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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.
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  • 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
    41801 1yr3:F (3.2) BS01 XAN 2.4.2.1 GO:0003824 ... P45563 15808857
    41802 1yr5:A (1.7) BS01 peptide ? GO:0000086 ... P0DP23 N/A
    41803 1yr5:A (1.7) BS02 CA ? GO:0000086 ... P0DP23 N/A
    41804 1yr5:A (1.7) BS03 CA ? GO:0000086 ... P0DP23 N/A
    41805 1yr5:A (1.7) BS04 CA ? GO:0000086 ... P0DP23 N/A
    41806 1yr5:A (1.7) BS05 CA ? GO:0000086 ... P0DP23 N/A
    41807 1yrc:A (1.4) BS01 HEM 1.14.15.1 GO:0004497 ... P00183 15858263
    41808 1yrc:A (1.4) BS02 CAM 1.14.15.1 GO:0004497 ... P00183 15858263
    41809 1yrd:A (1.7) BS01 HEM 1.14.15.1 GO:0004497 ... P00183 15858263
    41810 1yrd:A (1.7) BS02 CAM 1.14.15.1 GO:0004497 ... P00183 15858263
    41811 1yrh:A (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41812 1yrh:B (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41813 1yrh:C (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41814 1yrh:D (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41815 1yrh:E (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41816 1yrh:F (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41817 1yrh:G (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41818 1yrh:H (3.11) BS01 FMN 1.6.5.2 GO:0000166 ... Q9RYU4 16322580
    41819 1yro:A (1.9) BS01 CA ? GO:0004461 ... P29752 15736931
    41820 1yro:C (1.9) BS01 CA ? GO:0004461 ... P29752 15736931
    41821 1yrq:A (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41822 1yrq:A (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41823 1yrq:A (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41824 1yrq:B (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41825 1yrq:B (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41826 1yrq:B (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41827 1yrq:C (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41828 1yrq:C (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41829 1yrq:C (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41830 1yrq:D (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41831 1yrq:D (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41832 1yrq:D (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41833 1yrq:F (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41834 1yrq:F (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41835 1yrq:F (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41836 1yrq:G (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41837 1yrq:G (2.1) BS02 F3S 1.12.2.1 GO:0008901 ... P18187 15803334
    41838 1yrq:G (2.1) BS03 SF4 1.12.2.1 GO:0008901 ... P18187 15803334
    41839 1yrq:H (2.1) BS01 F3S 1.12.2.1 GO:0008901 ... P18188 15803334
    41840 1yrq:H (2.1) BS02 SF4 1.12.2.1 GO:0008901 ... P18188 15803334
    41841 1yrq:H (2.1) BS03 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41842 1yrq:H (2.1) BS04 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41843 1yrq:I (2.1) BS01 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41844 1yrq:I (2.1) BS02 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41845 1yrq:J (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18188 15803334
    41846 1yrq:J (2.1) BS02 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41847 1yrq:J (2.1) BS03 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41848 1yrq:K (2.1) BS01 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41849 1yrq:K (2.1) BS02 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41850 1yrq:M (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18188 15803334
    41851 1yrq:M (2.1) BS02 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41852 1yrq:M (2.1) BS03 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41853 1yrq:N (2.1) BS01 SF4 1.12.2.1 GO:0008901 ... P18188 15803334
    41854 1yrq:N (2.1) BS02 MG 1.12.2.1 GO:0008901 ... P18188 15803334
    41855 1yrq:N (2.1) BS03 FCO 1.12.2.1 GO:0008901 ... P18188 15803334
    41856 1yrr:A (2.0) BS01 PO4 3.5.1.25 GO:0006040 ... P0AF18 16630633
    41857 1yrr:B (2.0) BS01 PO4 3.5.1.25 GO:0006040 ... P0AF18 16630633
    41858 1yry:E (2.8) BS01 MSG 2.4.2.1 GO:0000255 ... P00491 16154528
    41859 1ys1:X (1.1) BS01 CA 3.1.1.3 GO:0004806 ... P22088 15850979
    41860 1ys1:X (1.1) BS02 2HR 3.1.1.3 GO:0004806 ... P22088 15850979
    41861 1ys2:X (1.5) BS01 CA 3.1.1.3 GO:0004806 ... P22088 15850979
    41862 1ys2:X (1.5) BS02 2HS 3.1.1.3 GO:0004806 ... P22088 15850979
    41863 1ys6:A (1.77) BS01 CA ? GO:0000156 ... P9WGM1 N/A
    41864 1ys6:B (1.77) BS01 CA ? GO:0000156 ... P9WGM1 N/A
    41865 1ys7:A (1.58) BS01 MG ? GO:0000156 ... P9WGM1 16434396
    41866 1ys7:B (1.58) BS01 MG ? GO:0000156 ... P9WGM1 16434396
    41867 1ysb:A (1.7) BS01 ZN 3.5.4.1 GO:0003824 ... Q12178 15879217
    41868 1ysb:B (1.7) BS01 ZN 3.5.4.1 GO:0003824 ... Q12178 15879217
    41869 1ysd:A (1.9) BS01 ZN 3.5.4.1 GO:0003824 ... Q12178 15879217
    41870 1ysd:B (1.9) BS01 ZN 3.5.4.1 GO:0003824 ... Q12178 15879217
    41871 1ysh:C (9.5) BS01 rna ? GO:0003723 ... Q5I7K9 15864315
    41872 1ysh:D (9.5) BS01 rna ? GO:0003735 ... P0DKK1 15864315
    41873 1ysh:D (9.5) BS02 rna ? GO:0003735 ... P0DKK1 15864315
    41874 1ysh:E (9.5) BS01 rna ? GO:0003735 ... Q69UI2 15864315
    41875 1ysh:E (9.5) BS02 rna ? GO:0003735 ... Q69UI2 15864315
    41876 1yso:A (1.73) BS01 CU1 1.15.1.1 GO:0004784 ... P00445 8652572
    41877 1yso:A (1.73) BS02 ZN 1.15.1.1 GO:0004784 ... P00445 8652572
    41878 1yst:L (3.0) BS01 BCL ? GO:0009772 ... P0C0Y8 15299304
    41879 1yst:L (3.0) BS02 BCL ? GO:0009772 ... P0C0Y8 15299304
    41880 1yst:L (3.0) BS03 BPH ? GO:0009772 ... P0C0Y8 15299304
    41881 1yst:L (3.0) BS04 U10 ? GO:0009772 ... P0C0Y8 15299304
    41882 1yst:L (3.0) BS05 MN ? GO:0009772 ... P0C0Y8 15299304
    41883 1yst:L (3.0) BS06 BCL ? GO:0009772 ... P0C0Y8 15299304
    41884 1yst:L (3.0) BS07 BCL ? GO:0009772 ... P0C0Y8 15299304
    41885 1yst:L (3.0) BS08 BPH ? GO:0009772 ... P0C0Y8 15299304
    41886 1yst:M (3.0) BS01 BCL ? GO:0009772 ... P0C0Y9 15299304
    41887 1yst:M (3.0) BS02 BPH ? GO:0009772 ... P0C0Y9 15299304
    41888 1yst:M (3.0) BS03 MN ? GO:0009772 ... P0C0Y9 15299304
    41889 1yst:M (3.0) BS04 BCL ? GO:0009772 ... P0C0Y9 15299304
    41890 1yst:M (3.0) BS05 BCL ? GO:0009772 ... P0C0Y9 15299304
    41891 1yst:M (3.0) BS06 BPH ? GO:0009772 ... P0C0Y9 15299304
    41892 1yst:M (3.0) BS07 SPO ? GO:0009772 ... P0C0Y9 15299304
    41893 1yst:M (3.0) BS08 U10 ? GO:0009772 ... P0C0Y9 15299304
    41894 1ysx:A (-1.00) BS01 4EB ? GO:0005615 ... P02768 15902208
    41895 1yt3:A (1.6) BS01 ZN 3.1.13.5 GO:0000166 ... P09155 16004870
    41896 1ytc:A (1.8) BS01 HEC ? GO:0005739 ... P00045 8639684
    41897 1ytf:C (2.5) BS01 dna ? GO:0005672 ... P32773 8610010 PDBbind: Kd=20pM
    41898 1ytm:A (2.2) BS01 MN 4.1.1.49 GO:0004611 ... O09460 15890557
    41899 1ytm:A (2.2) BS02 ATP 4.1.1.49 GO:0004611 ... O09460 15890557
    41900 1ytm:A (2.2) BS03 OXD 4.1.1.49 GO:0004611 ... O09460 15890557
    41901 1ytm:B (2.2) BS01 MN 4.1.1.49 GO:0004611 ... O09460 15890557
    41902 1ytm:B (2.2) BS02 ATP 4.1.1.49 GO:0004611 ... O09460 15890557
    41903 1ytm:B (2.2) BS03 OXD 4.1.1.49 GO:0004611 ... O09460 15890557
    41904 1ytv:A (1.8) BS01 peptide ? GO:0005515 ... P0AEX9 16511036
    41905 1ytv:A (1.8) BS02 GLC ? GO:0005515 ... P0AEX9 16511036
    41906 1ytv:A (1.8) BS03 GLC ? GO:0005515 ... P0AEX9 16511036
    41907 1ytv:B (1.8) BS01 peptide ? GO:0005515 ... P0AEX9 16511036
    41908 1ytv:B (1.8) BS02 GLC ? GO:0005515 ... P0AEX9 16511036
    41909 1ytv:B (1.8) BS03 GLC ? GO:0005515 ... P0AEX9 16511036
    41910 1yty:A (2.29) BS01 rna ? GO:0003676 ... P05455 16387655
    41911 1yty:A (2.29) BS02 rna ? GO:0003676 ... P05455 16387655
    41912 1yty:B (2.29) BS01 rna ? GO:0003676 ... P05455 16387655
    41913 1yty:B (2.29) BS02 rna ? GO:0003676 ... P05455 16387655
    41914 1ytz:C (3.0) BS01 CA ? GO:0003009 ... P02588 15784741
    41915 1ytz:C (3.0) BS02 CA ? GO:0003009 ... P02588 15784741
    41916 1ytz:C (3.0) BS03 CA ? GO:0003009 ... P02588 15784741
    41917 1ytz:C (3.0) BS04 CA ? GO:0003009 ... P02588 15784741
    41918 1ytz:C (3.0) BS05 DR6 ? GO:0003009 ... P02588 15784741
    41919 1ytz:I (3.0) BS01 DR6 ? GO:0003009 ... P68246 15784741
    41920 1ytz:I (3.0) BS02 DR6 ? GO:0003009 ... P68246 15784741
    41921 1ytz:T (3.0) BS01 DR6 ? GO:0005861 ... P12620 15784741
    41922 1yu0:A (1.56) BS01 CA ? GO:0005515 ... Q775D6 16170324
    41923 1yu4:A (1.87) BS01 MG ? GO:0005515 ... Q775D6 16170324
    41924 1yu4:B (1.87) BS01 MG ? GO:0005515 ... Q775D6 16170324
    41925 1yu4:C (1.87) BS01 MG ? GO:0005515 ... Q775D6 16170324
    41926 1yut:A (-1.00) BS01 CA ? GO:0001819 ... Q99584 16145699
    41927 1yut:A (-1.00) BS02 CA ? GO:0001819 ... Q99584 16145699
    41928 1yut:B (-1.00) BS01 CA ? GO:0001819 ... Q99584 16145699
    41929 1yut:B (-1.00) BS02 CA ? GO:0001819 ... Q99584 16145699
    41930 1yuu:A (-1.00) BS01 CA ? GO:0001819 ... Q99584 16145699
    41931 1yuu:A (-1.00) BS02 CA ? GO:0001819 ... Q99584 16145699
    41932 1yuu:B (-1.00) BS01 CA ? GO:0001819 ... Q99584 16145699
    41933 1yuu:B (-1.00) BS02 CA ? GO:0001819 ... Q99584 16145699
    41934 1yux:A (1.6) BS01 FE ? GO:0005506 ... P30820 15895271
    41935 1yux:A (1.6) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41936 1yux:A (1.6) BS03 FE ? GO:0005506 ... P30820 15895271
    41937 1yux:B (1.6) BS01 FE ? GO:0005506 ... P30820 15895271
    41938 1yux:B (1.6) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41939 1yux:B (1.6) BS03 FE ? GO:0005506 ... P30820 15895271
    41940 1yuz:A (1.4) BS01 FE ? GO:0005506 ... P30820 15895271
    41941 1yuz:A (1.4) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41942 1yuz:A (1.4) BS03 FE ? GO:0005506 ... P30820 15895271
    41943 1yuz:B (1.4) BS01 FE ? GO:0005506 ... P30820 15895271
    41944 1yuz:B (1.4) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41945 1yuz:B (1.4) BS03 FE ? GO:0005506 ... P30820 15895271
    41946 1yv0:C (7.0) BS01 MG ? GO:0003009 ... P02588 15784741
    41947 1yv0:C (7.0) BS02 MG ? GO:0003009 ... P02588 15784741
    41948 1yv1:A (1.5) BS01 FE2 ? GO:0005506 ... P30820 15895271
    41949 1yv1:A (1.5) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41950 1yv1:A (1.5) BS03 FE2 ? GO:0005506 ... P30820 15895271
    41951 1yv1:B (1.5) BS01 FE2 ? GO:0005506 ... P30820 15895271
    41952 1yv1:B (1.5) BS02 FE2 ? GO:0005506 ... P30820 15895271
    41953 1yv1:B (1.5) BS03 FE2 ? GO:0005506 ... P30820 15895271
    41954 1yv3:A (2.0) BS01 MG ? GO:0003774 ... P08799 15750603
    41955 1yv3:A (2.0) BS02 ADP ? GO:0003774 ... P08799 15750603
    41956 1yv3:A (2.0) BS03 BIT ? GO:0003774 ... P08799 15750603 BindingDB: IC50=4900nM
    41957 1yvl:A (3.0) BS01 peptide ? GO:0000122 ... P42224 15780933
    41958 1yvl:B (3.0) BS01 peptide ? GO:0000122 ... P42224 15780933
    41959 1yvm:A (1.6) BS01 CO 3.4.11.18 GO:0004177 ... P0AE18 15880695
    41960 1yvm:A (1.6) BS02 CO 3.4.11.18 GO:0004177 ... P0AE18 15880695
    41961 1yvm:A (1.6) BS03 TMG 3.4.11.18 GO:0004177 ... P0AE18 15880695 MOAD: Ki=0.4uM
    PDBbind: -logKd/Ki=6.40, Ki=0.4uM
    BindingDB: IC50=472nM
    41962 1yvn:A (2.1) BS01 ATP 3.6.4.- GO:0000011 ... P60010 N/A
    41963 1yvp:A (2.2) BS01 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41964 1yvp:A (2.2) BS02 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41965 1yvp:A (2.2) BS03 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41966 1yvp:A (2.2) BS04 MG ? GO:0003723 ... P42700 15907467
    41967 1yvp:B (2.2) BS01 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41968 1yvp:B (2.2) BS02 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41969 1yvp:B (2.2) BS03 rna ? GO:0003723 ... P42700 15907467 PDBbind: Kd=5.2nM
    41970 1yvp:B (2.2) BS04 MG ? GO:0003723 ... P42700 15907467
    41971 1yvq:A (1.8) BS01 HEM ? GO:0004601 ... P69905 N/A
    41972 1yvq:B (1.8) BS01 HEM ? GO:0004601 ... P68871 N/A
    41973 1yvq:C (1.8) BS01 HEM ? GO:0004601 ... P69905 N/A
    41974 1yvq:D (1.8) BS01 HEM ? GO:0004601 ... P68871 N/A
    41975 1yvt:A (1.8) BS01 HEM ? GO:0004601 ... P69905 N/A
    41976 1yvt:B (1.8) BS01 HEM ? GO:0004601 ... P68871 N/A
    41977 1yw2:A (2.01) BS01 PGJ 2.7.11.24 GO:0000077 ... P47811 15837333 MOAD: ic50=141nM
    PDBbind: -logKd/Ki=6.85, IC50=141nM
    41978 1ywa:A (0.89) BS01 HEM 1.7.6.1 GO:0005576 ... Q94734 16171383
    41979 1ywb:A (0.97) BS01 HEM 1.7.6.1 GO:0005576 ... Q94734 16171383
    41980 1ywc:A (1.0) BS01 HEM 1.7.6.1 GO:0005576 ... Q94734 16171383
    41981 1ywd:A (1.08) BS01 HEM 1.7.6.1 GO:0005576 ... Q94734 16171383
    41982 1ywf:A (1.71) BS01 PO4 ? GO:0004438 ... P96830 16271885
    41983 1ywg:O (2.6) BS01 NAD 1.2.1.12 GO:0000166 ... Q8T6B1 16131754
    41984 1ywg:P (2.6) BS01 NAD 1.2.1.12 GO:0000166 ... Q8T6B1 16131754
    41985 1ywg:Q (2.6) BS01 NAD 1.2.1.12 GO:0000166 ... Q8T6B1 16131754
    41986 1ywg:R (2.6) BS01 NAD 1.2.1.12 GO:0000166 ... Q8T6B1 16131754
    41987 1ywh:A (2.7) BS01 peptide ? GO:0001934 ... Q03405 15861141
    41988 1ywh:A (2.7) BS02 peptide ? GO:0001934 ... Q03405 15861141
    41989 1ywh:A (2.7) BS03 FUC ? GO:0001934 ... Q03405 15861141
    41990 1ywh:C (2.7) BS01 peptide ? GO:0001934 ... Q03405 15861141
    41991 1ywh:C (2.7) BS02 peptide ? GO:0001934 ... Q03405 15861141
    41992 1ywh:E (2.7) BS01 peptide ? GO:0001934 ... Q03405 15861141
    41993 1ywh:E (2.7) BS02 peptide ? GO:0001934 ... Q03405 15861141
    41994 1ywh:E (2.7) BS03 FUC ? GO:0001934 ... Q03405 15861141
    41995 1ywh:G (2.7) BS01 peptide ? GO:0001934 ... Q03405 15861141
    41996 1ywh:G (2.7) BS02 peptide ? GO:0001934 ... Q03405 15861141
    41997 1ywh:G (2.7) BS03 FUC ? GO:0001934 ... Q03405 15861141
    41998 1ywh:I (2.7) BS01 peptide ? GO:0001934 ... Q03405 15861141
    41999 1ywh:I (2.7) BS02 peptide ? GO:0001934 ... Q03405 15861141
    42000 1ywh:I (2.7) BS03 FUC ? GO:0001934 ... Q03405 15861141
    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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