data_MD1
#
_chem_comp.id MD1
_chem_comp.name "PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C20 H26 N10 O13 P2 S2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2003-09-29
_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 740.557
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code MD1
_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 1Q16
_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
MD1 PB PB P 0 1 N N R -124.383 -63.460 -23.952 1.132 3.620 0.590 PB MD1 1
MD1 O3B O3B O 0 1 N N N -125.661 -62.506 -23.795 -0.401 3.492 0.116 O3B MD1 2
MD1 O1B O1B O 0 1 N N N -124.714 -64.537 -24.914 1.581 5.166 0.544 O1B MD1 3
MD1 O2B O2B O 0 1 N N N -123.241 -62.633 -24.292 1.265 3.109 1.973 O2B MD1 4
MD1 O3A O3A O 0 1 N N N -124.138 -64.151 -22.521 2.072 2.759 -0.393 O3A MD1 5
MD1 C10 C10 C 0 1 N N N -125.038 -65.017 -21.838 3.473 2.586 -0.176 C10 MD1 6
MD1 C11 C11 C 0 1 N N R -124.204 -65.449 -20.603 4.059 1.718 -1.292 C11 MD1 7
MD1 O11 O11 O 0 1 N N N -123.833 -64.251 -19.915 3.952 2.408 -2.538 O11 MD1 8
MD1 C12 C12 C 0 1 N N N -125.016 -66.394 -19.613 5.509 1.433 -0.998 C12 MD1 9
MD1 S12 S12 S 0 1 N N N -126.665 -66.896 -19.972 6.622 2.763 -0.682 S12 MD1 10
MD1 C13 C13 C 0 1 N N N -124.514 -66.881 -18.368 5.948 0.182 -0.978 C13 MD1 11
MD1 S13 S13 S 0 1 N N N -125.634 -67.853 -17.434 7.588 -0.167 -0.435 S13 MD1 12
MD1 C14 C14 C 0 1 N N R -123.126 -66.665 -17.717 5.045 -0.941 -1.418 C14 MD1 13
MD1 N15 N15 N 0 1 N N N -123.452 -65.897 -16.498 4.635 -1.733 -0.245 N15 MD1 14
MD1 C16 C16 C 0 1 Y N N -122.394 -65.456 -15.700 5.554 -2.681 0.236 C16 MD1 15
MD1 C15 C15 C 0 1 Y N N -122.555 -65.245 -14.301 5.580 -3.072 1.582 C15 MD1 16
MD1 O14 O14 O 0 1 N N N -123.635 -65.459 -13.747 4.792 -2.601 2.386 O14 MD1 17
MD1 N17 N17 N 0 1 Y N N -121.417 -64.774 -13.587 6.501 -3.985 1.966 N17 MD1 18
MD1 C17 C17 C 0 1 Y N N -120.165 -64.512 -14.181 7.374 -4.499 1.056 C17 MD1 19
MD1 N16 N16 N 0 1 N N N -119.159 -64.068 -13.428 8.303 -5.421 1.472 N16 MD1 20
MD1 N18 N18 N 0 1 Y N N -120.027 -64.722 -15.518 7.354 -4.140 -0.208 N18 MD1 21
MD1 C20 C20 C 0 1 Y N N -121.076 -65.179 -16.307 6.462 -3.243 -0.658 C20 MD1 22
MD1 N8 N8 N 0 1 N N N -120.883 -65.374 -17.686 6.425 -2.880 -1.972 N8 MD1 23
MD1 C7 C7 C 0 1 N N N -122.053 -65.863 -18.493 5.785 -1.838 -2.376 C7 MD1 24
MD1 PA PA P 0 1 N N S -125.812 -60.939 -23.934 -1.817 3.830 0.804 PA MD1 25
MD1 O1A O1A O 0 1 N N N -124.811 -60.324 -23.057 -2.106 5.410 0.691 O1A MD1 26
MD1 O2A O2A O 0 1 N N N -127.255 -60.593 -23.723 -1.778 3.437 2.231 O2A MD1 27
MD1 "O5'" O5* O 0 1 N N N -125.360 -60.858 -25.484 -2.986 3.015 0.055 "O5'" MD1 28
MD1 "C5'" C5* C 0 1 N N N -126.299 -60.531 -26.494 -4.345 3.020 0.497 "C5'" MD1 29
MD1 "C4'" C4* C 0 1 N N R -125.662 -59.646 -27.528 -5.188 2.148 -0.435 "C4'" MD1 30
MD1 "O4'" O4* O 0 1 N N N -126.200 -60.013 -28.800 -4.789 0.773 -0.312 "O4'" MD1 31
MD1 "C1'" C1* C 0 1 N N R -126.893 -58.894 -29.383 -5.977 -0.028 -0.488 "C1'" MD1 32
MD1 N9 N9 N 0 1 Y N N -128.061 -59.487 -30.060 -5.798 -1.356 0.104 N9 MD1 33
MD1 C4 C4 C 0 1 Y N N -128.048 -59.914 -31.382 -6.476 -2.494 -0.238 C4 MD1 34
MD1 N3 N3 N 0 1 Y N N -126.966 -59.860 -32.277 -7.434 -2.776 -1.129 N3 MD1 35
MD1 C2 C2 C 0 1 Y N N -127.229 -60.355 -33.519 -7.915 -3.994 -1.246 C2 MD1 36
MD1 N2 N2 N 0 1 N N N -126.315 -60.379 -34.467 -8.896 -4.236 -2.175 N2 MD1 37
MD1 N1 N1 N 0 1 Y N N -128.494 -60.868 -33.843 -7.467 -5.023 -0.472 N1 MD1 38
MD1 C6 C6 C 0 1 Y N N -129.596 -60.930 -32.956 -6.502 -4.813 0.450 C6 MD1 39
MD1 O6 O6 O 0 1 N N N -130.678 -61.396 -33.311 -6.095 -5.727 1.147 O6 MD1 40
MD1 C5 C5 C 0 1 Y N N -129.339 -60.416 -31.642 -5.975 -3.508 0.586 C5 MD1 41
MD1 N7 N7 N 0 1 Y N N -130.144 -60.312 -30.525 -5.029 -2.950 1.380 N7 MD1 42
MD1 C8 C8 C 0 1 Y N N -129.354 -59.764 -29.623 -4.918 -1.685 1.095 C8 MD1 43
MD1 "C2'" C2* C 0 1 N N R -127.215 -57.940 -28.200 -7.067 0.767 0.275 "C2'" MD1 44
MD1 "O2'" O2* O 0 1 N N N -127.351 -56.549 -28.544 -8.368 0.471 -0.237 "O2'" MD1 45
MD1 "C3'" C3* C 0 1 N N S -126.014 -58.176 -27.259 -6.673 2.233 -0.032 "C3'" MD1 46
MD1 "O3'" O3* O 0 1 N N N -124.902 -57.315 -27.502 -7.456 2.746 -1.111 "O3'" MD1 47
MD1 H1B H1B H 0 1 N N N -123.956 -65.102 -25.007 1.519 5.567 -0.333 H1B MD1 48
MD1 H101 1H10 H 0 0 N N N -126.032 -64.571 -21.602 3.964 3.559 -0.178 H101 MD1 49
MD1 H102 2H10 H 0 0 N N N -125.440 -65.856 -22.451 3.635 2.099 0.786 H102 MD1 50
MD1 H11 H11 H 0 1 N N N -123.319 -66.034 -20.947 3.508 0.779 -1.348 H11 MD1 51
MD1 H1 H1 H 0 1 N N N -123.322 -64.515 -19.158 4.419 3.254 -2.561 H1 MD1 52
MD1 H12 H12 H 0 1 N N N -127.149 -67.460 -19.381 7.791 2.134 -0.469 H12 MD1 53
MD1 H13 H13 H 0 1 N N N -125.300 -68.177 -16.605 7.666 -1.505 -0.552 H13 MD1 54
MD1 H14 H14 H 0 1 N N N -122.652 -67.668 -17.609 4.162 -0.529 -1.907 H14 MD1 55
MD1 H15 H15 H 0 1 N N N -124.100 -66.437 -15.925 3.770 -1.606 0.175 H15 MD1 56
MD1 H17 H17 H 0 1 N N N -121.504 -64.613 -12.583 6.541 -4.273 2.891 H17 MD1 57
MD1 H161 1H16 H 0 0 N N N -118.253 -63.878 -13.857 8.331 -5.696 2.402 H161 MD1 58
MD1 H162 2H16 H 0 0 N N N -119.021 -64.717 -12.653 8.931 -5.797 0.836 H162 MD1 59
MD1 H7 H7 H 0 1 N N N -122.119 -65.649 -19.573 5.778 -1.601 -3.430 H7 MD1 60
MD1 H1A H1A H 0 1 N N N -124.901 -59.382 -23.140 -2.145 5.738 -0.218 H1A MD1 61
MD1 "H5'1" 1H5* H 0 0 N N N -126.755 -61.441 -26.948 -4.399 2.625 1.512 "H5'1" MD1 62
MD1 "H5'2" 2H5* H 0 0 N N N -127.225 -60.076 -26.070 -4.727 4.041 0.484 "H5'2" MD1 63
MD1 "H4'" H4* H 0 1 N N N -124.553 -59.766 -27.499 -5.062 2.479 -1.466 "H4'" MD1 64
MD1 "H1'" H1* H 0 1 N N N -126.339 -58.289 -30.139 -6.230 -0.112 -1.546 "H1'" MD1 65
MD1 HN21 1HN2 H 0 0 N N N -126.511 -60.749 -35.396 -9.224 -3.514 -2.733 HN21 MD1 66
MD1 HN22 2HN2 H 0 0 N N N -125.500 -60.871 -34.101 -9.260 -5.130 -2.273 HN22 MD1 67
MD1 HN1 HN1 H 0 1 N N N -128.621 -61.221 -34.791 -7.844 -5.910 -0.584 HN1 MD1 68
MD1 H8 H8 H 0 1 N N N -129.735 -59.558 -28.608 -4.235 -0.998 1.572 H8 MD1 69
MD1 "H2'" H2* H 0 1 N N N -128.215 -58.163 -27.760 -7.017 0.566 1.345 "H2'" MD1 70
MD1 H2 H2 H 0 1 N N N -127.547 -55.965 -27.820 -9.083 0.945 0.208 H2 MD1 71
MD1 "H3'" H3* H 0 1 N N N -126.270 -57.952 -26.197 -6.792 2.854 0.856 "H3'" MD1 72
MD1 H3 H3 H 0 1 N N N -125.119 -56.405 -27.335 -8.399 2.820 -0.912 H3 MD1 73
#
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
MD1 PB O3B SING N N 1
MD1 PB O1B SING N N 2
MD1 PB O2B DOUB N N 3
MD1 PB O3A SING N N 4
MD1 O3B PA SING N N 5
MD1 O1B H1B SING N N 6
MD1 O3A C10 SING N N 7
MD1 C10 C11 SING N N 8
MD1 C10 H101 SING N N 9
MD1 C10 H102 SING N N 10
MD1 C11 O11 SING N N 11
MD1 C11 C12 SING N N 12
MD1 C11 H11 SING N N 13
MD1 O11 H1 SING N N 14
MD1 C12 S12 SING N N 15
MD1 C12 C13 DOUB N Z 16
MD1 S12 H12 SING N N 17
MD1 C13 S13 SING N N 18
MD1 C13 C14 SING N N 19
MD1 S13 H13 SING N N 20
MD1 C14 N15 SING N N 21
MD1 C14 C7 SING N N 22
MD1 C14 H14 SING N N 23
MD1 N15 C16 SING N N 24
MD1 N15 H15 SING N N 25
MD1 C16 C15 SING Y N 26
MD1 C16 C20 DOUB Y N 27
MD1 C15 O14 DOUB N N 28
MD1 C15 N17 SING Y N 29
MD1 N17 C17 SING Y N 30
MD1 N17 H17 SING N N 31
MD1 C17 N16 SING N N 32
MD1 C17 N18 DOUB Y N 33
MD1 N16 H161 SING N N 34
MD1 N16 H162 SING N N 35
MD1 N18 C20 SING Y N 36
MD1 C20 N8 SING N N 37
MD1 N8 C7 DOUB N N 38
MD1 C7 H7 SING N N 39
MD1 PA O1A SING N N 40
MD1 PA O2A DOUB N N 41
MD1 PA "O5'" SING N N 42
MD1 O1A H1A SING N N 43
MD1 "O5'" "C5'" SING N N 44
MD1 "C5'" "C4'" SING N N 45
MD1 "C5'" "H5'1" SING N N 46
MD1 "C5'" "H5'2" SING N N 47
MD1 "C4'" "O4'" SING N N 48
MD1 "C4'" "C3'" SING N N 49
MD1 "C4'" "H4'" SING N N 50
MD1 "O4'" "C1'" SING N N 51
MD1 "C1'" N9 SING N N 52
MD1 "C1'" "C2'" SING N N 53
MD1 "C1'" "H1'" SING N N 54
MD1 N9 C4 SING Y N 55
MD1 N9 C8 SING Y N 56
MD1 C4 N3 SING Y N 57
MD1 C4 C5 DOUB Y N 58
MD1 N3 C2 DOUB Y N 59
MD1 C2 N2 SING N N 60
MD1 C2 N1 SING Y N 61
MD1 N2 HN21 SING N N 62
MD1 N2 HN22 SING N N 63
MD1 N1 C6 SING Y N 64
MD1 N1 HN1 SING N N 65
MD1 C6 O6 DOUB N N 66
MD1 C6 C5 SING Y N 67
MD1 C5 N7 SING Y N 68
MD1 N7 C8 DOUB Y N 69
MD1 C8 H8 SING N N 70
MD1 "C2'" "O2'" SING N N 71
MD1 "C2'" "C3'" SING N N 72
MD1 "C2'" "H2'" SING N N 73
MD1 "O2'" H2 SING N N 74
MD1 "C3'" "O3'" SING N N 75
MD1 "C3'" "H3'" SING N N 76
MD1 "O3'" H3 SING N N 77
#
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
MD1 SMILES ACDLabs 10.04 "O=C2NC(=NC=1N=CC(NC=12)C(/S)=C(/S)C(O)COP(=O)(O)OP(=O)(O)OCC5OC(n4cnc3c4N=C(N)NC3=O)C(O)C5O)N"
MD1 InChI InChI 1.03
;InChI=1S/C20H26N10O13P2S2/c21-19-26-14-8(16(34)28-19)25-5(1-23-14)12(46)13(47)6(31)2-40-44(36,37)43-45(38,39)41-3-7-10(32)11(33)18(42-7)30-4-24-9-15(30)27-20(22)29-17(9)35/h1,4-7,10-11,18,25,31-33,46-47H,2-3H2,(H,36,37)(H,38,39)(H3,21,26,28,34)(H3,22,27,29,35)/b13-12-/t5-,6-,7-,10-,11-,18-/m1/s1
;
MD1 InChIKey InChI 1.03 IRGDLSAXQOKWLX-XHEYTWMPSA-N
MD1 SMILES_CANONICAL CACTVS 3.385 "NC1=NC2=C(N[C@H](C=N2)C(\S)=C(S)/[C@H](O)CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1"
MD1 SMILES CACTVS 3.385 "NC1=NC2=C(N[CH](C=N2)C(S)=C(S)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5C(=O)NC(=Nc45)N)C(=O)N1"
MD1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.5 "c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@](=O)(O)OC[C@H](/C(=C(\[C@H]4C=NC5=C(N4)C(=O)NC(=N5)N)/S)/S)O)O)O)N=C(NC2=O)N"
MD1 SMILES "OpenEye OEToolkits" 1.7.5 "c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC(C(=C(C4C=NC5=C(N4)C(=O)NC(=N5)N)S)S)O)O)O)N=C(NC2=O)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
MD1 "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-[(S)-{[(R)-({(2R,3Z)-4-[(6R)-2-amino-4-oxo-3,4,5,6-tetrahydropteridin-6-yl]-2-hydroxy-3,4-disulfanylbut-3-en-1-yl}oxy)(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine"
MD1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0
"[(Z,2R)-4-[(6R)-2-amino-4-oxo-5,6-dihydro-3H-pteridin-6-yl]-2-hydroxy-3,4-bis-sulfanyl-but-3-enyl] [[(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] 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
MD1 "Create component" 2003-09-29 RCSB
MD1 "Modify descriptor" 2011-06-04 RCSB
MD1 "Modify descriptor" 2012-01-05 RCSB
MD1 "Modify coordinates" 2012-01-05 RCSB
#