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BioLiP
Download all results in tab-seperated text for 22 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 1d4s:A (2.5) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 8893827 MOAD: Ki=0.008nM
    2 1d4s:B (2.5) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 8893827
    3 1d4y:A (1.97) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 8893827 MOAD: Ki=0.008nM
    PDBbind: -logKd/Ki=11.10, Ki=0.008nM
    4 1d4y:B (1.97) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 8893827 PDBbind: -logKd/Ki=11.10, Ki=0.008nM
    5 2o4l:A (1.33) BS01 TPV ? GO:0004190 ... Q1G1C3 17360759 MOAD: Kd=608pM
    PDBbind: -logKd/Ki=9.22, Kd=608pM
    6 2o4l:B (1.33) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 17360759 PDBbind: -logKd/Ki=9.22, Kd=608pM
    7 2o4n:A (2.0) BS01 TPV 3.1.26.13 GO:0004190 ... Q90SN9 17360759 MOAD: Kd=15010pM
    PDBbind: -logKd/Ki=7.82, Kd=15nM
    8 2o4n:B (2.0) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P03367 17360759 PDBbind: -logKd/Ki=7.82, Kd=15nM
    9 2o4p:A (1.8) BS01 TPV ? GO:0004190 ... Q5RZ08 17360759 MOAD: Kd=19pM
    PDBbind: -logKd/Ki=10.72, Kd=19pM
    10 2o4p:B (1.8) BS01 TPV ? GO:0004190 ... Q5RZ08 17360759 PDBbind: -logKd/Ki=10.72, Kd=19pM
    11 3spk:A (1.24) BS01 TPV 3.1.26.13 GO:0004190 ... Q000H7 21871444 MOAD: ic50=3.02nM
    PDBbind: -logKd/Ki=8.52, IC50=3.02nM
    12 3spk:A (1.24) BS02 TPV 3.1.26.13 GO:0004190 ... Q000H7 21871444 MOAD: ic50=3.02nM
    PDBbind: -logKd/Ki=8.52, IC50=3.02nM
    13 3spk:B (1.24) BS01 TPV 3.1.26.13 GO:0004190 ... Q000H7 21871444 MOAD: ic50=3.02nM
    PDBbind: -logKd/Ki=8.52, IC50=3.02nM
    14 3spk:B (1.24) BS02 TPV 3.1.26.13 GO:0004190 ... Q000H7 21871444 MOAD: ic50=3.02nM
    PDBbind: -logKd/Ki=8.52, IC50=3.02nM
    15 4nju:A (1.8) BS01 TPV ? GO:0004190 ... Q9J006 24752271
    16 4nju:B (1.8) BS01 TPV ? GO:0004190 ... Q9J006 24752271
    17 4nju:C (1.8) BS01 TPV ? GO:0004190 ... Q9J006 24752271
    18 4nju:D (1.8) BS01 TPV ? GO:0004190 ... Q9J006 24752271
    19 6dif:A (1.2) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P04585 30288468 PDBbind: -logKd/Ki=10.72, Ki=0.019nM
    20 6dif:B (1.2) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P04585 30288468 MOAD: Ki=0.019nM
    PDBbind: -logKd/Ki=10.72, Ki=0.019nM
    21 6dil:A (1.482) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P04585 30288468 PDBbind: -logKd/Ki=8.12, Ki=7.6nM
    22 6dil:B (1.482) BS01 TPV 2.7.7.-
    2.7.7.49
    2.7.7.7
    3.1.-.-
    3.1.13.2
    3.1.26.13
    3.4.23.16    		 GO:0004190 ... P04585 30288468 MOAD: Ki=7.6nM
    PDBbind: -logKd/Ki=8.12, Ki=7.6nM
    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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