data_HAM
#
_chem_comp.id HAM
_chem_comp.name "HISTIDYL-ADENOSINE MONOPHOSPHATE"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H21 N8 O8 P"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_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 484.361
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HAM
_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 1KMM
_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.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
HAM P P P 0 1 N N N N N N 13.859 -22.140 -13.896 -2.115 -1.879 0.316 P HAM 1
HAM O1P O1P O 0 1 N N N N N N 14.615 -23.350 -13.483 -2.474 -3.363 0.079 O1P HAM 2
HAM O2P O2P O -1 1 N N N N N N 13.013 -21.482 -12.883 -1.912 -1.633 1.828 O2P HAM 3
HAM O3P O3P O 0 1 N N N N N N 12.952 -22.491 -15.255 -3.311 -0.945 -0.223 O3P HAM 4
HAM "O5'" O5* O 0 1 N N N N N N 14.952 -21.062 -14.356 -0.758 -1.522 -0.473 "O5'" HAM 5
HAM "C5'" C5* C 0 1 N N N N N N 15.606 -21.152 -15.629 0.284 -2.294 0.127 "C5'" HAM 6
HAM "C4'" C4* C 0 1 N N R N N N 17.031 -20.672 -15.522 1.608 -2.001 -0.580 "C4'" HAM 7
HAM "O4'" O4* O 0 1 N N N N N N 17.024 -19.271 -15.149 2.013 -0.635 -0.343 "O4'" HAM 8
HAM "C3'" C3* C 0 1 N N S N N N 17.847 -21.363 -14.441 2.743 -2.860 0.020 "C3'" HAM 9
HAM "O3'" O3* O 0 1 N N N N N N 18.451 -22.549 -14.952 2.979 -4.014 -0.789 "O3'" HAM 10
HAM "C2'" C2* C 0 1 N N R N N N 18.875 -20.301 -14.058 3.974 -1.923 0.002 "C2'" HAM 11
HAM "O2'" O2* O 0 1 N N N N N N 19.990 -20.248 -14.924 5.009 -2.472 -0.817 "O2'" HAM 12
HAM "C1'" C1* C 0 1 N N R N N N 18.060 -19.016 -14.211 3.434 -0.609 -0.604 "C1'" HAM 13
HAM N9 N9 N 0 1 Y N N N N N 17.447 -18.524 -12.979 4.051 0.547 0.050 N9 HAM 14
HAM C8 C8 C 0 1 Y N N N N N 16.229 -18.878 -12.447 3.549 1.234 1.115 C8 HAM 15
HAM N7 N7 N 0 1 Y N N N N N 15.928 -18.245 -11.338 4.356 2.203 1.439 N7 HAM 16
HAM C5 C5 C 0 1 Y N N N N N 17.025 -17.423 -11.115 5.427 2.194 0.610 C5 HAM 17
HAM C6 C6 C 0 1 Y N N N N N 17.319 -16.490 -10.099 6.582 2.984 0.479 C6 HAM 18
HAM N6 N6 N 0 1 N N N N N N 16.517 -16.238 -9.070 6.815 4.044 1.337 N6 HAM 19
HAM N1 N1 N 0 1 Y N N N N N 18.490 -15.822 -10.182 7.447 2.686 -0.485 N1 HAM 20
HAM C2 C2 C 0 1 Y N N N N N 19.311 -16.085 -11.215 7.232 1.676 -1.309 C2 HAM 21
HAM N3 N3 N 0 1 Y N N N N N 19.148 -16.941 -12.227 6.162 0.913 -1.227 N3 HAM 22
HAM C4 C4 C 0 1 Y N N N N N 17.971 -17.585 -12.117 5.242 1.135 -0.295 C4 HAM 23
HAM C C C 0 1 N N N N N N 12.442 -21.549 -16.022 -4.518 -0.995 0.362 C HAM 24
HAM O O O 0 1 N N N N N N 12.471 -20.314 -15.802 -4.708 -1.742 1.293 O HAM 25
HAM CA CA C 0 1 N N S N N N 11.582 -21.860 -17.307 -5.637 -0.121 -0.143 CA HAM 26
HAM N N N 1 1 N N N N N N 10.830 -20.642 -17.745 -6.926 -0.671 0.298 N HAM 27
HAM CB CB C 0 1 N N N N N N 12.416 -22.351 -18.504 -5.469 1.294 0.413 CB HAM 28
HAM CG CG C 0 1 Y N N N N N 11.643 -22.460 -19.803 -6.515 2.197 -0.187 CG HAM 29
HAM CD2 CD2 C 0 1 Y N N N N N 11.202 -21.474 -20.625 -7.394 2.955 0.496 CD2 HAM 30
HAM ND1 ND1 N 0 1 Y N N N N N 11.399 -23.684 -20.407 -6.731 2.392 -1.497 ND1 HAM 31
HAM CE1 CE1 C 0 1 Y N N N N N 10.826 -23.419 -21.570 -7.715 3.236 -1.650 CE1 HAM 32
HAM NE2 NE2 N 0 1 Y N N N N N 10.685 -22.104 -21.758 -8.155 3.614 -0.431 NE2 HAM 33
HAM "H5'1" 1H5* H 0 0 N N N N N N 15.545 -22.180 -16.055 0.049 -3.355 0.035 "H5'1" HAM 34
HAM "H5'2" 2H5* H 0 0 N N N N N N 15.043 -20.609 -16.424 0.369 -2.032 1.181 "H5'2" HAM 35
HAM "H4'" H4* H 0 1 N N N N N N 17.488 -20.886 -16.515 1.516 -2.189 -1.650 "H4'" HAM 36
HAM "H3'" H3* H 0 1 N N N N N N 17.247 -21.703 -13.564 2.500 -3.154 1.041 "H3'" HAM 37
HAM "HO3'" *HO3 H 0 0 N N N N N N 18.960 -22.980 -14.276 3.694 -4.510 -0.367 "HO3'" HAM 38
HAM "H2'" H2* H 0 1 N N N N N N 19.311 -20.491 -13.049 4.339 -1.753 1.015 "H2'" HAM 39
HAM "HO2'" *HO2 H 0 0 N N N N N N 20.570 -19.564 -14.599 5.260 -3.317 -0.420 "HO2'" HAM 40
HAM "H1'" H1* H 0 1 N N N N N N 18.773 -18.224 -14.538 3.621 -0.581 -1.678 "H1'" HAM 41
HAM H8 H8 H 0 1 N N N N N N 15.538 -19.620 -12.881 2.619 1.009 1.615 H8 HAM 42
HAM HN61 1HN6 H 0 0 N N N N N N 15.635 -16.723 -8.987 7.618 4.580 1.239 HN61 HAM 43
HAM HN62 2HN6 H 0 0 N N N N N N 16.777 -15.549 -8.378 6.174 4.255 2.034 HN62 HAM 44
HAM H2 H2 H 0 1 N N N N N N 20.255 -15.515 -11.235 7.961 1.469 -2.078 H2 HAM 45
HAM HA HA H 0 1 N N N N N N 10.889 -22.679 -17.004 -5.610 -0.089 -1.232 HA HAM 46
HAM HN1 1HN H 0 1 N N N N N N 11.284 -19.813 -17.280 -7.675 -0.086 -0.039 HN1 HAM 47
HAM HN2 2HN H 0 1 N N N N N N 9.853 -20.722 -17.434 -7.036 -1.605 -0.068 HN2 HAM 48
HAM HN3 3HN H 0 1 N N N N N N 10.896 -20.549 -18.757 -6.951 -0.701 1.307 HN3 HAM 49
HAM HB1 1HB H 0 1 N N N N N N 13.316 -21.707 -18.640 -5.585 1.275 1.497 HB1 HAM 50
HAM HB2 2HB H 0 1 N N N N N N 12.909 -23.321 -18.262 -4.477 1.669 0.160 HB2 HAM 51
HAM HD2 HD2 H 0 1 N N N N N N 11.252 -20.392 -20.416 -7.481 3.028 1.570 HD2 HAM 52
HAM HE1 HE1 H 0 1 N N N N N N 10.507 -24.192 -22.288 -8.109 3.578 -2.596 HE1 HAM 53
HAM HE2 HE2 H 0 1 N N N N N N 10.292 -21.665 -22.542 -8.876 4.236 -0.247 HE2 HAM 54
#
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
HAM P O1P DOUB N N 1
HAM P O2P SING N N 2
HAM P O3P SING N N 3
HAM P "O5'" SING N N 4
HAM O3P C SING N N 5
HAM "O5'" "C5'" SING N N 6
HAM "C5'" "C4'" SING N N 7
HAM "C5'" "H5'1" SING N N 8
HAM "C5'" "H5'2" SING N N 9
HAM "C4'" "O4'" SING N N 10
HAM "C4'" "C3'" SING N N 11
HAM "C4'" "H4'" SING N N 12
HAM "O4'" "C1'" SING N N 13
HAM "C3'" "O3'" SING N N 14
HAM "C3'" "C2'" SING N N 15
HAM "C3'" "H3'" SING N N 16
HAM "O3'" "HO3'" SING N N 17
HAM "C2'" "O2'" SING N N 18
HAM "C2'" "C1'" SING N N 19
HAM "C2'" "H2'" SING N N 20
HAM "O2'" "HO2'" SING N N 21
HAM "C1'" N9 SING N N 22
HAM "C1'" "H1'" SING N N 23
HAM N9 C8 SING Y N 24
HAM N9 C4 SING Y N 25
HAM C8 N7 DOUB Y N 26
HAM C8 H8 SING N N 27
HAM N7 C5 SING Y N 28
HAM C5 C6 SING Y N 29
HAM C5 C4 DOUB Y N 30
HAM C6 N6 SING N N 31
HAM C6 N1 DOUB Y N 32
HAM N6 HN61 SING N N 33
HAM N6 HN62 SING N N 34
HAM N1 C2 SING Y N 35
HAM C2 N3 DOUB Y N 36
HAM C2 H2 SING N N 37
HAM N3 C4 SING Y N 38
HAM C O DOUB N N 39
HAM C CA SING N N 40
HAM CA N SING N N 41
HAM CA CB SING N N 42
HAM CA HA SING N N 43
HAM N HN1 SING N N 44
HAM N HN2 SING N N 45
HAM N HN3 SING N N 46
HAM CB CG SING N N 47
HAM CB HB1 SING N N 48
HAM CB HB2 SING N N 49
HAM CG CD2 DOUB Y N 50
HAM CG ND1 SING Y N 51
HAM CD2 NE2 SING Y N 52
HAM CD2 HD2 SING N N 53
HAM ND1 CE1 DOUB Y N 54
HAM CE1 NE2 SING Y N 55
HAM CE1 HE1 SING N N 56
HAM NE2 HE2 SING N N 57
#
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
HAM SMILES ACDLabs 10.04 "[O-]P(=O)(OC(=O)C([NH3+])Cc1ncnc1)OCC4OC(n3cnc2c(ncnc23)N)C(O)C4O"
HAM SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P]([O-])(=O)OC(=O)[C@@H]([NH3+])Cc4c[nH]cn4)[C@@H](O)[C@H]3O
HAM SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P]([O-])(=O)OC(=O)[CH]([NH3+])Cc4c[nH]cn4)[CH](O)[CH]3O
HAM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1c(nc[nH]1)C[C@@H](C(=O)O[P@](=O)([O-])OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)[NH3+]
HAM SMILES "OpenEye OEToolkits" 1.5.0 c1c(nc[nH]1)CC(C(=O)OP(=O)([O-])OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)[NH3+]
HAM InChI InChI 1.03 InChI=1S/C16H21N8O8P/c17-8(1-7-2-19-4-20-7)16(27)32-33(28,29)30-3-9-11(25)12(26)15(31-9)24-6-23-10-13(18)21-5-22-14(10)24/h2,4-6,8-9,11-12,15,25-26H,1,3,17H2,(H,19,20)(H,28,29)(H2,18,21,22)/t8-,9+,11+,12+,15+/m0/s1
HAM InChIKey InChI 1.03 XTFBSLZFYLGYAT-OPYVMVOTSA-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
HAM "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-({[(2S)-2-ammonio-3-(1H-imidazol-4-yl)propanoyl]oxy}phosphinato)adenosine"
HAM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [(2S)-2-azaniumyl-3-(1H-imidazol-4-yl)propanoyl] 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
HAM 'Create component' 1999-07-08 RCSB
HAM 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id HAM
_pdbe_chem_comp_drugbank_details.drugbank_id DB04201
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Histidyl-Adenosine Monophosphate'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id HAM
_pdbe_chem_comp_synonyms.name 'Histidyl-Adenosine Monophosphate'
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HAM
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04201
_pdbe_chem_comp_drugbank_classification.parent "5'-acylphosphoadenosines"
_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 5'-acylphosphoadenosines. These are ribonucleoside derivatives containing an adenoside moiety, where the phosphate group is acylated."
#
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
HAM DB04201 'Histidine--tRNA ligase' 'Escherichia coli (strain K12)' P60906 unknown 1
HAM DB04201 'Histidine--tRNA ligase' 'Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)' P56194 unknown 2
#
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
HAM P P 7.571 2.178 1
HAM O1P O 8.998 2.639 2
HAM O2P O 6.144 1.717 3
HAM O3P O 7.110 3.605 4
HAM "O5'" O 8.032 0.751 5
HAM "C5'" C 7.027 -0.362 6
HAM "C4'" C 7.487 -1.790 7
HAM "O4'" O 6.604 -3.002 8
HAM "C3'" C 8.913 -2.256 9
HAM "O3'" O 10.129 -1.376 10
HAM "C2'" C 8.911 -3.756 11
HAM "O2'" O 10.123 -4.639 12
HAM "C1'" C 7.483 -4.217 13
HAM N9 N 7.018 -5.643 14
HAM C8 C 7.893 -6.850 15
HAM N7 N 7.018 -8.057 16
HAM C5 C 5.598 -7.600 17
HAM C6 C 4.299 -8.350 18
HAM N6 N 4.299 -9.850 19
HAM N1 N 3.000 -7.600 20
HAM C2 C 3.000 -6.100 21
HAM N3 N 4.299 -5.350 22
HAM C4 C 5.598 -6.100 23
HAM C C 8.116 4.718 24
HAM O O 9.582 4.404 25
HAM CA C 7.655 6.146 26
HAM N N 8.660 7.259 27
HAM CB C 6.188 6.460 28
HAM CG C 5.727 7.888 29
HAM CD2 C 4.301 8.354 30
HAM ND1 N 6.611 9.100 31
HAM CE1 C 5.731 10.315 32
HAM NE2 N 4.304 9.854 33
#
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
HAM P O1P DOUBLE NONE 1
HAM P O2P SINGLE BEGINDASH 2
HAM P O3P SINGLE NONE 3
HAM P "O5'" SINGLE NONE 4
HAM O3P C SINGLE NONE 5
HAM "O5'" "C5'" SINGLE NONE 6
HAM "C4'" "C5'" SINGLE BEGINDASH 7
HAM "C4'" "O4'" SINGLE NONE 8
HAM "C4'" "C3'" SINGLE NONE 9
HAM "O4'" "C1'" SINGLE NONE 10
HAM "C3'" "O3'" SINGLE BEGINWEDGE 11
HAM "C3'" "C2'" SINGLE NONE 12
HAM "C2'" "O2'" SINGLE BEGINWEDGE 13
HAM "C2'" "C1'" SINGLE NONE 14
HAM "C1'" N9 SINGLE BEGINDASH 15
HAM N9 C8 SINGLE NONE 16
HAM N9 C4 SINGLE NONE 17
HAM C8 N7 DOUBLE NONE 18
HAM N7 C5 SINGLE NONE 19
HAM C5 C6 DOUBLE NONE 20
HAM C5 C4 SINGLE NONE 21
HAM C6 N6 SINGLE NONE 22
HAM C6 N1 SINGLE NONE 23
HAM N1 C2 DOUBLE NONE 24
HAM C2 N3 SINGLE NONE 25
HAM N3 C4 DOUBLE NONE 26
HAM C O DOUBLE NONE 27
HAM C CA SINGLE NONE 28
HAM CA N SINGLE BEGINDASH 29
HAM CA CB SINGLE NONE 30
HAM CB CG SINGLE NONE 31
HAM CG CD2 DOUBLE NONE 32
HAM CG ND1 SINGLE NONE 33
HAM CD2 NE2 SINGLE NONE 34
HAM ND1 CE1 DOUBLE NONE 35
HAM CE1 NE2 SINGLE NONE 36
#
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
HAM MurckoScaffold S1 scaffold 'O=C(CCc1c[nH]cn1)O[PH](=O)OC[C@@H]1CC[C@H](n2cnc3cncnc32)O1' InChI=1S/C16H19N6O5P/c23-15(4-1-11-5-17-8-19-11)27-28(24)25-7-12-2-3-14(26-12)22-10-21-13-6-18-9-20-16(13)22/h5-6,8-10,12,14,28H,1-4,7H2,(H,17,19)/t12-,14+/m0/s1 PJUQETZNZORYKV-GXTWGEPZSA-N
HAM 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
HAM imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
HAM peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
HAM 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
HAM 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
HAM pyrimidine F6 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
HAM 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
HAM P S1 1
HAM O1P S1 1
HAM O3P S1 1
HAM "O5'" S1 1
HAM "C5'" S1 1
HAM "C4'" S1 1
HAM "O4'" S1 1
HAM "C3'" S1 1
HAM "C2'" S1 1
HAM "C1'" S1 1
HAM N9 S1 1
HAM C8 S1 1
HAM N7 S1 1
HAM C5 S1 1
HAM C6 S1 1
HAM N1 S1 1
HAM C2 S1 1
HAM N3 S1 1
HAM C4 S1 1
HAM C S1 1
HAM O S1 1
HAM CA S1 1
HAM CB S1 1
HAM CG S1 1
HAM CD2 S1 1
HAM ND1 S1 1
HAM CE1 S1 1
HAM NE2 S1 1
HAM N1 F1 1
HAM C6 F1 1
HAM C5 F1 1
HAM C4 F1 1
HAM N3 F1 1
HAM C2 F1 1
HAM N9 F1 1
HAM C8 F1 1
HAM N7 F1 1
HAM N6 F1 1
HAM C5 F2 1
HAM C4 F2 1
HAM N9 F2 1
HAM C8 F2 1
HAM N7 F2 1
HAM CG F2 2
HAM CD2 F2 2
HAM NE2 F2 2
HAM CE1 F2 2
HAM ND1 F2 2
HAM O F3 1
HAM C F3 1
HAM CA F3 1
HAM N F3 1
HAM O2P F4 1
HAM P F4 1
HAM O1P F4 1
HAM O3P F4 1
HAM "O5'" F4 1
HAM N7 F5 1
HAM C8 F5 1
HAM N9 F5 1
HAM C4 F5 1
HAM C5 F5 1
HAM C6 F5 1
HAM N1 F5 1
HAM C2 F5 1
HAM N3 F5 1
HAM C5 F6 1
HAM C6 F6 1
HAM N1 F6 1
HAM C2 F6 1
HAM N3 F6 1
HAM C4 F6 1
HAM "C2'" F7 1
HAM "C3'" F7 1
HAM "C4'" F7 1
HAM "O4'" F7 1
HAM "C1'" F7 1
HAM "C5'" F7 1
HAM "O5'" F7 1
HAM "O3'" F7 1
HAM "O2'" F7 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HAM
_pdbe_chem_comp_rdkit_properties.exactmw 484.122
_pdbe_chem_comp_rdkit_properties.amw 484.366
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 16
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 8
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 12
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 14
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 33
_pdbe_chem_comp_rdkit_properties.NumAtoms 54
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 17
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.438
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 214.731
_pdbe_chem_comp_rdkit_properties.tpsa 251.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP -4.232
_pdbe_chem_comp_rdkit_properties.CrippenMR 100.981
_pdbe_chem_comp_rdkit_properties.chi0v 16.185
_pdbe_chem_comp_rdkit_properties.chi1v 9.474
_pdbe_chem_comp_rdkit_properties.chi2v 4.170
_pdbe_chem_comp_rdkit_properties.chi3v 4.170
_pdbe_chem_comp_rdkit_properties.chi4v 2.654
_pdbe_chem_comp_rdkit_properties.chi0n 36.291
_pdbe_chem_comp_rdkit_properties.chi1n 18.013
_pdbe_chem_comp_rdkit_properties.chi2n 3.466
_pdbe_chem_comp_rdkit_properties.chi3n 3.466
_pdbe_chem_comp_rdkit_properties.chi4n 2.132
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.980
_pdbe_chem_comp_rdkit_properties.kappa1 8.664
_pdbe_chem_comp_rdkit_properties.kappa2 9.106
_pdbe_chem_comp_rdkit_properties.kappa3 4.861
_pdbe_chem_comp_rdkit_properties.Phi 2.391
#
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
HAM UniChem DrugBank DB04201
HAM UniChem ZINC ZINC000031976542
HAM UniChem PubChem 444222
HAM UniChem 'Probes And Drugs' PD059344
HAM UniChem PubChem 5288509
#
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
HAM P -1.243 -0.227 -4.226 ETKDGv3 1
HAM O1P -0.978 0.704 -5.386 ETKDGv3 2
HAM O2P -2.439 -1.334 -4.684 ETKDGv3 3
HAM O3P -1.776 0.713 -2.884 ETKDGv3 4
HAM "O5'" 0.206 -1.049 -3.856 ETKDGv3 5
HAM "C5'" -0.012 -1.861 -2.727 ETKDGv3 6
HAM "C4'" 1.299 -2.558 -2.339 ETKDGv3 7
HAM "O4'" 2.308 -1.586 -2.151 ETKDGv3 8
HAM "C3'" 1.143 -3.358 -1.043 ETKDGv3 9
HAM "O3'" 1.934 -4.525 -1.066 ETKDGv3 10
HAM "C2'" 1.610 -2.376 0.006 ETKDGv3 11
HAM "O2'" 2.245 -3.009 1.087 ETKDGv3 12
HAM "C1'" 2.589 -1.497 -0.769 ETKDGv3 13
HAM N9 2.507 -0.104 -0.330 ETKDGv3 14
HAM C8 1.614 0.920 -0.820 ETKDGv3 15
HAM N7 1.483 1.960 -0.037 ETKDGv3 16
HAM C5 2.303 1.683 1.090 ETKDGv3 17
HAM C6 2.457 2.355 2.230 ETKDGv3 18
HAM N6 1.831 3.618 2.454 ETKDGv3 19
HAM N1 3.279 1.746 3.252 ETKDGv3 20
HAM C2 3.827 0.565 3.074 ETKDGv3 21
HAM N3 3.621 -0.161 1.839 ETKDGv3 22
HAM C4 2.915 0.418 0.917 ETKDGv3 23
HAM C -2.566 0.196 -1.853 ETKDGv3 24
HAM O -3.098 -0.944 -1.957 ETKDGv3 25
HAM CA -2.744 0.993 -0.590 ETKDGv3 26
HAM N -4.172 1.149 -0.280 ETKDGv3 27
HAM CB -1.988 0.304 0.565 ETKDGv3 28
HAM CG -1.967 1.153 1.800 ETKDGv3 29
HAM CD2 -2.685 0.944 2.891 ETKDGv3 30
HAM ND1 -1.193 2.344 1.932 ETKDGv3 31
HAM CE1 -1.475 2.798 3.111 ETKDGv3 32
HAM NE2 -2.411 1.987 3.810 ETKDGv3 33
HAM "H5'1" -0.337 -1.249 -1.860 ETKDGv3 34
HAM "H5'2" -0.779 -2.638 -2.949 ETKDGv3 35
HAM "H4'" 1.595 -3.233 -3.172 ETKDGv3 36
HAM "H3'" 0.087 -3.656 -0.855 ETKDGv3 37
HAM "HO3'" 2.872 -4.263 -1.261 ETKDGv3 38
HAM "H2'" 0.746 -1.768 0.365 ETKDGv3 39
HAM "HO2'" 1.525 -3.430 1.626 ETKDGv3 40
HAM "H1'" 3.628 -1.861 -0.609 ETKDGv3 41
HAM H8 1.082 0.839 -1.758 ETKDGv3 42
HAM HN61 1.958 4.108 3.366 ETKDGv3 43
HAM HN62 1.245 4.070 1.717 ETKDGv3 44
HAM H2 4.432 0.130 3.857 ETKDGv3 45
HAM HA -2.300 2.001 -0.754 ETKDGv3 46
HAM HN1 -4.671 1.555 -1.105 ETKDGv3 47
HAM HN2 -4.602 0.227 -0.038 ETKDGv3 48
HAM HN3 -4.294 1.806 0.524 ETKDGv3 49
HAM HB1 -2.445 -0.686 0.788 ETKDGv3 50
HAM HB2 -0.935 0.123 0.261 ETKDGv3 51
HAM HD2 -3.377 0.129 3.061 ETKDGv3 52
HAM HE1 -1.043 3.703 3.515 ETKDGv3 53
HAM HE2 -2.812 2.133 4.762 ETKDGv3 54
#