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●TM-score ●TM-align ●US-align ●MM-align ●RNA-align ●NW-align ●LS-align ●EDTSurf ●MVP ●MVP-Fit ●SPICKER ●HAAD ●PSSpred ●3DRobot ●MR-REX ●I-TASSER-MR ●SVMSEQ ●NeBcon ●ResPRE ●TripletRes ●DeepPotential ●WDL-RF ●ATPbind ●DockRMSD ●DeepMSA ●FASPR ●EM-Refiner ●GPU-I-TASSER

●BioLiP ●E. coli ●GLASS ●GPCR-HGmod ●GPCR-RD ●GPCR-EXP ●Tara-3D ●TM-fold ●DECOYS ●POTENTIAL ●RW/RWplus ●EvoEF ●HPSF ●THE-DB ●ADDRESS ●Alpaca-Antibody ●CASP7 ●CASP8 ●CASP9 ●CASP10 ●CASP11 ●CASP12 ●CASP13 ●CASP14

BioLiP
Download all results in tab-seperated text for 1213 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 1agp:A (2.3) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 8357792
    2 1am4:D (2.7) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 9262406
    3 1am4:E (2.7) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 9262406
    4 1am4:F (2.7) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 9262406
    5 1b23:P (2.6) BS04 GNP ? GO:0003746 ... Q01698 10368282
    6 1cf4:A (-1.00) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 10360579
    7 1cip:A (1.5) BS02 GNP ? GO:0000287 ... P10824 10358003
    8 1ctq:A (1.26) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 10574788
    9 1day:A (2.2) BS02 GNP 2.7.11.1 GO:0004672 ... P28523 10581548
    10 1e0a:A (-1.00) BS01 GNP 3.6.5.2 GO:0000139 ... P60953 10802735
    11 1eft:A (2.5) BS02 GNP ? GO:0003746 ... Q01698 8069622
    12 1ek0:A (1.48) BS02 GNP ? GO:0003924 ... P36017 10756108
    13 1exm:A (1.7) BS02 GNP ? GO:0003746 ... P60338 N/A
    14 1f5n:A (1.7) BS02 GNP 3.6.1.-
    3.6.5.-    		 GO:0000139 ... P32455 10970849
    15 1g17:A (2.0) BS02 GNP ? GO:0003924 ... P07560 11099382
    16 1g17:B (2.0) BS02 GNP ? GO:0003924 ... P07560 11099382
    17 1g7t:A (2.0) BS01 GNP ? GO:0003743 ... O26359 11114334
    18 1gl6:A (2.8) BS01 GNP ? N/A Q04230 11214325
    19 1gl6:A (2.8) BS02 GNP ? N/A Q04230 11214325
    20 1gl6:B (2.8) BS01 GNP ? N/A Q04230 11214325
    21 1gl6:D (2.8) BS01 GNP ? N/A Q04230 11214325
    22 1gl6:E (2.8) BS01 GNP ? N/A Q04230 11214325
    23 1gl6:F (2.8) BS01 GNP ? N/A Q04230 11214325
    24 1gl6:G (2.8) BS01 GNP ? N/A Q04230 11214325
    25 1gua:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P62834 8756332 MOAD: Kd=40nM
    26 1he8:B (3.0) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 11136978
    27 1hoo:A (2.3) BS02 GNP 6.3.4.4 GO:0000166 ... P0A7D4 8663109
    28 1huq:A (1.8) BS02 GNP 3.6.5.2 GO:0003924 ... P35278 11278565
    29 1i4t:D (2.6) BS01 GNP 3.6.5.2 GO:0001764 ... P63000 11346801
    30 1iaq:A (2.9) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 11320243
    31 1iaq:B (2.9) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 11320243
    32 1iaq:C (2.9) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 11320243
    33 1ibr:A (2.3) BS02 GNP 3.6.5.- GO:0000054 ... P62826 10367892
    34 1ibr:C (2.3) BS02 GNP 3.6.5.- GO:0000054 ... P62826 10367892
    35 1jpj:A (2.3) BS01 GNP 3.6.5.4 GO:0003924 ... O07347 11566135
    36 1jpn:A (1.9) BS01 GNP 3.6.5.4 GO:0003924 ... O07347 11566135
    37 1jpn:B (1.9) BS01 GNP 3.6.5.4 GO:0003924 ... O07347 11566135
    38 1k5d:A (2.7) BS02 GNP 3.6.5.- GO:0000054 ... P62826 11832950
    39 1k5d:D (2.7) BS02 GNP 3.6.5.- GO:0000054 ... P62826 11832950
    40 1k5d:G (2.7) BS02 GNP 3.6.5.- GO:0000054 ... P62826 11832950
    41 1k5d:J (2.7) BS02 GNP 3.6.5.- GO:0000054 ... P62826 11832950
    42 1k8r:A (3.0) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 11709168
    43 1kk1:A (1.8) BS02 GNP 3.6.5.3 GO:0000049 ... Q9V1G0 11927566
    44 1kmq:A (1.55) BS03 GNP 3.6.5.2 GO:0000902 ... P61586 12777804
    45 1ky2:A (1.6) BS02 GNP ? GO:0003924 ... P32939 11937061
    46 1lf0:A (1.7) BS04 GNP 3.6.5.2 GO:0003924 ... P01112 12213964
    47 1lfd:B (2.1) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 9628477
    48 1lfd:D (2.1) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 9628477
    49 1m2o:A (2.5) BS02 GNP ? GO:0000139 ... P15303 12239560
    50 1m2o:B (2.5) BS02 GNP 3.6.5.- GO:0000139 ... P20606 12239560
    51 1m2o:D (2.5) BS02 GNP 3.6.5.- GO:0000139 ... P20606 12239560
    52 1mh1:A (1.38) BS02 GNP 3.6.5.2 GO:0001764 ... P63000 9033596
    53 1n6h:A (1.51) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 12433916
    54 1n6n:A (1.6) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 12433916
    55 1n6o:A (1.8) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 12433916
    56 1n6p:A (1.54) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 12433916
    57 1n6r:A (1.55) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 12433916
    58 1nf3:A (2.1) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 12606577 MOAD: Kd=50nM
    59 1nf3:B (2.1) BS02 GNP 3.6.5.2 GO:0000139 ... P60953 12606577 MOAD: Kd=50nM
    60 1nvv:Q (2.18) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12628188
    61 1nvw:Q (2.7) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12628188
    62 1ob2:A (3.35) BS05 GNP 3.6.1.48 GO:0003723 ... P0CE48 N/A
    63 1ob5:A (3.1) BS03 GNP 3.6.1.48 GO:0003746 ... Q01698 16257965
    64 1ob5:C (3.1) BS03 GNP 3.6.1.48 GO:0003746 ... Q01698 16257965
    65 1ob5:E (3.1) BS03 GNP 3.6.1.48 GO:0003746 ... Q01698 16257965
    66 1p2s:A (2.45) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12842038
    67 1p2t:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12842038
    68 1p2u:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12842038
    69 1p2v:A (2.3) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 12842038
    70 1puj:A (2.0) BS01 GNP ? GO:0003723 ... O31743 N/A
    71 1qbk:C (3.0) BS02 GNP 3.6.5.- GO:0000054 ... P62826 10353245
    72 1r2q:A (1.05) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 14684892
    73 1r4a:A (2.3) BS02 GNP ? GO:0000139 ... P61212 14718928
    74 1r4a:B (2.3) BS02 GNP ? GO:0000139 ... P61212 14718928
    75 1r4a:C (2.3) BS02 GNP ? GO:0000139 ... P61212 14718928
    76 1r4a:D (2.3) BS02 GNP ? GO:0000139 ... P61212 14718928
    77 1r5o:A (3.2) BS01 GNP 3.6.5.- GO:0000288 ... O74718 15099522
    78 1rrp:A (2.96) BS02 GNP 3.6.5.- GO:0000054 ... P62826 10078529
    79 1rrp:C (2.96) BS02 GNP 3.6.5.- GO:0000054 ... P62826 10078529
    80 1ryh:A (1.75) BS01 GNP 3.6.5.2 GO:0003924 ... P63000 14625275 PDBbind: -logKd/Ki=7.56, Kd=27.6nM
    81 1ryh:B (1.75) BS01 GNP 3.6.5.2 GO:0003924 ... P63000 14625275
    82 1s1c:A (2.6) BS02 GNP 3.6.5.2 GO:0000902 ... P61586 14660612
    83 1s1c:B (2.6) BS02 GNP 3.6.5.2 GO:0000902 ... P61586 14660612
    84 1svs:A (1.5) BS02 GNP 3.6.1.46 GO:0000287 ... P10824 15128951 MOAD: Kd=2.3nM
    85 1sz3:A (1.6) BS01 GNP 3.6.1.61
    3.6.1.69    		 GO:0005524 ... Q9RVK2 15123424
    86 1sz3:A (1.6) BS02 GNP 3.6.1.61
    3.6.1.69    		 GO:0005524 ... Q9RVK2 15123424
    87 1sz3:B (1.6) BS01 GNP 3.6.1.61
    3.6.1.69    		 GO:0005524 ... Q9RVK2 15123424
    88 1sz3:B (1.6) BS02 GNP 3.6.1.61
    3.6.1.69    		 GO:0005524 ... Q9RVK2 15123424
    89 1tq2:A (2.7) BS01 GNP 3.6.5.- GO:0003924 ... Q9QZ85 15350217
    90 1tq2:B (2.7) BS01 GNP 3.6.5.- GO:0003924 ... Q9QZ85 15350217
    91 1tq6:A (2.7) BS02 GNP 3.6.5.- GO:0003924 ... Q9QZ85 15350217
    92 1ttt:A (2.7) BS05 GNP ? GO:0003746 ... Q01698 7491491
    93 1ttt:B (2.7) BS05 GNP ? GO:0003746 ... Q01698 7491491
    94 1ttt:C (2.7) BS05 GNP ? GO:0003746 ... Q01698 7491491
    95 1tu3:A (2.31) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 15378032
    96 1tu3:B (2.31) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 15378032
    97 1tu3:C (2.31) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 15378032
    98 1tu3:D (2.31) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 15378032
    99 1tu3:E (2.31) BS02 GNP 3.6.5.2 GO:0003924 ... P20339 15378032
    100 1u8y:A (1.55) BS01 GNP 3.6.5.2 GO:0003924 ... P63320 15530367
    101 1u8y:B (1.55) BS01 GNP 3.6.5.2 GO:0003924 ... P63320 15530367
    102 1uad:A (2.1) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 12839989 MOAD: Ka=7260000M^-1
    103 1uad:B (2.1) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 12839989 MOAD: Ka=7260000M^-1
    104 1vg8:A (1.7) BS02 GNP 3.6.5.2 GO:0000045 ... P09527 15186776
    105 1vg8:B (1.7) BS02 GNP 3.6.5.2 GO:0000045 ... P09527 15186776
    106 1vg8:C (1.7) BS02 GNP 3.6.5.2 GO:0000045 ... P09527 15186776
    107 1vg8:D (1.7) BS02 GNP 3.6.5.2 GO:0000045 ... P09527 15186776
    108 1wf3:A (1.88) BS02 GNP ? GO:0000028 ... Q5SM23 N/A
    109 1x1s:A (2.2) BS01 GNP 3.6.5.2 GO:0003924 ... O08989 15994326
    110 1x3s:A (1.32) BS02 GNP ? GO:0003924 ... Q9NP72 N/A
    111 1xcm:A (1.84) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 N/A
    112 1xtr:A (2.65) BS02 GNP 3.6.5.- GO:0000139 ... Q15382 15728574
    113 1yu9:A (2.07) BS02 GNP 3.6.5.2 GO:0003924 ... P20338 16034420
    114 1yvd:A (1.93) BS02 GNP ? GO:0003924 ... P35285 16034420
    115 1yzk:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P62491 16034420
    116 1yzl:A (1.85) BS02 GNP ? GO:0003924 ... Q9R0M6 16034420
    117 1yzn:A (2.06) BS02 GNP ? GO:0003924 ... P01123 16034420
    118 1yzq:A (1.78) BS02 GNP ? GO:0003924 ... P20340 16034420
    119 1yzt:A (2.05) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    120 1yzt:B (2.05) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    121 1yzu:A (2.5) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    122 1yzu:B (2.5) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    123 1z06:A (1.81) BS02 GNP ? GO:0003924 ... O35963 16034420
    124 1z07:A (1.81) BS02 GNP 3.6.5.2 GO:0003924 ... P35278 16034420
    125 1z08:A (1.8) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    126 1z08:B (1.8) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    127 1z08:C (1.8) BS01 GNP ? GO:0003924 ... Q9UL25 16034420
    128 1z08:D (1.8) BS02 GNP ? GO:0003924 ... Q9UL25 16034420
    129 1z2c:A (3.0) BS02 GNP ? GO:0000281 ... P08134 15864301
    130 1z2c:C (3.0) BS02 GNP ? GO:0000281 ... P08134 15864301
    131 1zc3:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    132 1zc3:C (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    133 1zc4:A (2.5) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    134 1zc4:C (2.5) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    135 1zw6:A (1.5) BS04 GNP 3.6.5.2 GO:0003924 ... P01112 16531227
    136 221p:A (2.3) BS02 GNP 3.6.5.2 GO:0003924 ... P01112 2199064
    137 2aho:A (3.0) BS03 GNP 3.6.5.3 GO:0000049 ... Q980A5 16407071
    138 2atx:A (2.65) BS02 GNP 3.6.5.2 GO:0003924 ... P17081 16246732
    139 2atx:B (2.65) BS02 GNP 3.6.5.2 GO:0003924 ... P17081 16246732
    140 2bc9:A (2.8) BS02 GNP 3.6.1.-
    3.6.5.-    		 GO:0003924 ... P32455 16511497
    141 2bme:A (1.57) BS01 GNP 3.6.5.2 GO:0003924 ... P20338 15907487
    142 2bme:B (1.57) BS01 GNP 3.6.5.2 GO:0003924 ... P20338 15907487
    143 2bme:C (1.57) BS01 GNP 3.6.5.2 GO:0003924 ... P20338 15907487
    144 2bme:D (1.57) BS01 GNP 3.6.5.2 GO:0003924 ... P20338 15907487
    145 2bv3:A (2.5) BS01 GNP ? GO:0000287 ... P13551 16083884
    146 2bvn:A (2.3) BS01 GNP 3.6.1.48 GO:0003723 ... P0CE48 16257965
    147 2bvn:B (2.3) BS01 GNP 3.6.1.48 GO:0003723 ... P0CE48 16257965
    148 2c77:A (1.6) BS02 GNP 3.1.5.1 GO:0003746 ... P60339 16734421
    149 2c78:A (1.4) BS01 GNP 3.1.5.1 GO:0003723 ... Q5SHN6 16734421
    150 2cl0:X (1.8) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 16698776
    151 2dxf:A (1.7) BS01 GNP 2.7.4.6 GO:0004550 ... O58429 N/A
    152 2ew1:A (2.0) BS02 GNP ? GO:0000139 ... Q15771 N/A
    153 2f9m:A (1.95) BS02 GNP 3.6.5.2 GO:0001881 ... Q15907 16545962
    154 2fg5:A (2.801) BS02 GNP ? GO:0003924 ... Q13636 N/A
    155 2g6b:A (2.0) BS02 GNP ? GO:0003924 ... Q9ULW5 N/A
    156 2gco:A (1.4) BS02 GNP ? GO:0000281 ... P08134 17497936
    157 2gco:B (1.4) BS02 GNP ? GO:0000281 ... P08134 17497936
    158 2ic5:A (1.9) BS01 GNP 3.6.5.2 GO:0003924 ... P60763 N/A
    159 2j7p:A (1.97) BS01 GNP 3.6.5.4 GO:0003924 ... O07347 17184999
    160 2j7p:A (1.97) BS02 GNP 3.6.5.4 GO:0003924 ... O07347 17184999
    161 2j7p:B (1.97) BS01 GNP 3.6.5.4 GO:0003924 ... O07347 17184999
    162 2j7p:B (1.97) BS02 GNP 3.6.5.4 GO:0003924 ... O07347 17184999
    163 2j7p:D (1.97) BS01 GNP 3.6.5.4 GO:0003924 ... P83749 17184999
    164 2j7p:D (1.97) BS02 GNP 3.6.5.4 GO:0003924 ... P83749 17184999
    165 2j7p:E (1.97) BS01 GNP 3.6.5.4 GO:0003924 ... P83749 17184999
    166 2j7p:E (1.97) BS02 GNP 3.6.5.4 GO:0003924 ... P83749 17184999
    167 2ke5:A (-1.00) BS01 GNP 3.6.5.2 GO:0003924 ... P11234 19166349
    168 2kwi:A (-1.00) BS01 GNP 3.6.5.2 GO:0003924 ... P11234 20696399
    169 2lcf:A (-1.00) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 21930707
    170 2lwi:A (-1.00) BS01 GNP 3.6.5.2 GO:0003924 ... P01112 23630290
    171 2msd:B (-1.00) BS03 GNP 3.6.5.2 GO:0000139 ... P01116 25941399
    172 2mse:B (-1.00) BS01 GNP 3.6.5.2 GO:0000139 ... P01116 25941399
    173 2ocb:A (2.2) BS02 GNP ? GO:0003924 ... Q9NP90 N/A
    174 2p8w:S (11.3) BS01 GNP ? N/A P60339 17446867
    175 2p8w:T (11.3) BS01 GNP 3.6.5.- GO:0003746 ... P32324 17446867
    176 2p8x:S (9.7) BS01 GNP ? N/A P60339 17446867
    177 2p8x:T (9.7) BS02 GNP 3.6.5.- GO:0003746 ... P32324 17446867
    178 2p8z:S (8.9) BS01 GNP ? N/A P60339 17446867
    179 2p8z:T (8.9) BS03 GNP 3.6.5.- GO:0003746 ... P32324 17446867
    180 2pmd:A (2.65) BS02 GNP 3.6.5.3 GO:0000049 ... Q980A5 17825838
    181 2px0:A (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    182 2px0:B (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    183 2px0:B (3.0) BS02 GNP ? GO:0003924 ... Q01960 17699634
    184 2px0:C (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    185 2px0:D (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    186 2px0:E (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    187 2px0:F (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    188 2px0:G (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    189 2px0:H (3.0) BS01 GNP ? GO:0003924 ... Q01960 17699634
    190 2q3f:A (2.1) BS02 GNP 3.6.5.- GO:0005525 ... Q9NQL2 N/A
    191 2q3f:B (2.1) BS02 GNP 3.6.5.- GO:0005525 ... Q9NQL2 N/A
    192 2q9b:A (2.3) BS01 GNP 3.6.5.4 GO:0003924 ... P83749 17622352
    193 2q9c:A (2.2) BS01 GNP 3.6.5.4 GO:0003924 ... P83749 17622352
    194 2qtv:B (2.5) BS02 GNP 3.6.5.- GO:0003924 ... P20606 17981133
    195 2rex:B (2.3) BS03 GNP ? GO:0003924 ... Q92730 N/A
    196 2rex:D (2.3) BS03 GNP ? GO:0003924 ... Q92730 N/A
    197 2rga:A (1.9) BS03 GNP 3.6.5.2 GO:0003924 ... P01112 18073111
    198 2rgb:A (1.35) BS03 GNP 3.6.5.2 GO:0003924 ... P01112 18073111
    199 2rgc:A (1.6) BS03 GNP 3.6.5.2 GO:0003924 ... P01112 18073111
    200 2rgd:A (2.0) BS03 GNP 3.6.5.2 GO:0003924 ... P01112 18073111
    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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