.101 2.750 -0.890 0.159 C5 IM5 6
IM5 C6 C6 C 0 1 N N N -42.609 4.248 -1.752 3.951 -0.363 -0.352 C6 IM5 7
IM5 O6 O6 O 0 1 N N N -42.681 5.228 -0.970 4.867 -1.100 -0.677 O6 IM5 8
IM5 N7 N7 N 0 1 Y N N -45.101 3.421 -1.813 2.299 -2.167 0.420 N7 IM5 9
IM5 C8 C8 C 0 1 Y N N -45.733 2.408 -2.469 1.034 -2.090 0.918 C8 IM5 10
IM5 C9 C9 C 0 1 Y N N -44.841 1.680 -3.243 0.656 -0.798 0.987 C9 IM5 11
IM5 "N1'" "N1'" N 0 1 N N N -44.856 -0.791 -3.605 -1.537 0.023 0.337 "N1'" IM5 12
IM5 C10 C10 C 0 1 N N N -45.119 0.512 -4.164 -0.673 -0.288 1.484 C10 IM5 13
IM5 "C2'" "C2'" C 0 1 N N N -43.422 -1.095 -3.592 -1.965 -1.218 -0.359 "C2'" IM5 14
IM5 "C3'" "C3'" C 0 1 N N R -43.417 -2.332 -2.709 -3.232 -0.808 -1.140 "C3'" IM5 15
IM5 "O3'" "O3'" O 0 1 N N N -43.739 -3.468 -3.517 -2.895 -0.456 -2.484 "O3'" IM5 16
IM5 "C4'" "C4'" C 0 1 N N R -44.529 -2.117 -1.702 -3.787 0.418 -0.388 "C4'" IM5 17
IM5 "C5'" "C5'" C 0 1 N N N -43.974 -1.729 -0.348 -5.193 0.125 0.142 "C5'" IM5 18
IM5 "O5'" "O5'" O 0 1 N N N -45.068 -1.284 0.459 -5.735 1.308 0.732 "O5'" IM5 19
IM5 "C6'" "C6'" C 0 1 N N N -45.351 -0.948 -2.233 -2.809 0.647 0.784 "C6'" IM5 20
IM5 HN1 HN1 H 0 1 N N N -40.636 4.441 -2.118 4.881 1.360 -0.837 HN1 IM5 21
IM5 HN2 HN2 H 0 1 N N N -40.004 1.810 -4.346 4.002 3.519 -0.620 HN2 IM5 22
IM5 HN2A HN2A H 0 0 N N N -39.317 3.141 -3.477 2.451 3.747 -0.017 HN2A IM5 23
IM5 H8 H8 H 0 1 N N N -46.790 2.199 -2.396 0.428 -2.934 1.213 H8 IM5 24
IM5 H10 H10 H 0 1 N N N -46.180 0.551 -4.451 -1.147 -1.052 2.100 H10 IM5 25
IM5 H10A H10A H 0 0 N N N -44.492 0.630 -5.060 -0.518 0.613 2.077 H10A IM5 26
IM5 "H2'" "H2'" H 0 1 N N N -43.043 -1.313 -4.601 -1.188 -1.555 -1.045 "H2'" IM5 27
IM5 "H2'A" "H2'A" H 0 0 N N N -42.836 -0.276 -3.149 -2.200 -1.998 0.364 "H2'A" IM5 28
IM5 "H3'" "H3'" H 0 1 N N N -42.447 -2.446 -2.202 -3.960 -1.619 -1.132 "H3'" IM5 29
IM5 "HO3'" "HO3'" H 0 0 N N N -43.740 -4.250 -2.978 -2.499 -1.177 -2.992 "HO3'" IM5 30
IM5 "H4'" "H4'" H 0 1 N N N -45.154 -3.019 -1.619 -3.805 1.289 -1.044 "H4'" IM5 31
IM5 "H5'" "H5'" H 0 1 N N N -43.491 -2.598 0.122 -5.831 -0.196 -0.681 "H5'" IM5 32
IM5 "H5'A" "H5'A" H 0 0 N N N -43.239 -0.919 -0.463 -5.141 -0.664 0.891 "H5'A" IM5 33
IM5 "HO5'" "HO5'" H 0 0 N N N -44.747 -1.033 1.317 -6.627 1.195 1.090 "HO5'" IM5 34
IM5 "H6'" "H6'" H 0 1 N N N -45.172 -0.038 -1.642 -3.177 0.158 1.686 "H6'" IM5 35
IM5 "H6'A" "H6'A" H 0 0 N N N -46.425 -1.185 -2.225 -2.668 1.714 0.959 "H6'A" IM5 36
IM5 HN7 HN7 H 0 1 N N N -45.555 4.063 -1.195 2.799 -2.984 0.272 HN7 IM5 37
# #
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
IM5 C2 N1 SING N N 1
IM5 N1 C6 SING N N 2
IM5 N1 HN1 SING N N 3
IM5 N2 C2 SING N N 4
IM5 N3 C2 DOUB N N 5
IM5 N2 HN2 SING N N 6
IM5 N2 HN2A SING N N 7
IM5 N3 C4 SING N N 8
IM5 C9 C4 SING Y N 9
IM5 C4 C5 DOUB Y N 10
IM5 C5 N7 SING Y N 11
IM5 C5 C6 SING N N 12
IM5 C6 O6 DOUB N N 13
IM5 C8 N7 SING Y N 14
IM5 C9 C8 DOUB Y N 15
IM5 C8 H8 SING N N 16
IM5 C10 C9 SING N N 17
IM5 C10 "N1'" SING N N 18
IM5 "N1'" "C2'" SING N N 19
IM5 "N1'" "C6'" SING N N 20
IM5 C10 H10 SING N N 21
IM5 C10 H10A SING N N 22
IM5 "C2'" "C3'" SING N N 23
IM5 "C2'" "H2'" SING N N 24
IM5 "C2'" "H2'A" SING N N 25
IM5 "O3'" "C3'" SING N N 26
IM5 "C3'" "C4'" SING N N 27
IM5 "C3'" "H3'" SING N N 28
IM5 "O3'" "HO3'" SING N N 29
IM5 "C6'" "C4'" SING N N 30
IM5 "C4'" "C5'" SING N N 31
IM5 "C4'" "H4'" SING N N 32
IM5 "C5'" "O5'" SING N N 33
IM5 "C5'" "H5'" SING N N 34
IM5 "C5'" "H5'A" SING N N 35
IM5 "O5'" "HO5'" SING N N 36
IM5 "C6'" "H6'" SING N N 37
IM5 "C6'" "H6'A" SING N N 38
IM5 N7 HN7 SING N N 39
# #
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
IM5 SMILES ACDLabs 12.01 "O=C2NC(=Nc1c(cnc12)CN3CC(C(O)C3)CO)N"
IM5 InChI InChI 1.03 "InChI=1S/C12H17N5O3/c13-12-15-9-6(1-14-10(9)11(20)16-12)2-17-3-7(5-18)8(19)4-17/h1,7-8,14,18-19H,2-5H2,(H3,13,15,16,20)/t7-,8+/m1/s1"
IM5 InChIKey InChI 1.03 GSPTUGDLYPMLCQ-SFYZADRCSA-N
IM5 SMILES_CANONICAL CACTVS 3.370 "NC1=Nc2c(CN3C[C@H](O)[C@@H](CO)C3)c[nH]c2C(=O)N1"
IM5 SMILES CACTVS 3.370 "NC1=Nc2c(CN3C[CH](O)[CH](CO)C3)c[nH]c2C(=O)N1"
IM5 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1c(c2c([nH]1)C(=O)NC(=N2)N)CN3C[C@@H]([C@H](C3)O)CO"
IM5 SMILES "OpenEye OEToolkits" 1.7.6 "c1c(c2c([nH]1)C(=O)NC(=N2)N)CN3CC(C(C3)O)CO"
# #
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
IM5 "SYSTEMATIC NAME" ACDLabs 12.01 "2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one"
IM5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-azanyl-7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one"
# #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
IM5 "Create component" 2010-11-05 RCSB
IM5 "Modify aromatic_flag" 2011-06-04 RCSB
IM5 "Modify descriptor" 2011-06-04 RCSB
IM5 "Modify synonyms" 2011-12-05 RCSB
IM5 "Modify synonyms" 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id IM5
_pdbx_chem_comp_synonyms.name DADMe-ImmG
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##