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BioLiP
Download all results in tab-seperated text for 55 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 1die:A (2.5) BS03 NOJ 5.3.1.5 GO:0000287 ... P12070 2304904
    2 1die:B (2.5) BS03 NOJ 5.3.1.5 GO:0000287 ... P12070 2304904
    3 1dog:A (2.3) BS11 NOJ 3.2.1.3 GO:0004339 ... P69327 8431441 MOAD: Ki=96uM
    4 1dog:A (2.3) BS12 NOJ 3.2.1.3 GO:0004339 ... P69327 8431441 MOAD: Ki=96uM
    5 1i75:A (2.0) BS03 NOJ 2.4.1.19 GO:0003824 ... P05618 11275559
    6 1i75:A (2.0) BS04 NOJ 2.4.1.19 GO:0003824 ... P05618 11275559
    7 1i75:B (2.0) BS03 NOJ 2.4.1.19 GO:0003824 ... P05618 11275559
    8 1i75:B (2.0) BS04 NOJ 2.4.1.19 GO:0003824 ... P05618 11275559
    9 1oim:A (2.15) BS01 NOJ 3.2.1.21 GO:0004553 ... Q08638 14624580 MOAD: Ka=210000M^-1
    PDBbind: -logKd/Ki=5.32, Kd=4.8uM
    10 1oim:B (2.15) BS01 NOJ 3.2.1.21 GO:0004553 ... Q08638 14624580 MOAD: Ka=210000M^-1
    11 2j77:A (2.1) BS01 NOJ 3.2.1.21 GO:0004553 ... Q08638 17279749 MOAD: Kd=12.9uM
    PDBbind: -logKd/Ki=4.89, Kd=12.9uM
    12 2j77:B (2.1) BS01 NOJ 3.2.1.21 GO:0004553 ... Q08638 17279749 MOAD: Kd=12.9uM
    13 2jke:A (1.7) BS01 NOJ 3.2.1.3 GO:0000272 ... G8JZS4 18848471 MOAD: Ki=59uM
    PDBbind: -logKd/Ki=4.23, Ki=59uM
    14 2jke:B (1.7) BS01 NOJ 3.2.1.3 GO:0000272 ... G8JZS4 18848471 MOAD: Ki=59uM
    15 2pwd:A (1.8) BS02 NOJ 5.4.99.11 GO:0004556 ... Q2PS28 17597061 MOAD: Ki=40uM
    PDBbind: -logKd/Ki=4.40, Ki=40uM
    16 2pwd:B (1.8) BS02 NOJ 5.4.99.11 GO:0004556 ... Q2PS28 17597061 MOAD: Ki=40uM
    17 2x2j:A (2.35) BS01 NOJ 4.2.2.13 GO:0003824 ... Q9STC1 23902768
    18 2x2j:B (2.35) BS01 NOJ 4.2.2.13 GO:0003824 ... Q9STC1 23902768
    19 2x2j:C (2.35) BS01 NOJ 4.2.2.13 GO:0003824 ... Q9STC1 23902768
    20 2x2j:D (2.35) BS01 NOJ 4.2.2.13 GO:0003824 ... Q9STC1 23902768
    21 2xg9:A (1.8) BS01 NOJ 3.2.1.2 GO:0000272 ... P16098 21085740 PDBbind: -logKd/Ki=4.15, Ki=70uM
    22 2ya2:A (2.37) BS01 NOJ 3.2.1.41 GO:0004553 ... A0A0H2UNG0 21565699
    23 3gbe:A (1.7) BS01 NOJ 5.4.99.11 GO:0004556 ... D0VX20 19427862 MOAD: Ki=10uM
    PDBbind: -logKd/Ki=5.00, Ki=10uM
    24 3gxt:A (2.7) BS01 NOJ 3.2.1.22 GO:0003824 ... P06280 19374450 PDBbind: -logKd/Ki=4.74, Ki=18uM
    25 3gxt:B (2.7) BS01 NOJ 3.2.1.22 GO:0003824 ... P06280 19374450 PDBbind: -logKd/Ki=4.74, Ki=18uM
    26 3qfz:A (2.39) BS02 NOJ 2.4.1.20 GO:0003824 ... O66264 N/A PDBbind: -logKd/Ki=3.24, Ki=570uM
    27 3qfz:B (2.39) BS02 NOJ 2.4.1.20 GO:0003824 ... O66264 N/A PDBbind: -logKd/Ki=3.24, Ki=570uM
    28 3qg0:A (2.7) BS02 NOJ 2.4.1.20 GO:0003824 ... O66264 N/A
    29 3qg0:B (2.7) BS02 NOJ 2.4.1.20 GO:0003824 ... O66264 N/A
    30 3vig:A (0.99) BS01 NOJ 3.2.1.21 GO:0004553 ... Q8T0W7 22751668
    31 4hp0:A (1.19) BS01 NOJ 3.2.1.17 GO:0003796 ... P00698 23303182 PDBbind: -logKd/Ki=6.12, Kd=0.76uM
    32 4hpi:A (1.19) BS01 NOJ 3.2.1.17 GO:0003796 ... P00698 23303182 PDBbind: -logKd/Ki=4.85, Kd=14.2uM
    33 4iid:A (2.3) BS06 NOJ 3.2.1.21 GO:0004553 ... P48825 23537284 MOAD: Ki=2.4uM
    PDBbind: -logKd/Ki=5.62, Ki=2.4uM
    34 4iid:B (2.3) BS07 NOJ 3.2.1.21 GO:0004553 ... P48825 23537284 MOAD: Ki=2.4uM
    35 5bx3:A (1.96) BS01 NOJ 3.2.1.45 GO:0004348 ... F6BL85 27115290 MOAD: Ki=0.13uM
    36 5dky:A (1.6) BS01 NOJ 3.2.1.20 GO:0003824 ... G0SG42 26847925
    37 5iee:A (1.92) BS01 NOJ 3.2.1.207 GO:0003824 ... Q8BHN3 27462106 PDBbind: -logKd/Ki=4.94, IC50=11.4uM
    38 5ngl:A (1.85) BS01 NOJ ? GO:0004348 ... Q8A2J3 28461332
    39 5ngl:B (1.85) BS01 NOJ ? GO:0004348 ... Q8A2J3 28461332
    40 5ngl:C (1.85) BS01 NOJ ? GO:0004348 ... Q8A2J3 28461332
    41 5nn5:A (2.0) BS01 NOJ 3.2.1.20 GO:0000023 ... P10253 29061980 MOAD: Ki=3.4uM
    PDBbind: -logKd/Ki=5.47, Ki=3.4uM
    42 5ns8:A (1.55) BS01 NOJ N/A GO:0004553 ... N/A 30345395
    43 5ns8:B (1.55) BS01 NOJ N/A GO:0004553 ... N/A 30345395
    44 5ns8:C (1.55) BS01 NOJ N/A GO:0004553 ... N/A 30345395
    45 5wcz:A (1.58) BS01 NOJ 3.2.1.10 GO:0004556 ... O06994 29563521
    46 5wcz:B (1.58) BS01 NOJ 3.2.1.10 GO:0004556 ... O06994 29563521
    47 6f9j:A (1.67) BS01 NOJ 3.2.1.2 GO:0000272 ... A8CFR3 N/A
    48 6lgc:A (1.9) BS03 NOJ 3.2.1.20 GO:0005975 ... A0A077JI83 32381508
    49 6lgc:B (1.9) BS03 NOJ 3.2.1.20 GO:0005975 ... A0A077JI83 32381508
    50 6r5n:A (2.0) BS01 NOJ 3.2.1.21 GO:0004553 ... Q9I311 31877028 MOAD: Ki=4.4mM
    51 6r5n:B (2.0) BS01 NOJ 3.2.1.21 GO:0004553 ... Q9I311 31877028 MOAD: Ki=4.4mM
    52 7ec9:A (1.8) BS01 NOJ ? GO:0000272 ... Q9X274 36084911
    53 7ec9:B (1.8) BS01 NOJ ? GO:0000272 ... Q9X274 36084911
    54 7vkz:A (2.0) BS01 NOJ ? GO:0004553 ... I0AIT9 35065074
    55 7vkz:A (2.0) BS02 NOJ ? GO:0004553 ... I0AIT9 35065074
    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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