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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
    64601 1yhu:J (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64602 1yhu:J (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64603 1yhu:K (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64604 1yhu:K (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64605 1yhu:L (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64606 1yhu:M (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64607 1yhu:M (3.15) BS02 OXY ? GO:0005344 ... Q8IFK4 15710902
    64608 1yhu:N (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64609 1yhu:N (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    64610 1yhu:N (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64611 1yhu:N (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64612 1yhu:O (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64613 1yhu:O (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64614 1yhu:P (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64615 1yhu:Q (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64616 1yhu:Q (3.15) BS02 OXY ? GO:0005344 ... Q8IFK4 15710902
    64617 1yhu:R (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64618 1yhu:R (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    64619 1yhu:R (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64620 1yhu:R (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64621 1yhu:S (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64622 1yhu:S (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64623 1yhu:T (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64624 1yhu:U (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64625 1yhu:U (3.15) BS02 OXY ? GO:0005344 ... Q8IFK4 15710902
    64626 1yhu:V (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64627 1yhu:V (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    64628 1yhu:V (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64629 1yhu:V (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64630 1yhu:W (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64631 1yhu:W (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64632 1yhu:X (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64633 1yhy:A (2.7) BS01 MG 2.2.1.6 GO:0000287 ... P17597 16407096
    64634 1yhy:A (2.7) BS02 1MM 2.2.1.6 GO:0000287 ... P17597 16407096
    64635 1yhy:A (2.7) BS03 FAD 2.2.1.6 GO:0000287 ... P17597 16407096
    64636 1yhz:A (2.7) BS01 MG 2.2.1.6 GO:0000287 ... P17597 16407096
    64637 1yhz:A (2.7) BS02 1CS 2.2.1.6 GO:0000287 ... P17597 16407096
    64638 1yhz:A (2.7) BS03 FAD 2.2.1.6 GO:0000287 ... P17597 16407096
    64639 1yi0:A (2.7) BS01 MG 2.2.1.6 GO:0000287 ... P17597 16407096
    64640 1yi0:A (2.7) BS02 1SM 2.2.1.6 GO:0000287 ... P17597 16407096
    64641 1yi0:A (2.7) BS03 FAD 2.2.1.6 GO:0000287 ... P17597 16407096
    64642 1yi1:A (2.9) BS01 MG 2.2.1.6 GO:0000287 ... P17597 16407096
    64643 1yi1:A (2.9) BS02 1TB 2.2.1.6 GO:0000287 ... P17597 16407096 BindingDB: Ki=253nM
    64644 1yi1:A (2.9) BS03 FAD 2.2.1.6 GO:0000287 ... P17597 16407096
    64645 1yi2:1 (2.65) BS01 rna ? GO:0003723 ... P32410 15851032
    64646 1yi2:2 (2.65) BS01 rna ? GO:0003735 ... P22452 15851032
    64647 1yi2:3 (2.65) BS01 rna ? GO:0000049 ... P32411 15851032
    64648 1yi2:3 (2.65) BS02 MG ? GO:0000049 ... P32411 15851032
    64649 1yi2:A (2.65) BS01 rna ? GO:0002181 ... P20276 15851032
    64650 1yi2:A (2.65) BS02 MG ? GO:0002181 ... P20276 15851032
    64651 1yi2:B (2.65) BS01 rna ? GO:0003723 ... P20279 15851032
    64652 1yi2:C (2.65) BS01 rna ? GO:0003723 ... P12735 15851032
    64653 1yi2:D (2.65) BS01 rna ? GO:0000049 ... P14124 15851032
    64654 1yi2:D (2.65) BS02 rna ? GO:0000049 ... P14124 15851032
    64655 1yi2:E (2.65) BS01 rna ? GO:0002181 ... P14135 15851032
    64656 1yi2:F (2.65) BS01 rna ? GO:0001682 ... P12743 15851032
    64657 1yi2:H (2.65) BS01 rna ? GO:0000027 ... P60617 15851032
    64658 1yi2:I (2.65) BS01 rna ? GO:0003735 ... P14122 15851032
    64659 1yi2:J (2.65) BS01 rna ? GO:0003729 ... P29198 15851032
    64660 1yi2:K (2.65) BS01 rna ? GO:0003735 ... P22450 15851032
    64661 1yi2:L (2.65) BS01 rna ? GO:0003735 ... P12737 15851032
    64662 1yi2:M (2.65) BS01 rna ? GO:0002181 ... P60618 15851032
    64663 1yi2:N (2.65) BS01 rna ? GO:0000027 ... P14123 15851032
    64664 1yi2:N (2.65) BS02 rna ? GO:0000027 ... P14123 15851032
    64665 1yi2:O (2.65) BS01 rna ? GO:0003723 ... P12733 15851032
    64666 1yi2:P (2.65) BS01 rna ? GO:0003723 ... P14119 15851032
    64667 1yi2:Q (2.65) BS01 rna ? GO:0003735 ... P12734 15851032
    64668 1yi2:Q (2.65) BS02 rna ? GO:0003735 ... P12734 15851032
    64669 1yi2:R (2.65) BS01 rna ? GO:0002181 ... P10970 15851032
    64670 1yi2:S (2.65) BS01 rna ? GO:0000027 ... P12732 15851032
    64671 1yi2:T (2.65) BS01 rna ? GO:0002181 ... P10972 15851032
    64672 1yi2:T (2.65) BS02 MG ? GO:0002181 ... P10972 15851032
    64673 1yi2:U (2.65) BS01 rna ? GO:0003735 ... P14116 15851032
    64674 1yi2:V (2.65) BS01 rna ? GO:0003735 ... P10971 15851032
    64675 1yi2:W (2.65) BS01 rna ? GO:0000463 ... P14121 15851032
    64676 1yi2:W (2.65) BS02 rna ? GO:0000463 ... P14121 15851032
    64677 1yi2:X (2.65) BS01 rna ? GO:0002181 ... P18138 15851032
    64678 1yi2:Y (2.65) BS01 rna ? GO:0000166 ... P12736 15851032
    64679 1yi2:Y (2.65) BS02 MG ? GO:0000166 ... P12736 15851032
    64680 1yi2:Z (2.65) BS01 rna ? GO:0003735 ... P60619 15851032
    64681 1yi3:A (2.5) BS01 LY2 2.7.11.1 GO:0004672 ... P11309 15657054 MOAD: ic50=4uM
    PDBbind: -logKd/Ki=5.40, IC50=4.0uM
    BindingDB: IC50=820nM
    64682 1yi4:A (2.4) BS01 ADN 2.7.11.1 GO:0004672 ... P11309 15657054
    64683 1yi7:A (1.9) BS01 CA 3.2.1.37 GO:0004553 ... Q97DM1 N/A
    64684 1yi7:B (1.9) BS01 CA 3.2.1.37 GO:0004553 ... Q97DM1 N/A
    64685 1yi7:C (1.9) BS01 CA 3.2.1.37 GO:0004553 ... Q97DM1 N/A
    64686 1yi7:D (1.9) BS01 CA 3.2.1.37 GO:0004553 ... Q97DM1 N/A
    64687 1yi8:C (2.1) BS01 TRP 6.1.1.2 GO:0000166 ... Q9RVD6 15723076
    64688 1yi9:A (1.7) BS01 CU 1.14.17.3
    4.3.2.5    		 GO:0003824 ... P14925 16100265
    64689 1yi9:A (1.7) BS02 CU 1.14.17.3
    4.3.2.5    		 GO:0003824 ... P14925 16100265
    64690 1yia:B (3.7) BS01 HRP 6.1.1.2 GO:0000166 ... Q9RVD6 15723076
    64691 1yic:A (-1.00) BS01 HEC ? GO:0005515 ... P00044 9220987
    64692 1yid:B (2.4) BS01 ATP 6.1.1.2 GO:0000166 ... Q9RVD6 15998643 MOAD: Kd=10uM
    PDBbind: -logKd/Ki=5.00, Kd=10uM
    64693 1yie:A (2.4) BS01 HEM ? GO:0004601 ... P69905 15835899
    64694 1yie:B (2.4) BS01 HEM ? GO:0004601 ... P68871 15835899
    64695 1yie:B (2.4) BS02 OXY ? GO:0004601 ... P68871 15835899
    64696 1yie:C (2.4) BS01 HEM ? GO:0004601 ... P69905 15835899
    64697 1yie:C (2.4) BS02 OXY ? GO:0004601 ... P69905 15835899
    64698 1yie:D (2.4) BS01 HEM ? GO:0004601 ... P68871 15835899
    64699 1yie:D (2.4) BS02 OXY ? GO:0004601 ... P68871 15835899
    64700 1yih:A (2.0) BS01 HEM ? GO:0004601 ... P69905 15835899
    64701 1yih:B (2.0) BS01 HEM ? GO:0004601 ... P68871 15835899
    64702 1yih:B (2.0) BS02 OXY ? GO:0004601 ... P68871 15835899
    64703 1yih:C (2.0) BS01 HEM ? GO:0004601 ... P69905 15835899
    64704 1yih:D (2.0) BS01 HEM ? GO:0004601 ... P68871 15835899
    64705 1yih:D (2.0) BS02 OXY ? GO:0004601 ... P68871 15835899
    64706 1yii:A (1.42) BS01 CA ? GO:0001786 ... P17153 N/A
    64707 1yii:A (1.42) BS02 CA ? GO:0001786 ... P17153 N/A
    64708 1yii:A (1.42) BS03 CA ? GO:0001786 ... P17153 N/A
    64709 1yij:1 (2.6) BS01 rna ? GO:0003723 ... P32410 15851032
    64710 1yij:2 (2.6) BS01 rna ? GO:0003735 ... P22452 15851032
    64711 1yij:3 (2.6) BS01 rna ? GO:0000049 ... P32411 15851032
    64712 1yij:3 (2.6) BS02 MG ? GO:0000049 ... P32411 15851032
    64713 1yij:A (2.6) BS01 rna ? GO:0002181 ... P20276 15851032
    64714 1yij:A (2.6) BS02 MG ? GO:0002181 ... P20276 15851032
    64715 1yij:B (2.6) BS01 rna ? GO:0003723 ... P20279 15851032
    64716 1yij:C (2.6) BS01 rna ? GO:0003723 ... P12735 15851032
    64717 1yij:D (2.6) BS01 rna ? GO:0000049 ... P14124 15851032
    64718 1yij:D (2.6) BS02 rna ? GO:0000049 ... P14124 15851032
    64719 1yij:E (2.6) BS01 rna ? GO:0002181 ... P14135 15851032
    64720 1yij:F (2.6) BS01 rna ? GO:0001682 ... P12743 15851032
    64721 1yij:H (2.6) BS01 rna ? GO:0000027 ... P60617 15851032
    64722 1yij:I (2.6) BS01 rna ? GO:0003735 ... P14122 15851032
    64723 1yij:J (2.6) BS01 rna ? GO:0003729 ... P29198 15851032
    64724 1yij:K (2.6) BS01 rna ? GO:0003735 ... P22450 15851032
    64725 1yij:L (2.6) BS01 rna ? GO:0003735 ... P12737 15851032
    64726 1yij:M (2.6) BS01 rna ? GO:0002181 ... P60618 15851032
    64727 1yij:N (2.6) BS01 rna ? GO:0000027 ... P14123 15851032
    64728 1yij:N (2.6) BS02 rna ? GO:0000027 ... P14123 15851032
    64729 1yij:O (2.6) BS01 rna ? GO:0003723 ... P12733 15851032
    64730 1yij:P (2.6) BS01 rna ? GO:0003723 ... P14119 15851032
    64731 1yij:Q (2.6) BS01 rna ? GO:0003735 ... P12734 15851032
    64732 1yij:Q (2.6) BS02 rna ? GO:0003735 ... P12734 15851032
    64733 1yij:R (2.6) BS01 rna ? GO:0002181 ... P10970 15851032
    64734 1yij:S (2.6) BS01 rna ? GO:0000027 ... P12732 15851032
    64735 1yij:T (2.6) BS01 rna ? GO:0002181 ... P10972 15851032
    64736 1yij:T (2.6) BS02 MG ? GO:0002181 ... P10972 15851032
    64737 1yij:U (2.6) BS01 rna ? GO:0003735 ... P14116 15851032
    64738 1yij:V (2.6) BS01 rna ? GO:0003735 ... P10971 15851032
    64739 1yij:W (2.6) BS01 rna ? GO:0000463 ... P14121 15851032
    64740 1yij:W (2.6) BS02 rna ? GO:0000463 ... P14121 15851032
    64741 1yij:X (2.6) BS01 rna ? GO:0002181 ... P18138 15851032
    64742 1yij:Y (2.6) BS01 rna ? GO:0000166 ... P12736 15851032
    64743 1yij:Y (2.6) BS02 MG ? GO:0000166 ... P12736 15851032
    64744 1yij:Z (2.6) BS01 rna ? GO:0003735 ... P60619 15851032
    64745 1yik:A (1.75) BS01 MM1 3.2.1.17 GO:0003796 ... P00698 15701702
    64746 1yik:A (1.75) BS02 MM1 3.2.1.17 GO:0003796 ... P00698 15701702
    64747 1yil:A (1.6) BS01 MM2 3.2.1.17 GO:0003796 ... P00698 15701702
    64748 1yil:A (1.6) BS02 MM2 3.2.1.17 GO:0003796 ... P00698 15701702
    64749 1yim:A (1.9) BS01 CM4 ? N/A P03372 15745820 MOAD: ic50=1.5nM
    BindingDB: IC50=1.5nM
    64750 1yin:A (2.2) BS01 CM3 ? N/A P03372 15745820 MOAD: ic50=1.4nM
    BindingDB: IC50=0.8nM
    64751 1yio:A (2.2) BS01 MG ? GO:0000160 ... O30989 16154086
    64752 1yip:A (2.2) BS01 CU 1.14.17.3
    4.3.2.5    		 GO:0003824 ... P14925 16100265
    64753 1yip:A (2.2) BS02 CU 1.14.17.3
    4.3.2.5    		 GO:0003824 ... P14925 16100265
    64754 1yiq:A (2.2) BS01 CA 1.1.9.1 GO:0005509 ... Q4W6G0 16061256
    64755 1yiq:A (2.2) BS02 PQQ 1.1.9.1 GO:0005509 ... Q4W6G0 16061256
    64756 1yiq:A (2.2) BS03 HEC 1.1.9.1 GO:0005509 ... Q4W6G0 16061256
    64757 1yit:1 (2.8) BS01 rna ? GO:0003723 ... P32410 15851032
    64758 1yit:2 (2.8) BS01 rna ? GO:0003735 ... P22452 15851032
    64759 1yit:3 (2.8) BS01 rna ? GO:0000049 ... P32411 15851032
    64760 1yit:3 (2.8) BS02 MG ? GO:0000049 ... P32411 15851032
    64761 1yit:A (2.8) BS01 rna ? GO:0002181 ... P20276 15851032
    64762 1yit:B (2.8) BS01 rna ? GO:0003723 ... P20279 15851032
    64763 1yit:C (2.8) BS01 rna ? GO:0003723 ... P12735 15851032
    64764 1yit:D (2.8) BS01 rna ? GO:0000049 ... P14124 15851032
    64765 1yit:D (2.8) BS02 rna ? GO:0000049 ... P14124 15851032
    64766 1yit:E (2.8) BS01 rna ? GO:0002181 ... P14135 15851032
    64767 1yit:F (2.8) BS01 rna ? GO:0001682 ... P12743 15851032
    64768 1yit:H (2.8) BS01 rna ? GO:0000027 ... P60617 15851032
    64769 1yit:I (2.8) BS01 rna ? GO:0003735 ... P14122 15851032
    64770 1yit:J (2.8) BS01 rna ? GO:0003729 ... P29198 15851032
    64771 1yit:K (2.8) BS01 rna ? GO:0003735 ... P22450 15851032
    64772 1yit:L (2.8) BS01 rna ? GO:0003735 ... P12737 15851032
    64773 1yit:M (2.8) BS01 rna ? GO:0002181 ... P60618 15851032
    64774 1yit:N (2.8) BS01 rna ? GO:0000027 ... P14123 15851032
    64775 1yit:N (2.8) BS02 rna ? GO:0000027 ... P14123 15851032
    64776 1yit:O (2.8) BS01 rna ? GO:0003723 ... P12733 15851032
    64777 1yit:P (2.8) BS01 rna ? GO:0003723 ... P14119 15851032
    64778 1yit:Q (2.8) BS01 rna ? GO:0003735 ... P12734 15851032
    64779 1yit:Q (2.8) BS02 rna ? GO:0003735 ... P12734 15851032
    64780 1yit:R (2.8) BS01 rna ? GO:0002181 ... P10970 15851032
    64781 1yit:S (2.8) BS01 rna ? GO:0000027 ... P12732 15851032
    64782 1yit:T (2.8) BS01 rna ? GO:0002181 ... P10972 15851032
    64783 1yit:T (2.8) BS02 MG ? GO:0002181 ... P10972 15851032
    64784 1yit:U (2.8) BS01 rna ? GO:0003735 ... P14116 15851032
    64785 1yit:V (2.8) BS01 rna ? GO:0003735 ... P10971 15851032
    64786 1yit:W (2.8) BS01 rna ? GO:0000463 ... P14121 15851032
    64787 1yit:W (2.8) BS02 rna ? GO:0000463 ... P14121 15851032
    64788 1yit:X (2.8) BS01 rna ? GO:0002181 ... P18138 15851032
    64789 1yit:Y (2.8) BS01 rna ? GO:0000166 ... P12736 15851032
    64790 1yit:Y (2.8) BS02 MG ? GO:0000166 ... P12736 15851032
    64791 1yit:Z (2.8) BS01 rna ? GO:0003735 ... P60619 15851032
    64792 1yiv:A (2.1) BS01 EPE ? GO:0005504 ... P0C6G6 16041071
    64793 1yix:A (1.9) BS01 ZN 3.1.-.- GO:0004536 ... P0AFQ7 N/A
    64794 1yix:A (1.9) BS02 ZN 3.1.-.- GO:0004536 ... P0AFQ7 N/A
    64795 1yix:B (1.9) BS01 ZN 3.1.-.- GO:0004536 ... P0AFQ7 N/A
    64796 1yix:B (1.9) BS02 ZN 3.1.-.- GO:0004536 ... P0AFQ7 N/A
    64797 1yiy:A (1.9) BS01 PMP 2.6.1.-
    2.6.1.63
    2.6.1.7    		 GO:0005737 ... Q17CS8 15853804
    64798 1yiy:B (1.9) BS01 PMP 2.6.1.-
    2.6.1.63
    2.6.1.7    		 GO:0005737 ... Q17CS8 15853804
    64799 1yj0:A (2.95) BS01 ZN ? GO:0001786 ... P17153 N/A
    64800 1yj3:A (1.6) BS01 CO 3.4.11.18 GO:0004177 ... P9WK19 15882055
    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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