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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 903398 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
    879601 8v3k:A (1.47) BS02 DPO 4.2.3.37 GO:0016829 ... Q9K499 38420671
    879602 8v3k:A (1.47) BS03 BTM 4.2.3.37 GO:0016829 ... Q9K499 38420671
    879603 8v3m:A (1.8) BS01 ZN N/A N/A Q8NDL9 39020174
    879604 8v3n:A (2.3) BS01 ZN N/A N/A Q8NDL9 39020174
    879605 8v3n:A (2.3) BS02 A1AAG N/A N/A Q8NDL9 39020174
    879606 8v3o:A (2.3) BS01 peptide N/A N/A Q8NDL9 39020174
    879607 8v3o:A (2.3) BS02 ZN N/A N/A Q8NDL9 39020174
    879608 8v3p:A (2.36) BS01 peptide N/A N/A Q8NDL9 39020174
    879609 8v3p:A (2.36) BS02 ZN N/A N/A Q8NDL9 39020174
    879610 8v3q:A (3.1) BS01 peptide N/A N/A Q8NDL9 39020174
    879611 8v3q:A (3.1) BS02 ZN N/A N/A Q8NDL9 39020174
    879612 8v3q:A (3.1) BS03 GLU N/A N/A Q8NDL9 39020174
    879613 8v3r:A (3.4) BS01 peptide N/A N/A Q8NDL9 39020174
    879614 8v3r:A (3.4) BS02 ZN N/A N/A Q8NDL9 39020174
    879615 8v3r:A (3.4) BS03 GLU N/A N/A Q8NDL9 39020174
    879616 8v3s:A (3.6) BS01 peptide N/A N/A Q8NDL9 39020174
    879617 8v3s:A (3.6) BS02 ZN N/A N/A Q8NDL9 39020174
    879618 8v3s:A (3.6) BS03 GLU N/A N/A Q8NDL9 39020174
    879619 8v3w:C (2.9) BS01 peptide N/A N/A A0A031WFB8 39152109
    879620 8v3w:H (2.9) BS01 peptide N/A N/A A0A1X9K255 39152109
    879621 8v3w:W (2.9) BS01 peptide N/A N/A A0A031WFB8 39152109
    879622 8v3w:b (2.9) BS01 peptide N/A N/A A0A1X9K255 39152109
    879623 8v3w:t (2.9) BS01 peptide N/A N/A A0A031WFB8 39152109
    879624 8v3w:x (2.9) BS01 peptide N/A N/A A0A1X9K255 39152109
    879625 8v42:B (2.3) BS01 YD9 N/A N/A Q99986 38780468
    879626 8v42:D (2.3) BS01 YD9 N/A N/A Q99986 38780468
    879627 8v45:A (3.63) BS01 ATP N/A N/A N/A 39112702
    879628 8v45:A (3.63) BS02 ATP N/A N/A N/A 39112702
    879629 8v45:B (3.63) BS01 ATP N/A N/A N/A 39112702
    879630 8v45:B (3.63) BS02 ATP N/A N/A N/A 39112702
    879631 8v45:C (3.63) BS01 ATP N/A N/A N/A 39112702
    879632 8v45:C (3.63) BS02 ATP N/A N/A N/A 39112702
    879633 8v45:F (3.63) BS01 ATP N/A N/A N/A 39112702
    879634 8v45:F (3.63) BS02 ATP N/A N/A N/A 39112702
    879635 8v46:A (3.09) BS01 ATP N/A N/A N/A 39112702
    879636 8v46:B (3.09) BS01 ATP N/A N/A N/A 39112702
    879637 8v46:B (3.09) BS02 ATP N/A N/A N/A 39112702
    879638 8v47:A (4.08) BS01 ATP N/A N/A N/A 39112702
    879639 8v47:B (4.08) BS01 ATP N/A N/A N/A 39112702
    879640 8v47:B (4.08) BS02 ATP N/A N/A N/A 39112702
    879641 8v47:C (4.08) BS01 ATP N/A N/A N/A 39112702
    879642 8v47:H (4.08) BS01 ATP N/A N/A N/A 39112702
    879643 8v47:H (4.08) BS02 ATP N/A N/A N/A 39112702
    879644 8v48:A (3.68) BS01 ATP N/A N/A N/A 39112702
    879645 8v48:B (3.68) BS01 ATP N/A N/A N/A 39112702
    879646 8v48:B (3.68) BS02 ATP N/A N/A N/A 39112702
    879647 8v48:C (3.68) BS01 ATP N/A N/A N/A 39112702
    879648 8v48:C (3.68) BS02 ATP N/A N/A N/A 39112702
    879649 8v48:F (3.68) BS01 ATP N/A N/A N/A 39112702
    879650 8v48:F (3.68) BS02 ATP N/A N/A N/A 39112702
    879651 8v48:H (3.68) BS01 ATP N/A N/A N/A 39112702
    879652 8v48:K (3.68) BS01 ATP N/A N/A N/A 39112702
    879653 8v49:A (3.62) BS01 ATP N/A N/A N/A 39112702
    879654 8v49:B (3.62) BS01 ATP N/A N/A N/A 39112702
    879655 8v4a:A (1.96) BS01 YAE 4.1.99.1 GO:0006520 ... P28796 N/A
    879656 8v4a:B (1.96) BS01 YAR 4.1.99.1 GO:0006520 ... P28796 N/A
    879657 8v4a:C (1.96) BS01 YAE 4.1.99.1 GO:0006520 ... P28796 N/A
    879658 8v4a:D (1.96) BS01 YAR 4.1.99.1 GO:0006520 ... P28796 N/A
    879659 8v4g:A (2.0) BS01 NAP ? GO:0000166 ... A0A0U3AP28 38386885
    879660 8v4g:A (2.0) BS02 CDP ? GO:0000166 ... A0A0U3AP28 38386885
    879661 8v4g:B (2.0) BS01 NAP ? GO:0000166 ... A0A0U3AP28 38386885
    879662 8v4g:B (2.0) BS02 CDP ? GO:0000166 ... A0A0U3AP28 38386885
    879663 8v4h:A (2.2) BS01 YCX ? GO:0000166 ... A0A0U3AP28 38386885
    879664 8v4h:B (2.2) BS01 YCX ? GO:0000166 ... A0A0U3AP28 38386885
    879665 8v4h:B (2.2) BS02 PO4 ? GO:0000166 ... A0A0U3AP28 38386885
    879666 8v4j:A (1.31) BS01 J7D 5.3.1.28 GO:0005737 ... Q93UJ2 38598312
    879667 8v4j:A (1.31) BS02 ZN 5.3.1.28 GO:0005737 ... Q93UJ2 38598312
    879668 8v4k:A (3.1) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879669 8v4k:B (3.1) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879670 8v4k:C (3.1) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879671 8v4k:D (3.1) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879672 8v4k:E (3.1) BS01 ZN N/A N/A Q8NDL9 39020174
    879673 8v4k:E (3.1) BS02 GLU N/A N/A Q8NDL9 39020174
    879674 8v4l:A (2.9) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879675 8v4l:B (2.9) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879676 8v4l:C (2.9) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879677 8v4l:D (2.9) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879678 8v4l:E (2.9) BS01 GLU N/A N/A Q8NDL9 39020174
    879679 8v4l:E (2.9) BS02 ZN N/A N/A Q8NDL9 39020174
    879680 8v4m:A (3.0) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879681 8v4m:B (3.0) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879682 8v4m:C (3.0) BS01 GTP N/A GO:0000226 ... Q2XVP4 39020174
    879683 8v4m:D (3.0) BS01 G2P N/A GO:0000226 ... P02554 39020174
    879684 8v4m:E (3.0) BS01 GLU N/A N/A Q8NDL9 39020174
    879685 8v4m:E (3.0) BS02 ZN N/A N/A Q8NDL9 39020174
    879686 8v4o:A (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879687 8v4o:B (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879688 8v4o:C (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879689 8v4p:A (2.3) BS01 WPO 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879690 8v4p:A (2.3) BS02 WPO 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879691 8v4p:B (2.3) BS01 WPO 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879692 8v4p:C (2.3) BS01 WPO 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879693 8v4p:C (2.3) BS02 WPO 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879694 8v4r:A (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879695 8v4r:A (2.7) BS02 COA 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879696 8v4r:B (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879697 8v4r:B (2.7) BS02 COA 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879698 8v4r:C (2.7) BS01 AMP 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879699 8v4r:C (2.7) BS02 COA 6.2.1.1 GO:0003987 ... Q8NJN3 N/A
    879700 8v4s:A (2.49) BS01 GDP N/A N/A Q64663 39107314
    879701 8v4s:A (2.49) BS02 ZN N/A N/A Q64663 39107314
    879702 8v4s:A (2.49) BS03 ZN N/A N/A Q64663 39107314
    879703 8v4s:B (2.49) BS01 GDP N/A N/A Q64663 39107314
    879704 8v4s:B (2.49) BS02 ZN N/A N/A Q64663 39107314
    879705 8v4s:B (2.49) BS03 ZN N/A N/A Q64663 39107314
    879706 8v4s:C (2.49) BS01 GDP N/A N/A Q64663 39107314
    879707 8v4s:C (2.49) BS02 ZN N/A N/A Q64663 39107314
    879708 8v4s:C (2.49) BS03 ZN N/A N/A Q64663 39107314
    879709 8v4u:A (1.819) BS01 YDL 2.1.1.56
    2.1.1.57
    2.7.7.48
    2.7.7.50
    3.1.13.-
    3.4.19.12
    3.4.22.-
    3.4.22.69
    3.6.4.12
    3.6.4.13
    4.6.1.-    		 GO:0008233 ... P0DTD1 38687966
    879710 8v4u:B (1.819) BS01 YDL 2.1.1.56
    2.1.1.57
    2.7.7.48
    2.7.7.50
    3.1.13.-
    3.4.19.12
    3.4.22.-
    3.4.22.69
    3.6.4.12
    3.6.4.13
    4.6.1.-    		 GO:0008233 ... P0DTD1 38687966
    879711 8v4x:A (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879712 8v4x:A (2.486) BS02 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879713 8v4x:A (2.486) BS03 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879714 8v4x:A (2.486) BS04 A1AAB 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879715 8v4x:B (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879716 8v4x:B (2.486) BS02 A1AAB 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879717 8v4x:C (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879718 8v4x:C (2.486) BS02 A1AAB 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879719 8v4x:D (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879720 8v4x:D (2.486) BS02 A1AAB 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879721 8v4x:E (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879722 8v4x:F (2.486) BS01 peptide 3.4.22.- GO:0004197 ... Q9UDY8 38507740
    879723 8v4y:A (2.8) BS01 dna ? GO:0000786 ... P84233 38472177
    879724 8v4y:A (2.8) BS02 dna ? GO:0000786 ... P84233 38472177
    879725 8v4y:B (2.8) BS01 dna ? GO:0000786 ... P62799 38472177
    879726 8v4y:B (2.8) BS02 dna ? GO:0000786 ... P62799 38472177
    879727 8v4y:C (2.8) BS01 dna ? GO:0000786 ... P06897 38472177
    879728 8v4y:C (2.8) BS02 dna ? GO:0000786 ... P06897 38472177
    879729 8v4y:D (2.8) BS01 dna ? GO:0000786 ... P02281 38472177
    879730 8v4y:D (2.8) BS02 dna ? GO:0000786 ... P02281 38472177
    879731 8v4y:E (2.8) BS01 dna ? GO:0000786 ... P84233 38472177
    879732 8v4y:E (2.8) BS02 dna ? GO:0000786 ... P84233 38472177
    879733 8v4y:F (2.8) BS01 dna ? GO:0000786 ... P62799 38472177
    879734 8v4y:G (2.8) BS01 dna ? GO:0000786 ... P06897 38472177
    879735 8v4y:G (2.8) BS02 dna ? GO:0000786 ... P06897 38472177
    879736 8v4y:H (2.8) BS01 dna ? GO:0000786 ... P02281 38472177
    879737 8v4y:H (2.8) BS02 dna ? GO:0000786 ... P02281 38472177
    879738 8v4y:W (2.8) BS01 dna 3.6.4.- GO:0000183 ... O60264 38472177
    879739 8v4y:W (2.8) BS02 dna 3.6.4.- GO:0000183 ... O60264 38472177
    879740 8v4y:W (2.8) BS03 ADP 3.6.4.- GO:0000183 ... O60264 38472177
    879741 8v4y:W (2.8) BS04 BEF 3.6.4.- GO:0000183 ... O60264 38472177
    879742 8v54:A (4.1) BS01 dna N/A GO:0000262 ... P54098 38932681
    879743 8v54:A (4.1) BS02 dna N/A GO:0000262 ... P54098 38932681
    879744 8v55:A (4.2) BS01 dna N/A GO:0000262 ... P54098 38932681
    879745 8v55:A (4.2) BS02 dna N/A GO:0000262 ... P54098 38932681
    879746 8v5c:B (1.96) BS01 DXC N/A N/A P18013 39079629
    879747 8v5c:B (1.96) BS02 DXC N/A N/A P18013 39079629
    879748 8v5e:A (2.2) BS01 DXC N/A N/A P18013 39079629
    879749 8v5g:A (2.5) BS01 YDO 6.2.1.1 GO:0003987 ... J9VFT1 N/A
    879750 8v5g:B (2.5) BS01 YDO 6.2.1.1 GO:0003987 ... J9VFT1 N/A
    879751 8v5m:A (9.22) BS01 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879752 8v5m:A (9.22) BS02 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879753 8v5m:D (9.22) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879754 8v5n:A (8.56) BS01 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879755 8v5n:A (8.56) BS02 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879756 8v5n:D (8.56) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879757 8v5o:A (8.99) BS01 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879758 8v5o:A (8.99) BS02 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879759 8v5o:D (8.99) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879760 8v5r:A (3.0) BS01 dna N/A GO:0000262 ... P54098 38932681
    879761 8v5r:A (3.0) BS02 dna N/A GO:0000262 ... P54098 38932681
    879762 8v5r:A (3.0) BS03 MG N/A GO:0000262 ... P54098 38932681
    879763 8v5r:A (3.0) BS04 D3T N/A GO:0000262 ... P54098 38932681
    879764 8v5y:A (2.059) BS01 peptide ? GO:0003779 ... A0A1B2YLJ4 38662449
    879765 8v5y:B (2.059) BS01 peptide ? GO:0003779 ... A0A1B2YLJ4 38662449
    879766 8v6g:A (11.16) BS01 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879767 8v6g:A (11.16) BS02 rna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879768 8v6g:A (11.16) BS03 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879769 8v6g:A (11.16) BS04 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879770 8v6g:A (11.16) BS05 DGT 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879771 8v6g:A (11.16) BS06 MG 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879772 8v6g:C (11.16) BS01 dna ? GO:0003677 ... A0A1L8G3G3 38491139
    879773 8v6g:C (11.16) BS02 rna ? GO:0003677 ... A0A1L8G3G3 38491139
    879774 8v6g:C (11.16) BS03 SF4 ? GO:0003677 ... A0A1L8G3G3 38491139
    879775 8v6g:D (11.16) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879776 8v6h:A (11.11) BS01 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879777 8v6h:A (11.11) BS02 rna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879778 8v6h:A (11.11) BS03 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879779 8v6h:A (11.11) BS04 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879780 8v6h:A (11.11) BS05 DGT 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879781 8v6h:A (11.11) BS06 MG 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879782 8v6h:C (11.11) BS01 dna ? GO:0003677 ... A0A1L8G3G3 38491139
    879783 8v6h:C (11.11) BS02 rna ? GO:0003677 ... A0A1L8G3G3 38491139
    879784 8v6h:C (11.11) BS03 SF4 ? GO:0003677 ... A0A1L8G3G3 38491139
    879785 8v6h:D (11.11) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879786 8v6i:A (14.06) BS01 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879787 8v6i:A (14.06) BS02 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879788 8v6i:A (14.06) BS03 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879789 8v6i:A (14.06) BS04 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879790 8v6i:A (14.06) BS05 DGT 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879791 8v6i:A (14.06) BS06 MG 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879792 8v6i:C (14.06) BS01 dna ? GO:0003677 ... A0A1L8G3G3 38491139
    879793 8v6i:C (14.06) BS02 dna ? GO:0003677 ... A0A1L8G3G3 38491139
    879794 8v6i:C (14.06) BS03 SF4 ? GO:0003677 ... A0A1L8G3G3 38491139
    879795 8v6i:D (14.06) BS01 ZN 2.7.7.- GO:0000428 ... Q800A4 38491139
    879796 8v6j:A (11.11) BS01 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879797 8v6j:A (11.11) BS02 dna 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879798 8v6j:A (11.11) BS03 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879799 8v6j:A (11.11) BS04 ZN 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    879800 8v6j:A (11.11) BS05 DGT 2.7.7.7 GO:0000166 ... Q9DE46 38491139
    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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