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BioLiP
Download all results in tab-seperated text for 81 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 1hw5:A (1.82) BS01 CMP ? GO:0003677 ... P0ACJ8 11124966 Manual survey: Kb=2.0+-0.3M^-1 (11124966)
    2 1hw5:A (1.82) BS02 CMP ? GO:0003677 ... P0ACJ8 11124966 Manual survey: Kb=2.0+-0.3M^-1 (11124966)
    3 1hw5:B (1.82) BS01 CMP ? GO:0003677 ... P0ACJ8 11124966 Manual survey: Kb=2.0+-0.3M^-1 (11124966)
    4 1hw5:B (1.82) BS02 CMP ? GO:0003677 ... P0ACJ8 11124966 Manual survey: Kb=2.0+-0.3M^-1 (11124966)
    5 1o9f:A (2.7) BS01 peptide ? GO:0005737 ... P93343 12606564 Manual survey: Kd=0.7uM (12606564)
    6 1o9f:A (2.7) BS02 FSC ? GO:0005737 ... P93343 12606564 Manual survey: Kd=0.7uM (12606564)
    7 1w25:A (2.7) BS01 MG 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    8 1w25:A (2.7) BS02 C2E 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    PDBbind: -logKd/Ki=6.30, Ki=0.5uM
    9 1w25:A (2.7) BS03 C2E 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    PDBbind: -logKd/Ki=6.30, Ki=0.5uM
    10 1w25:A (2.7) BS04 C2E 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    PDBbind: -logKd/Ki=6.30, Ki=0.5uM
    11 1w25:B (2.7) BS01 MG 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    12 1w25:B (2.7) BS02 C2E 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    13 1w25:B (2.7) BS03 C2E 2.7.7.65 GO:0000160 ... B8GZM2 15569936 Manual survey: Ki=0.5uM (15569936)
    14 1xui:A (1.5) BS01 CA 3.4.21.4 GO:0004175 ... P00760 9468142 Manual survey: Ki=19uM (9468142)
    15 1xui:A (1.5) BS02 BAO 3.4.21.4 GO:0004175 ... P00760 9468142 Manual survey: Ki=19uM (9468142)
    16 2o99:A (1.7) BS01 GOA ? N/A P16528 17426033 Manual survey: Kd=0.9+-2uM (17426033)
    17 2o99:B (1.7) BS01 GOA ? N/A P16528 17426033 Manual survey: Kd=0.9+-2uM (17426033)
    18 2o99:C (1.7) BS01 GOA ? N/A P16528 17426033 Manual survey: Kd=0.9+-2uM (17426033)
    19 2o99:D (1.7) BS01 GOA ? N/A P16528 17426033 Manual survey: Kd=0.9+-2uM (17426033)
    20 2our:A (1.45) BS01 CMP 3.1.4.17 GO:0004114 ... Q9Y233 17389385 Manual survey: Km=56nM (17389385)
    21 2ouy:A (1.9) BS01 ZN 3.1.4.17 GO:0004114 ... Q9Y233 17389385 Manual survey: Km=56nM (17389385)
    22 2ouy:A (1.9) BS02 CMP 3.1.4.17 GO:0004114 ... Q9Y233 17389385 Manual survey: Km=56nM (17389385)
    23 2oz6:A (2.8) BS01 CMP ? GO:0000976 ... P55222 21665969 Manual survey: Kd=1.0uM (21665969)
    PDBbind: -logKd/Ki=5.26, Kd=5.5uM
    24 2oz6:A (2.8) BS02 CMP ? GO:0000976 ... P55222 21665969 Manual survey: Kd=1.0uM (21665969)
    PDBbind: -logKd/Ki=5.26, Kd=5.5uM
    25 2ptm:A (1.93) BS01 CMP ? N/A O76977 17562314 Manual survey: K1/2=1.1uM (17562314)
    26 2pw3:A (1.56) BS01 ZN 3.1.4.53 GO:0004114 ... Q08499 17582435 Manual survey: Km=56nM (17562314)
    27 2pw3:A (1.56) BS02 CMP 3.1.4.53 GO:0004114 ... Q08499 17582435 Manual survey: Km=56nM (17562314)
    28 2pw3:B (1.56) BS01 ZN 3.1.4.53 GO:0004114 ... Q08499 17582435 Manual survey: Km=56nM (17562314)
    29 2pw3:B (1.56) BS02 CMP 3.1.4.53 GO:0004114 ... Q08499 17582435 Manual survey: Km=56nM (17562314)
    30 3auj:A (2.1) BS01 GOL 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    31 3auj:A (2.1) BS02 CA 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    32 3auj:A (2.1) BS03 B12 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    33 3auj:L (2.1) BS01 GOL 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    34 3auj:L (2.1) BS02 CA 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    35 3auj:L (2.1) BS03 B12 4.2.1.28 GO:0003824 ... Q59470 22221669 Manual survey: Km=1.2+-0.2mM (22221669)
    36 3etq:A (1.9) BS01 CMP ? N/A O88703 19525958 Manual survey: Kd=920+-240nM (19525958)
    37 3etq:B (1.9) BS01 CMP ? N/A O88703 19525958 Manual survey: Kd=920+-240nM (19525958)
    38 3klo:A (2.802) BS01 C2E ? GO:0000166 ... Q9KKZ8 20150502 Manual survey: Kd=3.18uM (20150502)
    39 3klo:B (2.802) BS01 C2E ? GO:0000166 ... Q9KKZ8 20150502 Manual survey: Kd=3.18uM (20150502)
    40 3klo:C (2.802) BS01 C2E ? GO:0000166 ... Q9KKZ8 20150502 Manual survey: Kd=3.18uM (20150502)
    41 3klo:D (2.802) BS01 C2E ? GO:0000166 ... Q9KKZ8 20150502 Manual survey: Kd=3.18uM (20150502)
    42 3ocp:A (2.49) BS01 CMP 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=27+-3.6nM (21526164)
    MOAD: Kd=27nM
    PDBbind: -logKd/Ki=7.57, Kd=27nM
    43 3ocp:B (2.49) BS01 CMP 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=27+-3.6nM (21526164)
    MOAD: Kd=27nM
    44 3od0:A (2.9) BS01 PCG 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=12+-1.6nM (21526164)
    PDBbind: -logKd/Ki=7.92, Kd=12nM
    45 3od0:A (2.9) BS02 PCG 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=12+-1.6nM (21526164)
    PDBbind: -logKd/Ki=7.92, Kd=12nM
    46 3od0:B (2.9) BS01 PCG 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=12+-1.6nM (21526164)
    PDBbind: -logKd/Ki=7.92, Kd=12nM
    47 3ogj:A (2.751) BS01 CMP 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=27+-3.6nM (21526164)
    48 3ogj:B (2.751) BS01 CMP 2.7.11.12 N/A Q13976 21526164 Manual survey: Kd=27+-3.6nM (21526164)
    49 3pjt:A (2.5154) BS01 C2E ? N/A Q3KK31 21304926 Manual survey: Kd=13.1uM (21304926)
    PDBbind: -logKd/Ki=4.88, Kd=13.1uM
    50 3pjt:B (2.5154) BS01 C2E ? N/A Q3KK31 21304926 Manual survey: Kd=13.1uM (21304926)
    51 3q6k:A (2.52) BS01 SRO ? GO:0005576 ... Q5WPU9 21795673 Manual survey: Kd=4.3nM (21795673)
    PDBbind: -logKd/Ki=8.37, Kd=4.3nM
    52 3q6k:B (2.52) BS01 SRO ? GO:0005576 ... Q5WPU9 21795673 Manual survey: Kd=4.3nM (21795673)
    53 3qyy:A (1.9) BS01 C2E 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    MOAD: Kd=8.26uM
    PDBbind: -logKd/Ki=5.08, Kd=8.26uM
    54 3qyy:A (1.9) BS02 MG 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    55 3qyy:A (1.9) BS03 C2E 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    MOAD: Kd=8.26uM
    PDBbind: -logKd/Ki=5.08, Kd=8.26uM
    56 3qyy:B (1.9) BS01 C2E 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    MOAD: Kd=8.26uM
    PDBbind: -logKd/Ki=5.08, Kd=8.26uM
    57 3qyy:B (1.9) BS02 C2E 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    MOAD: Kd=8.26uM
    PDBbind: -logKd/Ki=5.08, Kd=8.26uM
    58 3qyy:B (1.9) BS03 MG 2.7.7.65 N/A Q8P559 22120736 Manual survey: Ki=6.54uM (22120736)
    59 3u0z:A (2.9) BS01 CMP ? N/A O88704 22006928 Manual survey: Kd=39.7nM (22006928)
    60 3u0z:B (2.9) BS01 CMP ? N/A O88704 22006928 Manual survey: Kd=39.7nM (22006928)
    61 3u10:A (2.3) BS01 CMP ? N/A Q9UL51 22006928 Manual survey: Kd=82.0nM (22006928)
    PDBbind: -logKd/Ki=5.44, Kd=3.6uM
    62 3u11:A (2.5) BS01 CMP ? N/A Q9Y3Q4 22006928 Manual survey: Kd=39.2nM (22006928)
    63 3u11:B (2.5) BS01 CMP ? N/A Q9Y3Q4 22006928 Manual survey: Kd=39.2nM (22006928)
    64 4dn0:A (2.3) BS01 C2E ? N/A A0A0H2ZD98 22605337 Manual survey: Kd=1.9uM (22605337)
    MOAD: Kd=1.9uM
    PDBbind: -logKd/Ki=5.72, Kd=1.9uM
    65 4dn0:A (2.3) BS02 C2E ? N/A A0A0H2ZD98 22605337 Manual survey: Kd=1.9uM (22605337)
    MOAD: Kd=1.9uM
    PDBbind: -logKd/Ki=5.72, Kd=1.9uM
    66 4ef4:A (2.147) BS01 C2E ? GO:0002218 ... Q86WV6 22579474 Manual survey: Kd=4.42uM (22579474)
    MOAD: Kd=4.42uM
    PDBbind: -logKd/Ki=5.35, Kd=4.42uM
    BindingDB: EC50=4500nM, Kd=1210nM
    67 4ef4:A (2.147) BS02 CA ? GO:0002218 ... Q86WV6 22579474 Manual survey: Kd=4.42uM (22579474)
    68 4ef4:B (2.147) BS01 C2E ? GO:0002218 ... Q86WV6 22579474 Manual survey: Kd=4.42uM (22579474)
    PDBbind: -logKd/Ki=5.35, Kd=4.42uM
    BindingDB: EC50=4500nM, Kd=1210nM
    69 4emt:A (1.5) BS01 C2E ? GO:0002218 ... Q86WV6 22728658 Manual survey: Kd=5uM (22728658)
    MOAD: Kd=4.63uM
    PDBbind: -logKd/Ki=5.30, Kd~5uM
    BindingDB: EC50=4500nM, Kd=1210nM
    70 4emt:B (1.5) BS01 C2E ? GO:0002218 ... Q86WV6 22728658 Manual survey: Kd=5uM (22728658)
    PDBbind: -logKd/Ki=5.30, Kd~5uM
    BindingDB: EC50=4500nM, Kd=1210nM
    71 4emt:B (1.5) BS02 CA ? GO:0002218 ... Q86WV6 22728658 Manual survey: Kd=5uM (22728658)
    72 4etz:A (2.05) BS01 C2E ? N/A Q9HZE7 22810222 Manual survey: Kd=0.5uM (22810222)
    MOAD: Kd~0.5uM
    PDBbind: -logKd/Ki=6.30, Kd=0.5uM
    73 4etz:B (2.05) BS01 C2E ? N/A Q9HZE7 22810222 Manual survey: Kd=0.5uM (22810222)
    MOAD: Kd~0.5uM
    74 4eu0:A (1.7) BS01 C2E ? N/A Q9HZE7 22810222 Manual survey: Kd=0.5uM (22810222)
    MOAD: Kd=0.4uM
    PDBbind: -logKd/Ki=6.40, Kd=0.4uM
    75 4euv:A (2.0) BS01 C2E ? N/A Q9HZE7 22810222 Manual survey: Kd=0.5uM (22810222)
    MOAD: Kd~0.5uM
    PDBbind: -logKd/Ki=6.30, Kd=0.5uM
    76 4f5y:A (2.396) BS01 CA ? GO:0002218 ... Q86WV6 22728660 Manual survey: Kd=3.7uM (22728660)
    77 4f5y:A (2.396) BS02 C2E ? GO:0002218 ... Q86WV6 22728660 Manual survey: Kd=3.7uM (22728660)
    PDBbind: -logKd/Ki=5.43, Kd=3.70uM
    BindingDB: EC50=4500nM, Kd=1210nM
    78 4f5y:B (2.396) BS01 C2E ? GO:0002218 ... Q86WV6 22728660 Manual survey: Kd=3.7uM (22728660)
    PDBbind: -logKd/Ki=5.43, Kd=3.70uM
    BindingDB: EC50=4500nM, Kd=1210nM
    79 4f5y:B (2.396) BS02 CA ? GO:0002218 ... Q86WV6 22728660 Manual survey: Kd=3.7uM (22728660)
    80 4f9g:A (2.95) BS01 C2E ? GO:0002218 ... Q86WV6 22705373 Manual survey: Km=2.4+-0.5mM (22705373)
    PDBbind: -logKd/Ki=5.62, Kd=2.4uM
    BindingDB: EC50=4500nM, Kd=1210nM
    81 4f9g:C (2.95) BS01 C2E ? GO:0002218 ... Q86WV6 22705373 Manual survey: Km=2.4+-0.5mM (22705373)
    PDBbind: -logKd/Ki=5.62, Kd=2.4uM
    BindingDB: EC50=4500nM, Kd=1210nM
    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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