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BioLiP
Download all results in tab-seperated text for 155 receptor-ligand interactions, whose format is explained at readme.txt.
  • Hover over PDB to view the title of the structure. Click PDB to view the structure at the RCSB PDB database. Resolution -1.00 means the resolution is unavailable, e.g., for NMR structures.
  • Click Site # to view the binding site structure. Hover over Site # to view the binding residues.
  • Hover over Ligand to view the full ligand name. Click Ligand to view the 2D diagram and other detail information of the ligand.
  • Hover over EC number to view the full name of enzymatic activity.
  • Hover over GO terms to view all GO terms.
  • Hover over UniProt to view the protein name.

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    # PDB
    (Resolution Å)     		Site # Ligand EC number GO terms UniProt PubMed Binding
    affinity
    1 5ndk:11 (2.95) BS01 rna ? GO:0002181 ... P60405 29208708
    2 5ndk:11 (2.95) BS02 rna ? GO:0002181 ... P60405 29208708
    3 5ndk:11 (2.95) BS03 MG ? GO:0002181 ... P60405 29208708
    4 5ndk:11 (2.95) BS04 MG ? GO:0002181 ... P60405 29208708
    5 5ndk:12 (2.95) BS01 rna ? GO:0003735 ... P80371 29208708
    6 5ndk:15 (2.95) BS01 rna ? GO:0003729 ... P60488 29208708
    7 5ndk:19 (2.95) BS01 rna ? GO:0002181 ... P60405 29208708
    8 5ndk:19 (2.95) BS02 rna ? GO:0002181 ... P60405 29208708
    9 5ndk:19 (2.95) BS03 MG ? GO:0002181 ... P60405 29208708
    10 5ndk:1A (2.95) BS01 rna ? GO:0000049 ... Q5SHN7 29208708
    11 5ndk:1E (2.95) BS01 rna ? GO:0003735 ... P80371 29208708
    12 5ndk:1I (2.95) BS01 rna ? GO:0000049 ... Q5SHN7 29208708
    13 5ndk:21 (2.95) BS01 rna ? GO:0003735 ... Q5SHN8 29208708
    14 5ndk:21 (2.95) BS02 MG ? GO:0003735 ... Q5SHN8 29208708
    15 5ndk:22 (2.95) BS01 rna ? GO:0003676 ... P80372 29208708
    16 5ndk:25 (2.95) BS01 rna ? GO:0003735 ... Q5SHP8 29208708
    17 5ndk:25 (2.95) BS02 rna ? GO:0003735 ... Q5SHP8 29208708
    18 5ndk:25 (2.95) BS03 MG ? GO:0003735 ... Q5SHP8 29208708
    19 5ndk:29 (2.95) BS01 rna ? GO:0003735 ... Q5SHN8 29208708
    20 5ndk:29 (2.95) BS02 MG ? GO:0003735 ... Q5SHN8 29208708
    21 5ndk:29 (2.95) BS03 MG ? GO:0003735 ... Q5SHN8 29208708
    22 5ndk:2A (2.95) BS01 rna ? GO:0003735 ... P80376 29208708
    23 5ndk:2A (2.95) BS02 MG ? GO:0003735 ... P80376 29208708
    24 5ndk:2E (2.95) BS01 rna ? GO:0003676 ... P80372 29208708
    25 5ndk:2I (2.95) BS01 rna ? GO:0003735 ... P80376 29208708
    26 5ndk:2I (2.95) BS02 MG ? GO:0003735 ... P80376 29208708
    27 5ndk:31 (2.95) BS01 rna ? GO:0003735 ... Q5SHN9 29208708
    28 5ndk:31 (2.95) BS02 MG ? GO:0003735 ... Q5SHN9 29208708
    29 5ndk:31 (2.95) BS03 MG ? GO:0003735 ... Q5SHN9 29208708
    30 5ndk:32 (2.95) BS01 rna ? GO:0003723 ... P80373 29208708
    31 5ndk:35 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ7 29208708
    32 5ndk:39 (2.95) BS01 rna ? GO:0003735 ... Q5SHN9 29208708
    33 5ndk:39 (2.95) BS02 MG ? GO:0003735 ... Q5SHN9 29208708
    34 5ndk:39 (2.95) BS03 MG ? GO:0003735 ... Q5SHN9 29208708
    35 5ndk:3A (2.95) BS01 rna ? GO:0000049 ... Q5SHN3 29208708
    36 5ndk:3E (2.95) BS01 rna ? GO:0003723 ... P80373 29208708
    37 5ndk:3E (2.95) BS02 MG ? GO:0003723 ... P80373 29208708
    38 5ndk:3I (2.95) BS01 rna ? GO:0000049 ... Q5SHN3 29208708
    39 5ndk:41 (2.95) BS01 rna ? GO:0000049 ... Q5SHQ0 29208708
    40 5ndk:41 (2.95) BS02 rna ? GO:0000049 ... Q5SHQ0 29208708
    41 5ndk:41 (2.95) BS03 rna ? GO:0000049 ... Q5SHQ0 29208708
    42 5ndk:41 (2.95) BS04 MG ? GO:0000049 ... Q5SHQ0 29208708
    43 5ndk:41 (2.95) BS05 MG ? GO:0000049 ... Q5SHQ0 29208708
    44 5ndk:42 (2.95) BS01 rna ? GO:0003723 ... Q5SHQ5 29208708
    45 5ndk:42 (2.95) BS02 MG ? GO:0003723 ... Q5SHQ5 29208708
    46 5ndk:45 (2.95) BS01 rna ? GO:0000049 ... P60489 29208708
    47 5ndk:45 (2.95) BS02 rna ? GO:0000049 ... P60489 29208708
    48 5ndk:45 (2.95) BS03 rna ? GO:0000049 ... P60489 29208708
    49 5ndk:45 (2.95) BS04 MG ? GO:0000049 ... P60489 29208708
    50 5ndk:49 (2.95) BS01 rna ? GO:0000049 ... Q5SHQ0 29208708
    51 5ndk:49 (2.95) BS02 rna ? GO:0000049 ... Q5SHQ0 29208708
    52 5ndk:49 (2.95) BS03 rna ? GO:0000049 ... Q5SHQ0 29208708
    53 5ndk:49 (2.95) BS04 MG ? GO:0000049 ... Q5SHQ0 29208708
    54 5ndk:4A (2.95) BS01 rna ? GO:0000049 ... P80377 29208708
    55 5ndk:4E (2.95) BS01 rna ? GO:0003723 ... Q5SHQ5 29208708
    56 5ndk:4E (2.95) BS02 MG ? GO:0003723 ... Q5SHQ5 29208708
    57 5ndk:4I (2.95) BS01 rna ? GO:0000049 ... P80377 29208708
    58 5ndk:4I (2.95) BS02 rna ? GO:0000049 ... P80377 29208708
    59 5ndk:51 (2.95) BS01 rna ? GO:0002181 ... P0DOY8 29208708
    60 5ndk:52 (2.95) BS01 rna ? GO:0003735 ... Q5SLP8 29208708
    61 5ndk:52 (2.95) BS02 MG ? GO:0003735 ... Q5SLP8 29208708
    62 5ndk:55 (2.95) BS01 rna ? GO:0003735 ... Q9Z9H5 29208708
    63 5ndk:58 (2.95) BS01 rna ? GO:0003729 ... P60488 29208708
    64 5ndk:59 (2.95) BS01 rna ? GO:0002181 ... P0DOY8 29208708
    65 5ndk:5A (2.95) BS01 rna ? GO:0003735 ... P0DOY6 29208708
    66 5ndk:5A (2.95) BS02 ZN ? GO:0003735 ... P0DOY6 29208708
    67 5ndk:5E (2.95) BS01 rna ? GO:0003735 ... Q5SLP8 29208708
    68 5ndk:5E (2.95) BS02 MG ? GO:0003735 ... Q5SLP8 29208708
    69 5ndk:5I (2.95) BS01 rna ? GO:0003735 ... P0DOY6 29208708
    70 5ndk:5I (2.95) BS02 ZN ? GO:0003735 ... P0DOY6 29208708
    71 5ndk:5I (2.95) BS03 MG ? GO:0003735 ... P0DOY6 29208708
    72 5ndk:61 (2.95) BS01 rna ? GO:0003735 ... Q5SLQ1 29208708
    73 5ndk:62 (2.95) BS01 rna ? GO:0000028 ... P17291 29208708
    74 5ndk:62 (2.95) BS02 rna ? GO:0000028 ... P17291 29208708
    75 5ndk:65 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ4 29208708
    76 5ndk:65 (2.95) BS02 rna ? GO:0003735 ... Q5SHQ4 29208708
    77 5ndk:68 (2.95) BS01 rna ? GO:0003735 ... Q5SHP8 29208708
    78 5ndk:68 (2.95) BS02 rna ? GO:0003735 ... Q5SHP8 29208708
    79 5ndk:69 (2.95) BS01 rna ? GO:0003735 ... Q5SLQ1 29208708
    80 5ndk:69 (2.95) BS02 rna ? GO:0003735 ... Q5SLQ1 29208708
    81 5ndk:6A (2.95) BS01 rna ? GO:0003735 ... Q5SJ76 29208708
    82 5ndk:6A (2.95) BS02 rna ? GO:0003735 ... Q5SJ76 29208708
    83 5ndk:6E (2.95) BS01 rna ? GO:0000028 ... P17291 29208708
    84 5ndk:6E (2.95) BS02 rna ? GO:0000028 ... P17291 29208708
    85 5ndk:6I (2.95) BS01 rna ? GO:0003735 ... Q5SJ76 29208708
    86 5ndk:6I (2.95) BS02 rna ? GO:0003735 ... Q5SJ76 29208708
    87 5ndk:72 (2.95) BS01 rna ? GO:0003735 ... P0DOY9 29208708
    88 5ndk:75 (2.95) BS01 rna ? GO:0003735 ... P60490 29208708
    89 5ndk:75 (2.95) BS02 rna ? GO:0003735 ... P60490 29208708
    90 5ndk:78 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ7 29208708
    91 5ndk:78 (2.95) BS02 MG ? GO:0003735 ... Q5SHQ7 29208708
    92 5ndk:7A (2.95) BS01 rna ? GO:0003735 ... Q5SJH3 29208708
    93 5ndk:7E (2.95) BS01 rna ? GO:0003735 ... P0DOY9 29208708
    94 5ndk:7I (2.95) BS01 rna ? GO:0003735 ... Q5SJH3 29208708
    95 5ndk:82 (2.95) BS01 rna ? GO:0000049 ... P80374 29208708
    96 5ndk:85 (2.95) BS01 rna ? GO:0000027 ... P60491 29208708
    97 5ndk:88 (2.95) BS01 rna ? GO:0000049 ... P60489 29208708
    98 5ndk:88 (2.95) BS02 rna ? GO:0000049 ... P60489 29208708
    99 5ndk:88 (2.95) BS03 rna ? GO:0000049 ... P60489 29208708
    100 5ndk:88 (2.95) BS04 MG ? GO:0000049 ... P60489 29208708
    101 5ndk:88 (2.95) BS05 MG ? GO:0000049 ... P60489 29208708
    102 5ndk:8A (2.95) BS01 rna ? GO:0003735 ... P0DOY7 29208708
    103 5ndk:8E (2.95) BS01 rna ? GO:0000049 ... P80374 29208708
    104 5ndk:8E (2.95) BS02 rna ? GO:0000049 ... P80374 29208708
    105 5ndk:8I (2.95) BS01 rna ? GO:0003735 ... P0DOY7 29208708
    106 5ndk:95 (2.95) BS01 rna ? GO:0003723 ... P60492 29208708
    107 5ndk:98 (2.95) BS01 rna ? GO:0003735 ... Q9Z9H5 29208708
    108 5ndk:9A (2.95) BS01 rna ? GO:0003735 ... Q5SLQ0 29208708
    109 5ndk:9I (2.95) BS01 rna ? GO:0003735 ... Q5SLQ0 29208708
    110 5ndk:A5 (2.95) BS01 rna ? GO:0003735 ... Q5SHP3 29208708
    111 5ndk:A5 (2.95) BS02 MG ? GO:0003735 ... Q5SHP3 29208708
    112 5ndk:A8 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ4 29208708
    113 5ndk:A8 (2.95) BS02 rna ? GO:0003735 ... Q5SHQ4 29208708
    114 5ndk:AA (2.95) BS01 rna ? GO:0000028 ... Q5SHP2 29208708
    115 5ndk:AI (2.95) BS01 rna ? GO:0000028 ... Q5SHP2 29208708
    116 5ndk:B5 (2.95) BS01 rna ? GO:0000027 ... Q5SHP0 29208708
    117 5ndk:B8 (2.95) BS01 rna ? GO:0003735 ... P60490 29208708
    118 5ndk:B8 (2.95) BS02 rna ? GO:0003735 ... P60490 29208708
    119 5ndk:BA (2.95) BS01 rna ? GO:0003723 ... P80380 29208708
    120 5ndk:BI (2.95) BS01 rna ? GO:0003723 ... P80380 29208708
    121 5ndk:C5 (2.95) BS01 rna ? GO:0003723 ... Q5SHP9 29208708
    122 5ndk:C5 (2.95) BS02 MG ? GO:0003723 ... Q5SHP9 29208708
    123 5ndk:C8 (2.95) BS01 rna ? GO:0000027 ... P60491 29208708
    124 5ndk:C8 (2.95) BS02 MG ? GO:0000027 ... P60491 29208708
    125 5ndk:D5 (2.95) BS01 rna ? GO:0003723 ... Q5SHZ1 29208708
    126 5ndk:D5 (2.95) BS02 rna ? GO:0003723 ... Q5SHZ1 29208708
    127 5ndk:D8 (2.95) BS01 rna ? GO:0003723 ... P60492 29208708
    128 5ndk:E5 (2.95) BS01 rna ? GO:0003735 ... P60493 29208708
    129 5ndk:E5 (2.95) BS02 rna ? GO:0003735 ... P60493 29208708
    130 5ndk:E5 (2.95) BS03 rna ? GO:0003735 ... P60493 29208708
    131 5ndk:E8 (2.95) BS01 rna ? GO:0003735 ... Q5SHP3 29208708
    132 5ndk:F5 (2.95) BS01 rna ? GO:0003735 ... P60494 29208708
    133 5ndk:F8 (2.95) BS01 rna ? GO:0000027 ... Q5SHP0 29208708
    134 5ndk:G5 (2.95) BS01 rna ? GO:0003735 ... Q5SHP6 29208708
    135 5ndk:G8 (2.95) BS01 rna ? GO:0003723 ... Q5SHP9 29208708
    136 5ndk:H5 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ6 29208708
    137 5ndk:H5 (2.95) BS02 rna ? GO:0003735 ... Q5SHQ6 29208708
    138 5ndk:H8 (2.95) BS01 rna ? GO:0003723 ... Q5SHZ1 29208708
    139 5ndk:I5 (2.95) BS01 rna ? GO:0003735 ... Q5SJE1 29208708
    140 5ndk:I8 (2.95) BS01 rna ? GO:0003735 ... P60493 29208708
    141 5ndk:I8 (2.95) BS02 rna ? GO:0003735 ... P60493 29208708
    142 5ndk:I8 (2.95) BS03 rna ? GO:0003735 ... P60493 29208708
    143 5ndk:J5 (2.95) BS01 rna ? GO:0003735 ... P80339 29208708
    144 5ndk:J8 (2.95) BS01 rna ? GO:0003735 ... P60494 29208708
    145 5ndk:K8 (2.95) BS01 rna ? GO:0003735 ... Q5SHP6 29208708
    146 5ndk:K8 (2.95) BS02 MG ? GO:0003735 ... Q5SHP6 29208708
    147 5ndk:L5 (2.95) BS01 rna ? GO:0003735 ... P80340 29208708
    148 5ndk:L5 (2.95) BS02 MG ? GO:0003735 ... P80340 29208708
    149 5ndk:L8 (2.95) BS01 rna ? GO:0003735 ... Q5SHQ6 29208708
    150 5ndk:L8 (2.95) BS02 rna ? GO:0003735 ... Q5SHQ6 29208708
    151 5ndk:M5 (2.95) BS01 rna ? GO:0003735 ... Q5SKU1 29208708
    152 5ndk:M8 (2.95) BS01 rna ? GO:0003735 ... Q5SJE1 29208708
    153 5ndk:N8 (2.95) BS01 rna ? GO:0003735 ... P80339 29208708
    154 5ndk:P8 (2.95) BS01 rna ? GO:0003735 ... P80340 29208708
    155 5ndk:Q8 (2.95) BS01 rna ? GO:0003735 ... Q5SKU1 29208708
    Reference:
  • Chengxin Zhang, Xi Zhang, Peter L Freddolino, and Yang Zhang. BioLiP2: an updated structure database for biologically relevent ligand-protein interactions, Nucleic Acids Research, gkad630 (2023).
  • Jianyi Yang, Ambrish Roy, and Yang Zhang. BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions, Nucleic Acids Research, 41: D1096-D1103 (2013) (download the PDF file).

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