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BioLiP
Download all results in tab-seperated text for 35 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 3ccm:1 (2.55) BS01 rna ? GO:0003723 ... P32410 18455733 PDBbind: Kd=100uM
    2 3ccm:2 (2.55) BS01 rna ? GO:0003735 ... P22452 18455733 PDBbind: Kd=100uM
    3 3ccm:3 (2.55) BS01 rna ? GO:0000049 ... P32411 18455733 PDBbind: Kd=100uM
    4 3ccm:A (2.55) BS01 rna ? GO:0002181 ... P20276 18455733 PDBbind: Kd=100uM
    5 3ccm:A (2.55) BS02 MG ? GO:0002181 ... P20276 18455733
    6 3ccm:B (2.55) BS01 rna ? GO:0003723 ... P20279 18455733 PDBbind: Kd=100uM
    7 3ccm:C (2.55) BS01 rna ? GO:0003723 ... P12735 18455733 PDBbind: Kd=100uM
    8 3ccm:D (2.55) BS01 rna ? GO:0000049 ... P14124 18455733 PDBbind: Kd=100uM
    9 3ccm:D (2.55) BS02 rna ? GO:0000049 ... P14124 18455733 PDBbind: Kd=100uM
    10 3ccm:E (2.55) BS01 rna ? GO:0002181 ... P14135 18455733 PDBbind: Kd=100uM
    11 3ccm:F (2.55) BS01 rna ? GO:0001682 ... P12743 18455733 PDBbind: Kd=100uM
    12 3ccm:H (2.55) BS01 rna ? GO:0000027 ... P60617 18455733 PDBbind: Kd=100uM
    13 3ccm:I (2.55) BS01 rna ? GO:0003735 ... P14122 18455733 PDBbind: Kd=100uM
    14 3ccm:J (2.55) BS01 rna ? GO:0003729 ... P29198 18455733 PDBbind: Kd=100uM
    15 3ccm:K (2.55) BS01 rna ? GO:0003735 ... P22450 18455733 PDBbind: Kd=100uM
    16 3ccm:L (2.55) BS01 rna ? GO:0003735 ... P12737 18455733 PDBbind: Kd=100uM
    17 3ccm:M (2.55) BS01 rna ? GO:0002181 ... P60618 18455733 PDBbind: Kd=100uM
    18 3ccm:N (2.55) BS01 rna ? GO:0000027 ... P14123 18455733 PDBbind: Kd=100uM
    19 3ccm:N (2.55) BS02 rna ? GO:0000027 ... P14123 18455733 PDBbind: Kd=100uM
    20 3ccm:O (2.55) BS01 rna ? GO:0003723 ... P12733 18455733 PDBbind: Kd=100uM
    21 3ccm:P (2.55) BS01 rna ? GO:0003723 ... P14119 18455733 PDBbind: Kd=100uM
    22 3ccm:Q (2.55) BS01 rna ? GO:0003735 ... P12734 18455733 PDBbind: Kd=100uM
    23 3ccm:Q (2.55) BS02 rna ? GO:0003735 ... P12734 18455733 PDBbind: Kd=100uM
    24 3ccm:R (2.55) BS01 rna ? GO:0002181 ... P10970 18455733 PDBbind: Kd=100uM
    25 3ccm:S (2.55) BS01 rna ? GO:0000027 ... P12732 18455733 PDBbind: Kd=100uM
    26 3ccm:T (2.55) BS01 rna ? GO:0002181 ... P10972 18455733 PDBbind: Kd=100uM
    27 3ccm:T (2.55) BS02 MG ? GO:0002181 ... P10972 18455733
    28 3ccm:U (2.55) BS01 rna ? GO:0003735 ... P14116 18455733 PDBbind: Kd=100uM
    29 3ccm:V (2.55) BS01 rna ? GO:0003735 ... P10971 18455733 PDBbind: Kd=100uM
    30 3ccm:W (2.55) BS01 rna ? GO:0000463 ... P14121 18455733 PDBbind: Kd=100uM
    31 3ccm:W (2.55) BS02 rna ? GO:0000463 ... P14121 18455733 PDBbind: Kd=100uM
    32 3ccm:X (2.55) BS01 rna ? GO:0002181 ... P18138 18455733 PDBbind: Kd=100uM
    33 3ccm:Y (2.55) BS01 rna ? GO:0000166 ... P12736 18455733 PDBbind: Kd=100uM
    34 3ccm:Y (2.55) BS02 MG ? GO:0000166 ... P12736 18455733
    35 3ccm:Z (2.55) BS01 rna ? GO:0003735 ... P60619 18455733 PDBbind: Kd=100uM
    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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