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BioLiP Library
Download all results in tab-seperated text for 88 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 1e8v:A (2.0) BS02 DAN 3.2.1.18 GO:0004308 ... Q9Q2W5 11062565
    2 1e8v:B (2.0) BS02 DAN 3.2.1.18 GO:0004308 ... Q9Q2W5 11062565
    3 1eus:A (2.0) BS01 DAN 3.2.1.18 GO:0004308 ... Q02834 8591030
    4 1f8b:A (1.8) BS02 DAN 3.2.1.18 GO:0004308 ... P03472 11274459 MOAD: Ki=4uM
    PDBbind: -logKd/Ki=5.40, Ki=4.0uM
    BindingDB: IC50=13000nM
    5 1ivf:A (2.4) BS02 DAN 3.2.1.18 GO:0004308 ... P06820 7880809
    6 1ivf:B (2.4) BS03 DAN 3.2.1.18 GO:0004308 ... P06820 7880809
    7 1ms0:A (2.5) BS03 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 PDBbind: -logKd/Ki=2.91, Ki=1.23mM
    BindingDB: Ki=12300000nM
    8 1ms0:B (2.5) BS03 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 BindingDB: Ki=12300000nM
    9 1ms1:A (1.8) BS01 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 BindingDB: Ki=12300000nM
    10 1ms1:B (1.8) BS01 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 BindingDB: Ki=12300000nM
    11 1ms8:A (2.0) BS01 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 BindingDB: Ki=12300000nM
    12 1ms8:B (2.0) BS01 DAN 3.2.1.18 GO:0004308 ... Q26966 12419220 BindingDB: Ki=12300000nM
    13 1mz6:A (2.9) BS01 DAN 3.2.1.18 GO:0004308 ... O44049 10619840
    14 1n1t:A (1.6) BS01 DAN 3.2.1.18 GO:0004308 ... O44049 12507479 PDBbind: -logKd/Ki=3.85, Ki=140uM
    15 1n1v:A (2.1) BS01 DAN 3.2.1.18 GO:0004308 ... O44049 12507479 MOAD: Ki=140uM
    PDBbind: -logKd/Ki=3.85, Ki=140uM
    16 1nnb:A (2.8) BS02 DAN 3.2.1.18 GO:0004308 ... P03472 8371267 PDBbind: -logKd/Ki=5.00, Ki=10uM
    BindingDB: IC50=13000nM
    17 1nsd:A (1.8) BS02 DAN 3.2.1.18 GO:0004308 ... P27907 8069621
    18 1nsd:B (1.8) BS02 DAN 3.2.1.18 GO:0004308 ... P27907 8069621
    19 1rv0:L (2.5) BS01 DAN ? GO:0019031 ... Q82500 14764886
    20 1sli:A (2.0) BS01 DAN 4.2.2.15 GO:0004308 ... Q27701 9562562
    21 1usr:A (2.0) BS02 DAN 3.2.1.18 GO:0004308 ... P32884 15016893
    22 1usr:B (2.0) BS02 DAN 3.2.1.18 GO:0004308 ... P32884 15016893
    23 1usx:A (2.7) BS02 DAN 3.2.1.18 GO:0004308 ... P32884 15016893
    24 1usx:B (2.7) BS03 DAN 3.2.1.18 GO:0004308 ... P32884 15016893
    25 1usx:C (2.7) BS02 DAN 3.2.1.18 GO:0004308 ... P32884 15016893
    26 1v3d:A (2.28) BS02 DAN 3.2.1.18 GO:0004308 ... Q6WJ03 14729348
    27 1v3d:B (2.28) BS02 DAN 3.2.1.18 GO:0004308 ... Q6WJ03 14729348
    28 1vcu:A (2.85) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 15501818 PDBbind: -logKd/Ki=3.85, Ki=0.14mM
    BindingDB: Ki=25000nM, IC50=37000nM
    29 1vcu:B (2.85) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 15501818 BindingDB: Ki=25000nM, IC50=37000nM
    30 1w0o:A (1.9) BS01 DAN 3.2.1.18 GO:0004308 ... P0C6E9 15226294 MOAD: Kd~37uM
    BindingDB: IC50=8600nM
    31 1w8n:A (2.1) BS02 DAN 3.2.1.18 GO:0004308 ... Q02834 15527797
    32 1wcq:A (2.1) BS01 DAN 3.2.1.18 GO:0004308 ... Q02834 16206228 MOAD: Ki=0.55uM
    PDBbind: -logKd/Ki=6.26, Ki=0.55uM
    33 1wcq:B (2.1) BS01 DAN 3.2.1.18 GO:0004308 ... Q02834 16206228 MOAD: Ki=0.55uM
    34 1wcq:C (2.1) BS01 DAN 3.2.1.18 GO:0004308 ... Q02834 16206228 MOAD: Ki=0.55uM
    35 1z4v:A (2.3) BS02 DAN 3.2.1.18 GO:0004308 ... P04850 15893670
    36 1z4w:A (2.7) BS02 DAN 3.2.1.18 GO:0004308 ... P04850 15893670
    37 1z4z:A (2.5) BS02 DAN 3.2.1.18 GO:0004308 ... P04850 15893670
    38 1z50:A (2.8) BS02 DAN 3.2.1.18 GO:0004308 ... P04850 15893670
    39 2cex:B (2.2) BS01 DAN ? GO:0030288 ... P44542 16702222 MOAD: Kd=20uM
    PDBbind: -logKd/Ki=4.70, Kd=20uM
    40 2f25:A (1.95) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    41 2f25:B (1.95) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    42 2f27:A (2.15) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    43 2f27:B (2.15) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    44 2f29:A (2.921) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    45 2f29:B (2.921) BS01 DAN 3.2.1.18 GO:0004308 ... Q9Y3R4 N/A BindingDB: Ki=25000nM, IC50=37000nM
    46 2htr:A (2.5) BS01 DAN 3.2.1.18 GO:0004308 ... Q07599 16915235
    47 2htw:A (3.5) BS01 DAN 3.2.1.18 GO:0004308 ... Q6XV46 16915235
    48 2qwc:A (1.6) BS02 DAN 3.2.1.18 GO:0004308 ... P03472 9655825 MOAD: Ki=280uM
    PDBbind: -logKd/Ki=3.55, Ki=280uM
    BindingDB: IC50=13000nM
    49 2sim:A (1.6) BS01 DAN 3.2.1.18 GO:0004308 ... P29768 8656428 MOAD: Ki=0.38mM
    PDBbind: -logKd/Ki=3.42, Ki=0.38mM
    50 2vk6:A (1.5) BS02 DAN 3.2.1.18 GO:0004308 ... Q59310 18218621 PDBbind: -logKd/Ki=5.30, Ki=5uM
    51 2vvz:A (2.5) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 18765901 BindingDB: IC50=4800nM, Ki=1.6e+3nM
    52 2vvz:B (2.5) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 18765901 BindingDB: IC50=4800nM, Ki=1.6e+3nM
    53 2vw1:A (2.39) BS01 DAN 3.2.1.18 GO:0004308 ... Q54727 18835278 MOAD: Ki=0.3mM
    PDBbind: -logKd/Ki=3.52, Ki=0.3mM
    54 2ya6:A (2.0) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 21514303 MOAD: Ki=2uM
    PDBbind: -logKd/Ki=5.70, Ki=2uM
    BindingDB: IC50=4800nM, Ki=1.6e+3nM
    55 2ya6:B (2.0) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 21514303 MOAD: Ki=2uM
    BindingDB: IC50=4800nM, Ki=1.6e+3nM
    56 3h73:A (1.7) BS01 DAN 3.2.1.18 GO:0004308 ... P62576 19284989
    57 3h73:B (1.7) BS01 DAN 3.2.1.18 GO:0004308 ... P62576 19284989
    58 4m4v:A (1.84) BS01 DAN 3.2.1.18 GO:0004308 ... Q4WQS0 N/A
    59 4x47:A (2.0) BS01 DAN N/A GO:0004308 ... N/A 26154892 MOAD: ic50=1.41mM
    PDBbind: -logKd/Ki=2.85, IC50=1.41mM
    60 4xog:A (2.09) BS01 DAN 3.2.1.18 GO:0004308 ... Q54727 N/A
    61 4yw1:B (2.25) BS01 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    62 4yw3:B (2.05) BS01 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    63 4yz2:A (2.06) BS01 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    64 4yz2:B (2.06) BS01 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    65 4yz5:A (2.27) BS02 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    66 4yz5:B (2.27) BS02 DAN 3.2.1.18 GO:0004308 ... A0A0H2UQE4 26370075
    67 6ckl:A (2.684) BS02 DAN 2.7.7.43 GO:0005737 ... P0A0Z8 31583886 PDBbind: -logKd/Ki=3.89, IC50=130uM
    68 6ckl:A (2.684) BS03 DAN 2.7.7.43 GO:0005737 ... P0A0Z8 31583886 PDBbind: -logKd/Ki=3.89, IC50=130uM
    69 6ckl:B (2.684) BS01 DAN 2.7.7.43 GO:0005737 ... P0A0Z8 31583886 PDBbind: -logKd/Ki=3.89, IC50=130uM
    70 6ckl:B (2.684) BS02 DAN 2.7.7.43 GO:0005737 ... P0A0Z8 31583886 PDBbind: -logKd/Ki=3.89, IC50=130uM
    71 6ckl:C (2.684) BS01 DAN 2.7.7.43 GO:0005737 ... P0A0Z8 31583886
    72 6hfy:A (1.65) BS05 DAN 3.2.1.18 GO:0004308 ... Q6XV27 N/A
    73 6hfy:B (1.65) BS05 DAN 3.2.1.18 GO:0004308 ... Q6XV27 N/A
    74 6hfy:C (1.65) BS05 DAN 3.2.1.18 GO:0004308 ... Q6XV27 N/A
    75 6hfy:D (1.65) BS05 DAN 3.2.1.18 GO:0004308 ... Q6XV27 N/A
    76 6mrv:A (1.8) BS01 DAN ? GO:0004308 ... A0A4S2B4D9 31548686
    77 6mrv:B (1.8) BS01 DAN ? GO:0004308 ... A0A4S2B4D9 31548686
    78 6s0e:A (1.9) BS01 DAN N/A N/A N/A 31645552 PDBbind: -logKd/Ki=5.50, Ki=3.17uM
    79 6s0e:B (1.9) BS01 DAN N/A N/A N/A 31645552
    80 6tvi:AAA (1.0) BS01 DAN 3.2.1.18 GO:0004308 ... P29768 N/A
    81 7a54:A (2.7) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 33150981 BindingDB: IC50=4800nM, Ki=1.6e+3nM
    82 7a54:B (2.7) BS01 DAN 3.2.1.18 GO:0004308 ... P62575 33150981 BindingDB: IC50=4800nM, Ki=1.6e+3nM
    83 7lbv:A (1.7) BS01 DAN 3.2.1.18 GO:0004308 ... A0A8B2VIR8 34792586
    84 8axi:A (1.25) BS02 DAN ? GO:0046872 ... B2ULI1 37005422
    85 8axi:B (1.25) BS02 DAN ? GO:0046872 ... B2ULI1 37005422
    86 8axs:B (1.3) BS02 DAN N/A N/A N/A 37005422
    87 8gfp:A (2.07) BS01 DAN N/A GO:0000270 ... N/A 37209283
    88 8t1y:A (2.14) BS01 DAN 3.2.1.18 GO:0004308 ... Q7MX62 37747935
    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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