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BioLiP
Download all results in tab-seperated text for 60 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 5gmk:A (3.4) BS01 rna ? GO:0000244 ... P33334 27445308
    2 5gmk:A (3.4) BS02 rna ? GO:0000244 ... P33334 27445308
    3 5gmk:A (3.4) BS03 rna ? GO:0000244 ... P33334 27445308
    4 5gmk:A (3.4) BS04 rna ? GO:0000244 ... P33334 27445308
    5 5gmk:A (3.4) BS05 rna ? GO:0000244 ... P33334 27445308
    6 5gmk:A (3.4) BS06 rna ? GO:0000244 ... P33334 27445308
    7 5gmk:A (3.4) BS07 peptide ? GO:0000244 ... P33334 27445308
    8 5gmk:C (3.4) BS01 rna ? GO:0000244 ... P36048 27445308
    9 5gmk:C (3.4) BS02 GTP ? GO:0000244 ... P36048 27445308
    10 5gmk:C (3.4) BS03 MG ? GO:0000244 ... P36048 27445308
    11 5gmk:F (3.4) BS01 rna ? GO:0000349 ... P28320 27445308
    12 5gmk:F (3.4) BS02 rna ? GO:0000349 ... P28320 27445308
    13 5gmk:F (3.4) BS03 rna ? GO:0000349 ... P28320 27445308
    14 5gmk:F (3.4) BS04 rna ? GO:0000349 ... P28320 27445308
    15 5gmk:F (3.4) BS05 ZN ? GO:0000349 ... P28320 27445308
    16 5gmk:G (3.4) BS01 rna ? GO:0000398 ... P53854 27445308
    17 5gmk:G (3.4) BS02 rna ? GO:0000398 ... P53854 27445308
    18 5gmk:H (3.4) BS01 rna ? GO:0000350 ... P21374 27445308
    19 5gmk:H (3.4) BS02 rna ? GO:0000350 ... P21374 27445308
    20 5gmk:H (3.4) BS03 rna ? GO:0000350 ... P21374 27445308
    21 5gmk:I (3.4) BS01 rna ? GO:0000384 ... P53277 27445308
    22 5gmk:I (3.4) BS02 rna ? GO:0000384 ... P53277 27445308
    23 5gmk:P (3.4) BS01 rna ? GO:0000350 ... P28004 27445308
    24 5gmk:P (3.4) BS02 rna ? GO:0000350 ... P28004 27445308
    25 5gmk:Q (3.4) BS01 rna ? GO:0000398 ... P38241 27445308
    26 5gmk:Q (3.4) BS02 rna ? GO:0000398 ... P38241 27445308
    27 5gmk:Q (3.4) BS03 ZN ? GO:0000398 ... P38241 27445308
    28 5gmk:Q (3.4) BS04 ZN ? GO:0000398 ... P38241 27445308
    29 5gmk:R (3.4) BS01 rna ? GO:0000387 ... Q12046 27445308
    30 5gmk:R (3.4) BS02 rna ? GO:0000387 ... Q12046 27445308
    31 5gmk:R (3.4) BS03 rna ? GO:0000387 ... Q12046 27445308
    32 5gmk:R (3.4) BS04 ZN ? GO:0000387 ... Q12046 27445308
    33 5gmk:S (3.4) BS01 rna ? GO:0000398 ... Q03772 27445308
    34 5gmk:S (3.4) BS02 rna ? GO:0000398 ... Q03772 27445308
    35 5gmk:S (3.4) BS03 rna ? GO:0000398 ... Q03772 27445308
    36 5gmk:T (3.4) BS01 rna ? GO:0000282 ... P25337 27445308
    37 5gmk:T (3.4) BS02 rna ? GO:0000282 ... P25337 27445308
    38 5gmk:T (3.4) BS03 ZN ? GO:0000282 ... P25337 27445308
    39 5gmk:T (3.4) BS04 ZN ? GO:0000282 ... P25337 27445308
    40 5gmk:T (3.4) BS05 ZN ? GO:0000282 ... P25337 27445308
    41 5gmk:Z (3.4) BS01 peptide ? GO:0000398 ... P53333 27445308
    42 5gmk:a (3.4) BS01 rna ? GO:0000398 ... P40567 27445308
    43 5gmk:c (3.4) BS01 rna ? GO:0000350 ... Q03654 27445308
    44 5gmk:d (3.4) BS01 rna ? GO:0000398 ... Q12309 27445308
    45 5gmk:e (3.4) BS01 rna ? GO:0000243 ... Q06217 27445308
    46 5gmk:g (3.4) BS01 rna ? GO:0000243 ... Q06217 27445308
    47 5gmk:h (3.4) BS01 rna ? GO:0000243 ... P54999 27445308
    48 5gmk:i (3.4) BS01 rna ? GO:0000243 ... Q12330 27445308
    49 5gmk:j (3.4) BS01 rna ? GO:0000243 ... P40204 27445308
    50 5gmk:k (3.4) BS01 rna ? GO:0000243 ... P40018 27445308
    51 5gmk:l (3.4) BS01 rna ? GO:0000243 ... P43321 27445308
    52 5gmk:m (3.4) BS01 rna ? GO:0000243 ... Q02260 27445308
    53 5gmk:n (3.4) BS01 rna ? GO:0000348 ... P40968 27445308
    54 5gmk:n (3.4) BS02 rna ? GO:0000348 ... P40968 27445308
    55 5gmk:s (3.4) BS01 rna ? GO:0000243 ... P40018 27445308
    56 5gmk:u (3.4) BS01 rna ? GO:0000243 ... Q12330 27445308
    57 5gmk:w (3.4) BS01 rna ? GO:0000243 ... P54999 27445308
    58 5gmk:x (3.4) BS01 rna ? GO:0000243 ... P40204 27445308
    59 5gmk:y (3.4) BS01 rna ? GO:0000243 ... P43321 27445308
    60 5gmk:z (3.4) BS01 rna ? GO:0000243 ... Q02260 27445308
    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)(download the PDF file).
  • 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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