data_AM2
#
_chem_comp.id AM2
_chem_comp.name APRAMYCIN
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAD
_chem_comp.formula "C21 H41 N5 O11"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "NEBRAMYCIN II; 4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-02-17
_chem_comp.pdbx_modified_date 2020-05-26
_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 539.577
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code AM2
_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 1YRJ
_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
AM2 CA1 CA1 C 0 1 N N S 28.355 -2.367 35.495 2.810 -1.613 0.449 CA1 AM2 1
AM2 CA2 CA2 C 0 1 N N R 28.660 -0.854 35.684 2.051 -2.834 -0.075 CA2 AM2 2
AM2 CA3 CA3 C 0 1 N N N 27.367 -0.022 35.845 0.843 -2.356 -0.888 CA3 AM2 3
AM2 CA4 CA4 C 0 1 N N S 26.446 -0.300 34.644 0.013 -1.391 -0.033 CA4 AM2 4
AM2 CA5 CA5 C 0 1 N N R 26.119 -1.843 34.568 0.927 -0.286 0.505 CA5 AM2 5
AM2 CA6 CA6 C 0 1 N N R 25.153 -2.192 33.396 0.098 0.675 1.367 CA6 AM2 6
AM2 CA7 CA7 C 0 1 N N S 23.880 -1.287 33.454 -1.109 1.153 0.553 CA7 AM2 7
AM2 CA8 CA8 C 0 1 N N R 24.292 0.253 33.588 -1.869 -0.066 0.026 CA8 AM2 8
AM2 CA9 CA9 C 0 1 N N N 22.292 -2.931 32.267 -2.748 2.846 0.521 CA9 AM2 9
AM2 OA4 OA4 O 0 1 N N N 27.381 -2.611 34.446 1.962 -0.853 1.307 OA4 AM2 10
AM2 OA5 OA5 O 0 1 N N N 25.209 0.478 34.742 -1.020 -0.827 -0.840 OA5 AM2 11
AM2 NA2 NA2 N 0 1 N N N 29.598 -0.610 36.832 2.937 -3.636 -0.929 NA2 AM2 12
AM2 NA7 NA7 N 0 1 N N N 22.978 -1.598 32.279 -1.994 1.953 1.410 NA7 AM2 13
AM2 OA6 OA6 O 0 1 N N N 25.840 -2.104 32.164 -0.354 -0.001 2.542 OA6 AM2 14
AM2 OA8 OA8 O 0 1 N N N 23.157 1.120 33.779 -3.021 0.368 -0.699 OA8 AM2 15
AM2 OA1 OA1 O 0 1 N N N 27.893 -3.006 36.679 3.223 -0.802 -0.652 OA1 AM2 16
AM2 CB1 CB1 C 0 1 N N R 23.417 2.497 33.376 -3.812 -0.795 -0.955 CB1 AM2 17
AM2 CB2 CB2 C 0 1 N N R 22.260 3.503 33.698 -4.928 -0.444 -1.941 CB2 AM2 18
AM2 CB3 CB3 C 0 1 N N S 21.012 3.245 32.793 -5.789 0.675 -1.347 CB3 AM2 19
AM2 CB4 CB4 C 0 1 N N S 21.457 3.371 31.303 -6.261 0.242 0.046 CB4 AM2 20
AM2 CB5 CB5 C 0 1 N N S 22.598 2.314 30.990 -5.045 -0.160 0.883 CB5 AM2 21
AM2 CB6 CB6 C 0 1 N N N 23.166 2.369 29.549 -5.505 -0.563 2.285 CB6 AM2 22
AM2 OB1 OB1 O 0 1 N N N 23.727 2.525 31.907 -4.378 -1.261 0.268 OB1 AM2 23
AM2 NB4 NB4 N 0 1 N N N 20.281 3.163 30.428 -6.961 1.357 0.698 NB4 AM2 24
AM2 OB2 OB2 O 0 1 N N N 21.951 3.424 35.094 -4.356 -0.004 -3.174 OB2 AM2 25
AM2 OB3 OB3 O 0 1 N N N 19.987 4.207 33.095 -6.921 0.911 -2.186 OB3 AM2 26
AM2 OB6 OB6 O 0 1 N N N 22.476 1.509 28.623 -4.363 -0.820 3.106 OB6 AM2 27
AM2 CC1 CC1 C 0 1 N N R 28.119 -4.459 36.825 4.205 0.107 -0.151 CC1 AM2 28
AM2 CC2 CC2 C 0 1 N N R 29.571 -4.647 37.341 5.598 -0.502 -0.323 CC2 AM2 29
AM2 CC3 CC3 C 0 1 N N S 29.872 -6.158 37.525 6.650 0.471 0.214 CC3 AM2 30
AM2 CC4 CC4 C 0 1 N N R 28.877 -6.776 38.540 6.569 1.788 -0.561 CC4 AM2 31
AM2 CC5 CC5 C 0 1 N N N 27.406 -6.619 38.019 5.176 2.397 -0.390 CC5 AM2 32
AM2 CC6 CC6 C 0 1 N N S 27.110 -5.106 37.834 4.125 1.424 -0.927 CC6 AM2 33
AM2 NC4 NC4 N 0 1 N N N 29.169 -8.202 38.725 7.579 2.722 -0.046 NC4 AM2 34
AM2 NC6 NC6 N 0 1 N N N 25.736 -4.970 37.350 2.787 2.008 -0.762 NC6 AM2 35
AM2 OC2 OC2 O 0 1 N N N 30.477 -4.071 36.391 5.673 -1.731 0.401 OC2 AM2 36
AM2 OC3 OC3 O 0 1 N N N 31.204 -6.282 37.997 7.951 -0.097 0.054 OC3 AM2 37
AM2 HA1 HA1 H 0 1 N N N 29.339 -2.805 35.209 3.688 -1.943 1.006 HA1 AM2 38
AM2 HA2 HA2 H 0 1 N N N 29.169 -0.514 34.752 1.709 -3.439 0.765 HA2 AM2 39
AM2 HA31 1HA3 H 0 0 N N N 26.861 -0.205 36.821 1.188 -1.839 -1.784 HA31 AM2 40
AM2 HA32 2HA3 H 0 0 N N N 27.574 1.065 35.980 0.231 -3.213 -1.171 HA32 AM2 41
AM2 HA4 HA4 H 0 1 N N N 26.974 0.009 33.712 -0.431 -1.933 0.802 HA4 AM2 42
AM2 HA5 HA5 H 0 1 N N N 25.593 -2.124 35.510 1.368 0.260 -0.329 HA5 AM2 43
AM2 HA6 HA6 H 0 1 N N N 24.798 -3.244 33.496 0.710 1.531 1.650 HA6 AM2 44
AM2 HA7 HA7 H 0 1 N N N 23.283 -1.510 34.368 -0.767 1.760 -0.285 HA7 AM2 45
AM2 HA8 HA8 H 0 1 N N N 24.795 0.499 32.624 -2.182 -0.688 0.865 HA8 AM2 46
AM2 HA91 1HA9 H 0 0 N N N 21.627 -3.160 31.401 -2.055 3.486 -0.024 HA91 AM2 47
AM2 HA92 2HA9 H 0 0 N N N 23.053 -3.738 32.371 -3.327 2.252 -0.187 HA92 AM2 48
AM2 HA93 3HA9 H 0 0 N N N 21.719 -3.059 33.215 -3.423 3.464 1.113 HA93 AM2 49
AM2 HA21 1HA2 H 0 0 N N N 29.798 0.382 36.956 3.716 -3.918 -0.354 HA21 AM2 50
AM2 HA22 2HA2 H 0 0 N N N 30.456 -1.151 36.730 2.430 -4.476 -1.165 HA22 AM2 51
AM2 H2 H2 H 0 1 N N N 23.501 -1.480 31.411 -1.399 2.540 1.974 H2 AM2 52
AM2 H1 H1 H 0 1 N N N 25.251 -2.316 31.449 -0.877 0.637 3.047 H1 AM2 53
AM2 HB1 HB1 H 0 1 N N N 24.285 2.843 33.983 -3.181 -1.574 -1.383 HB1 AM2 54
AM2 HB2 HB2 H 0 1 N N N 22.592 4.542 33.468 -5.547 -1.324 -2.120 HB2 AM2 55
AM2 HB3 HB3 H 0 1 N N N 20.599 2.225 32.977 -5.197 1.587 -1.265 HB3 AM2 56
AM2 HB4 HB4 H 0 1 N N N 21.870 4.388 31.111 -6.937 -0.609 -0.047 HB4 AM2 57
AM2 HB5 HB5 H 0 1 N N N 22.109 1.319 31.117 -4.360 0.684 0.955 HB5 AM2 58
AM2 HB61 1HB6 H 0 0 N N N 23.184 3.418 29.172 -6.091 0.246 2.722 HB61 AM2 59
AM2 HB62 2HB6 H 0 0 N N N 24.259 2.151 29.548 -6.117 -1.463 2.223 HB62 AM2 60
AM2 HB41 1HB4 H 0 0 N N N 20.571 3.245 29.453 -7.750 1.585 0.114 HB41 AM2 61
AM2 HB42 2HB4 H 0 0 N N N 19.510 3.791 30.657 -7.335 0.997 1.564 HB42 AM2 62
AM2 H5 H5 H 0 1 N N N 21.249 4.034 35.289 -3.824 -0.736 -3.513 H5 AM2 63
AM2 H6 H6 H 0 1 N N N 19.228 4.050 32.544 -6.578 1.181 -3.049 H6 AM2 64
AM2 HB6 HB6 H 0 1 N N N 22.824 1.542 27.739 -4.697 -1.070 3.978 HB6 AM2 65
AM2 HC1 HC1 H 0 1 N N N 27.964 -4.962 35.842 4.019 0.296 0.906 HC1 AM2 66
AM2 HC2 HC2 H 0 1 N N N 29.693 -4.140 38.326 5.784 -0.691 -1.380 HC2 AM2 67
AM2 HC3 HC3 H 0 1 N N N 29.757 -6.700 36.557 6.464 0.661 1.271 HC3 AM2 68
AM2 HC4 HC4 H 0 1 N N N 28.986 -6.241 39.512 6.755 1.599 -1.619 HC4 AM2 69
AM2 HC51 1HC5 H 0 0 N N N 27.214 -7.209 37.092 5.119 3.335 -0.942 HC51 AM2 70
AM2 HC52 2HC5 H 0 0 N N N 26.661 -7.123 38.678 4.990 2.586 0.667 HC52 AM2 71
AM2 HC6 HC6 H 0 1 N N N 27.228 -4.573 38.806 4.311 1.234 -1.984 HC6 AM2 72
AM2 HC41 1HC4 H 0 0 N N N 28.514 -8.608 39.393 7.490 3.571 -0.584 HC41 AM2 73
AM2 HC42 2HC4 H 0 0 N N N 30.139 -8.361 38.995 7.309 2.948 0.900 HC42 AM2 74
AM2 HC61 1HC6 H 0 0 N N N 25.079 -5.391 38.006 2.818 2.925 -1.182 HC61 AM2 75
AM2 HC62 2HC6 H 0 0 N N N 25.626 -5.350 36.409 2.157 1.453 -1.322 HC62 AM2 76
AM2 H3 H3 H 0 1 N N N 31.365 -4.186 36.706 6.565 -2.081 0.267 H3 AM2 77
AM2 H4 H4 H 0 1 N N N 31.388 -7.207 38.109 7.959 -0.923 0.557 H4 AM2 78
#
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
AM2 CA1 CA2 SING N N 1
AM2 CA1 OA4 SING N N 2
AM2 CA1 OA1 SING N N 3
AM2 CA1 HA1 SING N N 4
AM2 CA2 CA3 SING N N 5
AM2 CA2 NA2 SING N N 6
AM2 CA2 HA2 SING N N 7
AM2 CA3 CA4 SING N N 8
AM2 CA3 HA31 SING N N 9
AM2 CA3 HA32 SING N N 10
AM2 CA4 CA5 SING N N 11
AM2 CA4 OA5 SING N N 12
AM2 CA4 HA4 SING N N 13
AM2 CA5 CA6 SING N N 14
AM2 CA5 OA4 SING N N 15
AM2 CA5 HA5 SING N N 16
AM2 CA6 CA7 SING N N 17
AM2 CA6 OA6 SING N N 18
AM2 CA6 HA6 SING N N 19
AM2 CA7 CA8 SING N N 20
AM2 CA7 NA7 SING N N 21
AM2 CA7 HA7 SING N N 22
AM2 CA8 OA5 SING N N 23
AM2 CA8 OA8 SING N N 24
AM2 CA8 HA8 SING N N 25
AM2 CA9 NA7 SING N N 26
AM2 CA9 HA91 SING N N 27
AM2 CA9 HA92 SING N N 28
AM2 CA9 HA93 SING N N 29
AM2 NA2 HA21 SING N N 30
AM2 NA2 HA22 SING N N 31
AM2 NA7 H2 SING N N 32
AM2 OA6 H1 SING N N 33
AM2 OA8 CB1 SING N N 34
AM2 OA1 CC1 SING N N 35
AM2 CB1 CB2 SING N N 36
AM2 CB1 OB1 SING N N 37
AM2 CB1 HB1 SING N N 38
AM2 CB2 CB3 SING N N 39
AM2 CB2 OB2 SING N N 40
AM2 CB2 HB2 SING N N 41
AM2 CB3 CB4 SING N N 42
AM2 CB3 OB3 SING N N 43
AM2 CB3 HB3 SING N N 44
AM2 CB4 CB5 SING N N 45
AM2 CB4 NB4 SING N N 46
AM2 CB4 HB4 SING N N 47
AM2 CB5 CB6 SING N N 48
AM2 CB5 OB1 SING N N 49
AM2 CB5 HB5 SING N N 50
AM2 CB6 OB6 SING N N 51
AM2 CB6 HB61 SING N N 52
AM2 CB6 HB62 SING N N 53
AM2 NB4 HB41 SING N N 54
AM2 NB4 HB42 SING N N 55
AM2 OB2 H5 SING N N 56
AM2 OB3 H6 SING N N 57
AM2 OB6 HB6 SING N N 58
AM2 CC1 CC2 SING N N 59
AM2 CC1 CC6 SING N N 60
AM2 CC1 HC1 SING N N 61
AM2 CC2 CC3 SING N N 62
AM2 CC2 OC2 SING N N 63
AM2 CC2 HC2 SING N N 64
AM2 CC3 CC4 SING N N 65
AM2 CC3 OC3 SING N N 66
AM2 CC3 HC3 SING N N 67
AM2 CC4 CC5 SING N N 68
AM2 CC4 NC4 SING N N 69
AM2 CC4 HC4 SING N N 70
AM2 CC5 CC6 SING N N 71
AM2 CC5 HC51 SING N N 72
AM2 CC5 HC52 SING N N 73
AM2 CC6 NC6 SING N N 74
AM2 CC6 HC6 SING N N 75
AM2 NC4 HC41 SING N N 76
AM2 NC4 HC42 SING N N 77
AM2 NC6 HC61 SING N N 78
AM2 NC6 HC62 SING N N 79
AM2 OC2 H3 SING N N 80
AM2 OC3 H4 SING N N 81
#
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
AM2 SMILES ACDLabs 10.04 "O3C(OC1OC(CO)C(N)C(O)C1O)C(NC)C(O)C4OC(OC2C(N)CC(N)C(O)C2O)C(N)CC34"
AM2 SMILES_CANONICAL CACTVS 3.341 "CN[C@H]1[C@@H](O)[C@H]2O[C@H](O[C@@H]3[C@@H](N)C[C@@H](N)[C@H](O)[C@H]3O)[C@H](N)C[C@@H]2O[C@@H]1O[C@H]4O[C@H](CO)[C@@H](N)[C@H](O)[C@H]4O"
AM2 SMILES CACTVS 3.341 "CN[CH]1[CH](O)[CH]2O[CH](O[CH]3[CH](N)C[CH](N)[CH](O)[CH]3O)[CH](N)C[CH]2O[CH]1O[CH]4O[CH](CO)[CH](N)[CH](O)[CH]4O"
AM2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CN[C@H]1[C@H]([C@@H]2[C@H](C[C@H]([C@H](O2)O[C@@H]3[C@H](C[C@H]([C@@H]([C@H]3O)O)N)N)N)O[C@@H]1O[C@@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)N)O)O)O"
AM2 SMILES "OpenEye OEToolkits" 1.5.0 "CNC1C(C2C(CC(C(O2)OC3C(CC(C(C3O)O)N)N)N)OC1OC4C(C(C(C(O4)CO)N)O)O)O"
AM2 InChI InChI 1.03 "InChI=1S/C21H41N5O11/c1-26-11-14(30)18-8(33-20(11)37-21-16(32)13(29)10(25)9(4-27)34-21)3-7(24)19(36-18)35-17-6(23)2-5(22)12(28)15(17)31/h5-21,26-32H,2-4,22-25H2,1H3/t5-,6+,7-,8+,9-,10-,11+,12+,13+,14-,15-,16-,17-,18+,19+,20-,21-/m1/s1"
AM2 InChIKey InChI 1.03 XZNUGFQTQHRASN-XQENGBIVSA-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
AM2 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4S,5S,6S)-5-amino-2-{[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-4-hydroxy-3-(methylamino)octahydropyrano[3,2-b]pyran-2-yl]oxy}-6-(hydroxymethyl)tetrahydro-2H-pyran-3,4-diol (non-preferred name)"
AM2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4S,5S,6S)-2-[[(2R,3S,4R,4aR,6S,7R,8aS)-7-amino-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxy-cyclohexyl]oxy-4-hydroxy-3-methylamino-2,3,4,4a,6,7,8,8a-octahydropyrano[2,3-e]pyran-2-yl]oxy]-5-amino-6-(hydroxymethyl)oxane-3,4-diol"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
AM2 "Create component" 2005-02-17 RCSB
AM2 "Modify descriptor" 2011-06-04 RCSB
AM2 "Modify synonyms" 2020-05-26 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 AM2 "NEBRAMYCIN II" ? ?
2 AM2 "4-O-(3ALPHA-AMINO-6ALPHA-((4-AMINO-4-DEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY)-2,3,4,5ABETA,6,7,8,8AALPHA-OCTAHYDRO-8BETA-HYDROXY-7BETA-(METHYLAMINO)PYRANO(3,2-B)PYRAN-2ALPHA-YL)-2-DEOXY-D-STREPTAMINE" ? ?
#