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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 594392 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
    202801 5dat:O7 (3.15) BS02 rna ? GO:0000448 ... P49166 N/A
    202802 5dat:O7 (3.15) BS03 rna ? GO:0000448 ... P49166 N/A
    202803 5dat:O7 (3.15) BS04 OHX ? GO:0000448 ... P49166 N/A
    202804 5dat:O7 (3.15) BS05 ZN ? GO:0000448 ... P49166 N/A
    202805 5dat:O7 (3.15) BS06 MG ? GO:0000448 ... P49166 N/A
    202806 5dat:O7 (3.15) BS07 OHX ? GO:0000448 ... P49166 N/A
    202807 5dat:O7 (3.15) BS08 OHX ? GO:0000448 ... P49166 N/A
    202808 5dat:O8 (3.15) BS01 rna ? GO:0002181 ... P49167 N/A
    202809 5dat:O9 (3.15) BS01 rna ? GO:0002181 ... P04650 N/A
    202810 5dat:O9 (3.15) BS02 rna ? GO:0002181 ... P04650 N/A
    202811 5dat:O9 (3.15) BS03 MG ? GO:0002181 ... P04650 N/A
    202812 5dat:Q0 (3.15) BS01 rna ? GO:0003735 ... P0CH08 N/A
    202813 5dat:Q0 (3.15) BS02 ZN ? GO:0003735 ... P0CH08 N/A
    202814 5dat:Q0 (3.15) BS03 MG ? GO:0003735 ... P0CH08 N/A
    202815 5dat:Q2 (3.15) BS01 rna ? GO:0002181 ... P0CX27 N/A
    202816 5dat:Q2 (3.15) BS02 ZN ? GO:0002181 ... P0CX27 N/A
    202817 5dat:Q2 (3.15) BS03 OHX ? GO:0002181 ... P0CX27 N/A
    202818 5dat:Q3 (3.15) BS01 rna ? GO:0002181 ... P0CX25 N/A
    202819 5dat:Q3 (3.15) BS02 ZN ? GO:0002181 ... P0CX25 N/A
    202820 5dat:S0 (3.15) BS01 rna ? GO:0000028 ... P32905 N/A
    202821 5dat:S1 (3.15) BS01 rna ? GO:0000462 ... P33442 N/A
    202822 5dat:S2 (3.15) BS01 rna ? GO:0000054 ... P25443 N/A
    202823 5dat:S3 (3.15) BS01 rna ? GO:0000054 ... P05750 N/A
    202824 5dat:S4 (3.15) BS01 rna ? GO:0002181 ... P0CX35 N/A
    202825 5dat:S5 (3.15) BS01 rna ? GO:0000028 ... P26783 N/A
    202826 5dat:S6 (3.15) BS01 rna ? GO:0000462 ... P0CX37 N/A
    202827 5dat:S7 (3.15) BS01 rna ? GO:0002181 ... P26786 N/A
    202828 5dat:S8 (3.15) BS01 rna ? GO:0000462 ... P0CX39 N/A
    202829 5dat:S8 (3.15) BS02 rna ? GO:0000462 ... P0CX39 N/A
    202830 5dat:S8 (3.15) BS03 OHX ? GO:0000462 ... P0CX39 N/A
    202831 5dat:S9 (3.15) BS01 rna ? GO:0000462 ... O13516 N/A
    202832 5dat:S9 (3.15) BS02 OHX ? GO:0000462 ... O13516 N/A
    202833 5dat:SM (3.15) BS01 rna ? GO:0000723 ... P39015 N/A
    202834 5dat:SM (3.15) BS02 rna ? GO:0000723 ... P39015 N/A
    202835 5dat:SR (3.15) BS01 rna ? GO:0001965 ... P38011 N/A
    202836 5dat:SR (3.15) BS02 OHX ? GO:0001965 ... P38011 N/A
    202837 5dat:c0 (3.15) BS01 rna ? GO:0000054 ... Q08745 N/A
    202838 5dat:c1 (3.15) BS01 rna ? GO:0000028 ... P0CX47 N/A
    202839 5dat:c2 (3.15) BS01 rna ? GO:0003735 ... P48589 N/A
    202840 5dat:c3 (3.15) BS01 rna ? GO:0000462 ... P05756 N/A
    202841 5dat:c3 (3.15) BS02 rna ? GO:0000462 ... P05756 N/A
    202842 5dat:c3 (3.15) BS03 OHX ? GO:0000462 ... P05756 N/A
    202843 5dat:c4 (3.15) BS01 rna ? GO:0000028 ... P06367 N/A
    202844 5dat:c5 (3.15) BS01 rna ? GO:0000028 ... Q01855 N/A
    202845 5dat:c5 (3.15) BS02 OHX ? GO:0000028 ... Q01855 N/A
    202846 5dat:c6 (3.15) BS01 rna ? GO:0000462 ... P0CX51 N/A
    202847 5dat:c7 (3.15) BS01 rna ? GO:0000028 ... P02407 N/A
    202848 5dat:c8 (3.15) BS01 rna ? GO:0000054 ... P0CX55 N/A
    202849 5dat:c8 (3.15) BS02 MG ? GO:0000054 ... P0CX55 N/A
    202850 5dat:c9 (3.15) BS01 rna ? GO:0000028 ... P07280 N/A
    202851 5dat:c9 (3.15) BS02 MG ? GO:0000028 ... P07280 N/A
    202852 5dat:d0 (3.15) BS01 rna ? GO:0000462 ... P38701 N/A
    202853 5dat:d1 (3.15) BS01 rna ? GO:0000447 ... P0C0V8 N/A
    202854 5dat:d2 (3.15) BS01 rna ? GO:0003735 ... P0C0W1 N/A
    202855 5dat:d3 (3.15) BS01 rna ? GO:0000462 ... P0CX29 N/A
    202856 5dat:d4 (3.15) BS01 rna ? GO:0000462 ... P0CX31 N/A
    202857 5dat:d5 (3.15) BS01 rna ? GO:0002181 ... Q3E792 N/A
    202858 5dat:d6 (3.15) BS01 rna ? GO:0003735 ... P39939 N/A
    202859 5dat:d6 (3.15) BS02 ZN ? GO:0003735 ... P39939 N/A
    202860 5dat:d6 (3.15) BS03 MG ? GO:0003735 ... P39939 N/A
    202861 5dat:d7 (3.15) BS01 rna ? GO:0000028 ... P35997 N/A
    202862 5dat:d8 (3.15) BS01 rna ? GO:0000028 ... Q3E7X9 N/A
    202863 5dat:d9 (3.15) BS01 rna ? GO:0002181 ... P41057 N/A
    202864 5dat:d9 (3.15) BS02 ZN ? GO:0002181 ... P41057 N/A
    202865 5dat:e0 (3.15) BS01 rna ? GO:0002181 ... P0CX33 N/A
    202866 5dat:e1 (3.15) BS01 rna ? GO:0003735 ... P05759 N/A
    202867 5dat:f (3.15) BS01 rna ? GO:0002182 ... P23301 N/A
    202868 5dat:l2 (3.15) BS01 rna ? GO:0002181 ... P0CX45 N/A
    202869 5dat:l2 (3.15) BS02 rna ? GO:0002181 ... P0CX45 N/A
    202870 5dat:l2 (3.15) BS03 MG ? GO:0002181 ... P0CX45 N/A
    202871 5dat:l2 (3.15) BS04 MG ? GO:0002181 ... P0CX45 N/A
    202872 5dat:l2 (3.15) BS05 MG ? GO:0002181 ... P0CX45 N/A
    202873 5dat:l3 (3.15) BS01 rna ? GO:0000027 ... P14126 N/A
    202874 5dat:l3 (3.15) BS02 MG ? GO:0000027 ... P14126 N/A
    202875 5dat:l3 (3.15) BS03 OHX ? GO:0000027 ... P14126 N/A
    202876 5dat:l3 (3.15) BS04 OHX ? GO:0000027 ... P14126 N/A
    202877 5dat:l4 (3.15) BS01 rna ? GO:0002181 ... P10664 N/A
    202878 5dat:l4 (3.15) BS02 rna ? GO:0002181 ... P10664 N/A
    202879 5dat:l4 (3.15) BS03 OHX ? GO:0002181 ... P10664 N/A
    202880 5dat:l5 (3.15) BS01 rna ? GO:0000027 ... P26321 N/A
    202881 5dat:l5 (3.15) BS02 rna ? GO:0000027 ... P26321 N/A
    202882 5dat:l5 (3.15) BS03 MG ? GO:0000027 ... P26321 N/A
    202883 5dat:l5 (3.15) BS04 OHX ? GO:0000027 ... P26321 N/A
    202884 5dat:l5 (3.15) BS05 OHX ? GO:0000027 ... P26321 N/A
    202885 5dat:l6 (3.15) BS01 rna ? GO:0000027 ... Q02326 N/A
    202886 5dat:l7 (3.15) BS01 rna ? GO:0000463 ... P05737 N/A
    202887 5dat:l7 (3.15) BS02 rna ? GO:0000463 ... P05737 N/A
    202888 5dat:l7 (3.15) BS03 OHX ? GO:0000463 ... P05737 N/A
    202889 5dat:l8 (3.15) BS01 rna ? GO:0000470 ... P17076 N/A
    202890 5dat:l8 (3.15) BS02 rna ? GO:0000470 ... P17076 N/A
    202891 5dat:l9 (3.15) BS01 rna ? GO:0002181 ... P05738 N/A
    202892 5dat:m0 (3.15) BS01 rna ? GO:0000027 ... P41805 N/A
    202893 5dat:m0 (3.15) BS02 rna ? GO:0000027 ... P41805 N/A
    202894 5dat:m0 (3.15) BS03 MG ? GO:0000027 ... P41805 N/A
    202895 5dat:m0 (3.15) BS04 OHX ? GO:0000027 ... P41805 N/A
    202896 5dat:m0 (3.15) BS05 OHX ? GO:0000027 ... P41805 N/A
    202897 5dat:m0 (3.15) BS06 OHX ? GO:0000027 ... P41805 N/A
    202898 5dat:m1 (3.15) BS01 rna ? GO:0000027 ... Q3E757 N/A
    202899 5dat:m1 (3.15) BS02 rna ? GO:0000027 ... Q3E757 N/A
    202900 5dat:m3 (3.15) BS01 rna ? GO:0002181 ... Q12690 N/A
    202901 5dat:m3 (3.15) BS02 rna ? GO:0002181 ... Q12690 N/A
    202902 5dat:m4 (3.15) BS01 rna ? GO:0000027 ... P36105 N/A
    202903 5dat:m5 (3.15) BS01 rna ? GO:0002181 ... P05748 N/A
    202904 5dat:m5 (3.15) BS02 rna ? GO:0002181 ... P05748 N/A
    202905 5dat:m5 (3.15) BS03 OHX ? GO:0002181 ... P05748 N/A
    202906 5dat:m5 (3.15) BS04 MG ? GO:0002181 ... P05748 N/A
    202907 5dat:m6 (3.15) BS01 rna ? GO:0000470 ... P26784 N/A
    202908 5dat:m6 (3.15) BS02 MG ? GO:0000470 ... P26784 N/A
    202909 5dat:m7 (3.15) BS01 rna ? GO:0000448 ... P05740 N/A
    202910 5dat:m7 (3.15) BS02 rna ? GO:0000448 ... P05740 N/A
    202911 5dat:m7 (3.15) BS03 MG ? GO:0000448 ... P05740 N/A
    202912 5dat:m8 (3.15) BS01 rna ? GO:0002181 ... P0CX49 N/A
    202913 5dat:m9 (3.15) BS01 rna ? GO:0002181 ... P0CX82 N/A
    202914 5dat:m9 (3.15) BS02 rna ? GO:0002181 ... P0CX82 N/A
    202915 5dat:n0 (3.15) BS01 rna ? GO:0002181 ... P0CX23 N/A
    202916 5dat:n0 (3.15) BS02 rna ? GO:0002181 ... P0CX23 N/A
    202917 5dat:n1 (3.15) BS01 rna ? GO:0002181 ... Q02753 N/A
    202918 5dat:n1 (3.15) BS02 rna ? GO:0002181 ... Q02753 N/A
    202919 5dat:n1 (3.15) BS03 MG ? GO:0002181 ... Q02753 N/A
    202920 5dat:n1 (3.15) BS04 OHX ? GO:0002181 ... Q02753 N/A
    202921 5dat:n2 (3.15) BS01 rna ? GO:0002181 ... P05749 N/A
    202922 5dat:n3 (3.15) BS01 rna ? GO:0002181 ... P0CX41 N/A
    202923 5dat:n3 (3.15) BS02 rna ? GO:0002181 ... P0CX41 N/A
    202924 5dat:n4 (3.15) BS01 rna ? GO:0002181 ... P04449 N/A
    202925 5dat:n4 (3.15) BS02 rna ? GO:0002181 ... P04449 N/A
    202926 5dat:n5 (3.15) BS01 rna ? GO:0000027 ... P04456 N/A
    202927 5dat:n5 (3.15) BS02 rna ? GO:0000027 ... P04456 N/A
    202928 5dat:n6 (3.15) BS01 rna ? GO:0002181 ... P05743 N/A
    202929 5dat:n6 (3.15) BS02 rna ? GO:0002181 ... P05743 N/A
    202930 5dat:n7 (3.15) BS01 rna ? GO:0002181 ... P0C2H6 N/A
    202931 5dat:n8 (3.15) BS01 rna ? GO:0002181 ... P02406 N/A
    202932 5dat:n9 (3.15) BS01 rna ? GO:0002181 ... P05747 N/A
    202933 5dat:n9 (3.15) BS02 OHX ? GO:0002181 ... P05747 N/A
    202934 5dat:o0 (3.15) BS01 rna ? GO:0002181 ... P14120 N/A
    202935 5dat:o1 (3.15) BS01 rna ? GO:0002181 ... P0C2H8 N/A
    202936 5dat:o2 (3.15) BS01 rna ? GO:0002181 ... P38061 N/A
    202937 5dat:o2 (3.15) BS02 MG ? GO:0002181 ... P38061 N/A
    202938 5dat:o3 (3.15) BS01 rna ? GO:0000027 ... P05744 N/A
    202939 5dat:o3 (3.15) BS02 MG ? GO:0000027 ... P05744 N/A
    202940 5dat:o3 (3.15) BS03 OHX ? GO:0000027 ... P05744 N/A
    202941 5dat:o4 (3.15) BS01 rna ? GO:0002181 ... P87262 N/A
    202942 5dat:o5 (3.15) BS01 rna ? GO:0000463 ... P0CX84 N/A
    202943 5dat:o5 (3.15) BS02 rna ? GO:0000463 ... P0CX84 N/A
    202944 5dat:o6 (3.15) BS01 rna ? GO:0002181 ... P05745 N/A
    202945 5dat:o7 (3.15) BS01 rna ? GO:0000448 ... P49166 N/A
    202946 5dat:o7 (3.15) BS02 rna ? GO:0000448 ... P49166 N/A
    202947 5dat:o7 (3.15) BS03 ZN ? GO:0000448 ... P49166 N/A
    202948 5dat:o7 (3.15) BS04 OHX ? GO:0000448 ... P49166 N/A
    202949 5dat:o8 (3.15) BS01 rna ? GO:0002181 ... P49167 N/A
    202950 5dat:o9 (3.15) BS01 rna ? GO:0002181 ... P04650 N/A
    202951 5dat:o9 (3.15) BS02 rna ? GO:0002181 ... P04650 N/A
    202952 5dat:o9 (3.15) BS03 OHX ? GO:0002181 ... P04650 N/A
    202953 5dat:q0 (3.15) BS01 rna ? GO:0003735 ... P0CH08 N/A
    202954 5dat:q0 (3.15) BS02 ZN ? GO:0003735 ... P0CH08 N/A
    202955 5dat:q2 (3.15) BS01 rna ? GO:0002181 ... P0CX27 N/A
    202956 5dat:q2 (3.15) BS02 ZN ? GO:0002181 ... P0CX27 N/A
    202957 5dat:q2 (3.15) BS03 OHX ? GO:0002181 ... P0CX27 N/A
    202958 5dat:q3 (3.15) BS01 rna ? GO:0002181 ... P0CX25 N/A
    202959 5dat:q3 (3.15) BS02 rna ? GO:0002181 ... P0CX25 N/A
    202960 5dat:q3 (3.15) BS03 ZN ? GO:0002181 ... P0CX25 N/A
    202961 5dat:s0 (3.15) BS01 rna ? GO:0000028 ... P32905 N/A
    202962 5dat:s1 (3.15) BS01 rna ? GO:0000462 ... P33442 N/A
    202963 5dat:s1 (3.15) BS02 rna ? GO:0000462 ... P33442 N/A
    202964 5dat:s1 (3.15) BS03 OHX ? GO:0000462 ... P33442 N/A
    202965 5dat:s2 (3.15) BS01 rna ? GO:0000054 ... P25443 N/A
    202966 5dat:s3 (3.15) BS01 rna ? GO:0000054 ... P05750 N/A
    202967 5dat:s4 (3.15) BS01 rna ? GO:0002181 ... P0CX35 N/A
    202968 5dat:s4 (3.15) BS02 MG ? GO:0002181 ... P0CX35 N/A
    202969 5dat:s5 (3.15) BS01 rna ? GO:0000028 ... P26783 N/A
    202970 5dat:s5 (3.15) BS02 MG ? GO:0000028 ... P26783 N/A
    202971 5dat:s6 (3.15) BS01 rna ? GO:0000462 ... P0CX37 N/A
    202972 5dat:s7 (3.15) BS01 rna ? GO:0002181 ... P26786 N/A
    202973 5dat:s8 (3.15) BS01 rna ? GO:0000462 ... P0CX39 N/A
    202974 5dat:s8 (3.15) BS02 rna ? GO:0000462 ... P0CX39 N/A
    202975 5dat:s8 (3.15) BS03 OHX ? GO:0000462 ... P0CX39 N/A
    202976 5dat:s9 (3.15) BS01 rna ? GO:0000462 ... O13516 N/A
    202977 5dat:s9 (3.15) BS02 OHX ? GO:0000462 ... O13516 N/A
    202978 5dat:sM (3.15) BS01 rna ? GO:0000723 ... P39015 N/A
    202979 5dat:sM (3.15) BS02 rna ? GO:0000723 ... P39015 N/A
    202980 5dat:sM (3.15) BS03 MG ? GO:0000723 ... P39015 N/A
    202981 5dat:sR (3.15) BS01 rna ? GO:0001965 ... P38011 N/A
    202982 5dat:sR (3.15) BS02 OHX ? GO:0001965 ... P38011 N/A
    202983 5db0:A (1.5) BS01 58P ? GO:0005634 ... O00255 26744767 MOAD: ic50=46nM
    PDBbind: -logKd/Ki=7.43, IC50=37nM
    202984 5db0:A (1.5) BS02 6E6 ? GO:0005634 ... O00255 26744767 MOAD: ic50=42nM
    202985 5db1:A (1.86) BS01 58O ? GO:0005634 ... O00255 26744767 MOAD: ic50=22nM
    PDBbind: -logKd/Ki=7.66, IC50=22nM
    202986 5db2:A (1.54) BS01 58R ? GO:0005634 ... O00255 26744767 MOAD: ic50=25nM
    PDBbind: -logKd/Ki=7.60, IC50=25nM
    202987 5db3:A (1.71) BS01 58Q ? GO:0005634 ... O00255 26744767 MOAD: ic50=12nM
    PDBbind: -logKd/Ki=7.92, IC50=12nM
    202988 5db5:A (2.75) BS01 PLP 2.8.1.7
    3.13.1.-
    4.4.1.16    		 GO:0001887 ... P77444 N/A
    202989 5db5:A (2.75) BS02 CYS 2.8.1.7
    3.13.1.-
    4.4.1.16    		 GO:0001887 ... P77444 N/A
    202990 5db5:A (2.75) BS03 PLP 2.8.1.7
    3.13.1.-
    4.4.1.16    		 GO:0001887 ... P77444 N/A
    202991 5db5:B (2.75) BS01 PLP 2.8.1.7
    3.13.1.-
    4.4.1.16    		 GO:0001887 ... P77444 N/A
    202992 5db5:B (2.75) BS02 PLP 2.8.1.7
    3.13.1.-
    4.4.1.16    		 GO:0001887 ... P77444 N/A
    202993 5db6:A (2.83) BS01 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202994 5db6:A (2.83) BS02 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202995 5db6:A (2.83) BS03 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202996 5db7:A (2.209) BS01 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202997 5db7:A (2.209) BS02 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202998 5db7:A (2.209) BS03 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    202999 5db8:A (2.547) BS01 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    203000 5db8:A (2.547) BS02 dna 2.7.7.7
    4.2.99.-
    4.2.99.18    		 GO:0001701 ... P06746 26517568
    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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