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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 45686 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.
  • The sequence is converted from residues with experimentally determined coordinates in the structure; residues not observed in the 3D structure are excluded.
  • 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)     		Site
    #     		DNA
    sequence         		EC
    number     		GO
    terms     		UniProt PubMed Binding
    affinity
    1601 1nk4:A
    (1.6)    		 BS01 >1nk4:B
    gcgatcagg
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1602 1nk4:A
    (1.6)    		 BS02 >1nk4:C
    gctgatcgca
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1603 1nk5:A
    (2.1)    		 BS01 >1nk5:B
    catggcattgataa
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1604 1nk5:A
    (2.1)    		 BS02 >1nk5:C
    atatcaatgccatg
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1605 1nk6:A
    (2.1)    		 BS01 >1nk6:B
    gcatgatcc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1606 1nk6:A
    (2.1)    		 BS02 >1nk6:C
    gatcatgca
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1607 1nk7:A
    (1.9)    		 BS01 >1nk7:B
    gcatcatgcg
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1608 1nk7:A
    (1.9)    		 BS02 >1nk7:C
    gcatgatgca
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1609 1nk8:A
    (1.9)    		 BS01 >1nk8:B
    gcgatcagcgc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1610 1nk8:A
    (1.9)    		 BS02 >1nk8:C (identical to 1nk0:C, 1nk9:C)
    cgtgctgatcgc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1611 1nk9:A
    (1.9)    		 BS01 >1nk9:B
    gcgatcagcgcg
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1612 1nk9:A
    (1.9)    		 BS02 >1nk9:C (identical to 1nk0:C, 1nk8:C)
    cgtgctgatcgc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1613 1nkb:A
    (2.0)    		 BS01 >1nkb:B
    gcgatcagcgcgt
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1614 1nkb:A
    (2.0)    		 BS02 >1nkb:C
    tacgtgctgatcgc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1615 1nkc:A
    (1.8)    		 BS01 >1nkc:B
    gcgatcagcgcgtac
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1616 1nkc:A
    (1.8)    		 BS02 >1nkc:C
    gtacgtgctgatcgc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1617 1nke:A
    (1.8)    		 BS01 >1nke:B (identical to 2hhu:B)
    gcgatcagccc
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1618 1nke:A
    (1.8)    		 BS02 >1nke:C
    gtgctgatcgca
    		 2.7.7.7 GO:0003676 ... P52026 15035983
    1619 1nkp:A
    (1.8)    		 BS01 >1nkp:F (identical to 1nkp:G, 1nkp:H, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0003700 ... P01106 12553908 PDBbind: Kd=90nM
    1620 1nkp:A
    (1.8)    		 BS02 >1nkp:G (identical to 1nkp:F, 1nkp:H, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0003700 ... P01106 12553908 PDBbind: Kd=90nM
    1621 1nkp:B
    (1.8)    		 BS01 >1nkp:F (identical to 1nkp:G, 1nkp:H, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908 PDBbind: Kd=90nM
    1622 1nkp:B
    (1.8)    		 BS02 >1nkp:G (identical to 1nkp:F, 1nkp:H, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908 PDBbind: Kd=90nM
    1623 1nkp:D
    (1.8)    		 BS01 >1nkp:H (identical to 1nkp:F, 1nkp:G, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0003700 ... P01106 12553908 PDBbind: Kd=90nM
    1624 1nkp:D
    (1.8)    		 BS02 >1nkp:J (identical to 1nkp:F, 1nkp:G, 1nkp:H)
    cgagtagcacgtgctactc
    		 ? GO:0003700 ... P01106 12553908 PDBbind: Kd=90nM
    1625 1nkp:E
    (1.8)    		 BS01 >1nkp:H (identical to 1nkp:F, 1nkp:G, 1nkp:J)
    cgagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908 PDBbind: Kd=90nM
    1626 1nkp:E
    (1.8)    		 BS02 >1nkp:J (identical to 1nkp:F, 1nkp:G, 1nkp:H)
    cgagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908 PDBbind: Kd=90nM
    1627 1nlw:A
    (2.0)    		 BS01 >1nlw:F (identical to 1nlw:G, 1nlw:H, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0000122 ... Q05195 12553908
    1628 1nlw:A
    (2.0)    		 BS02 >1nlw:G (identical to 1nlw:F, 1nlw:H, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0000122 ... Q05195 12553908
    1629 1nlw:B
    (2.0)    		 BS01 >1nlw:F (identical to 1nlw:G, 1nlw:H, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908
    1630 1nlw:B
    (2.0)    		 BS02 >1nlw:G (identical to 1nlw:F, 1nlw:H, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908
    1631 1nlw:D
    (2.0)    		 BS01 >1nlw:H (identical to 1nlw:F, 1nlw:G, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0000122 ... Q05195 12553908
    1632 1nlw:D
    (2.0)    		 BS02 >1nlw:J (identical to 1nlw:F, 1nlw:G, 1nlw:H)
    gagtagcacgtgctactc
    		 ? GO:0000122 ... Q05195 12553908
    1633 1nlw:E
    (2.0)    		 BS01 >1nlw:H (identical to 1nlw:F, 1nlw:G, 1nlw:J)
    gagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908
    1634 1nlw:E
    (2.0)    		 BS02 >1nlw:J (identical to 1nlw:F, 1nlw:G, 1nlw:H)
    gagtagcacgtgctactc
    		 ? GO:0046983 ... P61244 12553908
    1635 1nne:A
    (3.11)    		 BS01 >1nne:C (identical to 1ewq:C, 1fw6:C)
    gcgacgctagcgtgcggctcgtc
    		 ? GO:0003677 ... Q56215 12582174
    1636 1nne:A
    (3.11)    		 BS02 >1nne:D (identical to 1ewq:D, 1fw6:D)
    ggacgagccgccgctagcgtcg
    		 ? GO:0003677 ... Q56215 12582174
    1637 1nne:B
    (3.11)    		 BS01 >1nne:C (identical to 1ewq:C, 1fw6:C)
    gcgacgctagcgtgcggctcgtc
    		 ? GO:0003677 ... Q56215 12582174
    1638 1nne:B
    (3.11)    		 BS02 >1nne:D (identical to 1ewq:D, 1fw6:D)
    ggacgagccgccgctagcgtcg
    		 ? GO:0003677 ... Q56215 12582174
    1639 1nnj:A
    (1.9)    		 BS01 >1nnj:D (identical to 1pji:D)
    ctctttStttctcg
    		 3.2.2.23
    4.2.99.18    		 GO:0003676 ... P42371 16243784 PDBbind: Kd=6nM
    1640 1nnj:A
    (1.9)    		 BS02 >1nnj:E (identical to 3c58:C, 4cis:C, 6fl1:C, 6h0s:C, 4pcz:C, 4pd2:C, 4pdg:C, 4pdi:C, 1pji:E, 1pjj:E, 1pm5:E, 6rnm:E, 6rno:E, 6rnr:E, 6ro2:C, 6rok:E, 6rp0:C, 6rp7:E, 1tdz:C, 1xc8:C, 2xzu:C)
    gcgagaaacaaaga
    		 3.2.2.23
    4.2.99.18    		 GO:0003676 ... P42371 16243784 PDBbind: Kd=6nM
    1641 1nop:A
    (2.3)    		 BS01 >1nop:D (identical to 1rff:D, 1rff:F, 1rg1:D, 1rg1:F, 7z3x:D)
    gtt
    		 3.1.4.- GO:0005634 ... Q9NUW8 12618186
    1642 1nop:B
    (2.3)    		 BS01 >1nop:F (identical to 2dwm:E, 2dwm:G, 4ljr:D)
    t
    		 3.1.4.- GO:0005634 ... Q9NUW8 12618186
    1643 1noy:B
    (2.2)    		 BS01 >1noy:S (identical to 1cbv:D, 2d7d:D, 5d8f:C, 5ith:B, 6jdg:E, 6jip:B, 5k83:I, 5k83:J, 5k83:H, 1krp:B, 1ksp:B, 1lau:D, 7lwa:B, 4mgu:C, 5odn:P, 5odn:L, 5odp:N, 5odp:P, 8q44:C, 3udg:H, 3udg:I, 8v08:C, 8v08:D, 3vdy:D, 3vdy:G, 1xf2:T, 1xi1:C, 1xi1:D, 7z3x:E)
    ttt
    		 2.7.7.7
    3.1.11.-    		 GO:0003676 ... P04415 8679562
    1644 1nvp:A
    (2.1)    		 BS01 >1nvp:E
    gggggggctataaaagg
    		 ? GO:0003677 ... P20226 12972251
    1645 1nvp:A
    (2.1)    		 BS02 >1nvp:F
    ccttttatagccccccc
    		 ? GO:0003677 ... P20226 12972251
    1646 1nvp:C
    (2.1)    		 BS01 >1nvp:F
    ccttttatagccccccc
    		 ? GO:0005672 ... P52655 12972251
    1647 1nwq:A
    (2.8)    		 BS01 >1nwq:B
    ttcctattgcgcaatccagtt
    		 ? GO:0003700 ... P05554 12578822
    1648 1nwq:A
    (2.8)    		 BS02 >1nwq:D
    aaactggattgcgcaatagga
    		 ? GO:0003700 ... P05554 12578822
    1649 1nwq:C
    (2.8)    		 BS01 >1nwq:B
    ttcctattgcgcaatccagtt
    		 ? GO:0003700 ... P05554 12578822
    1650 1nwq:C
    (2.8)    		 BS02 >1nwq:D
    aaactggattgcgcaatagga
    		 ? GO:0003700 ... P05554 12578822
    1651 1nzb:A
    (3.1)    		 BS01 >1nzb:C (identical to 1nzb:G, 1q3u:C, 1q3u:G)
    cgataacutcgtataatgtatgctatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1652 1nzb:A
    (3.1)    		 BS02 >1nzb:D (identical to 1nzb:H, 1ouq:D, 1ouq:H, 1q3u:D, 1q3u:H, 1q3v:D, 1q3v:H)
    ggataacttcgtatagcatacattatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1653 1nzb:B
    (3.1)    		 BS01 >1nzb:C (identical to 1nzb:G, 1q3u:C, 1q3u:G)
    cgataacutcgtataatgtatgctatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1654 1nzb:B
    (3.1)    		 BS02 >1nzb:D (identical to 1nzb:H, 1ouq:D, 1ouq:H, 1q3u:D, 1q3u:H, 1q3v:D, 1q3v:H)
    ggataacttcgtatagcatacattatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1655 1nzb:E
    (3.1)    		 BS01 >1nzb:G (identical to 1nzb:C, 1q3u:C, 1q3u:G)
    cgataacutcgtataatgtatgctatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1656 1nzb:E
    (3.1)    		 BS02 >1nzb:H (identical to 1nzb:D, 1ouq:D, 1ouq:H, 1q3u:D, 1q3u:H, 1q3v:D, 1q3v:H)
    ggataacttcgtatagcatacattatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1657 1nzb:F
    (3.1)    		 BS01 >1nzb:G (identical to 1nzb:C, 1q3u:C, 1q3u:G)
    cgataacutcgtataatgtatgctatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1658 1nzb:F
    (3.1)    		 BS02 >1nzb:H (identical to 1nzb:D, 1ouq:D, 1ouq:H, 1q3u:D, 1q3u:H, 1q3v:D, 1q3v:H)
    ggataacttcgtatagcatacattatacgaagttatc
    		 ? GO:0003677 ... P06956 12954782
    1659 1o3q:A
    (3.0)    		 BS01 >1o3q:B
    aaaaatgtgat
    		 ? GO:0003677 ... P0ACJ8 11724532
    1660 1o3q:A
    (3.0)    		 BS02 >1o3q:C
    ctagatcacattttt
    		 ? GO:0003677 ... P0ACJ8 11724532
    1661 1o3r:A
    (3.0)    		 BS01 >1o3r:B (identical to 1o3s:B)
    aaaaatgcgat
    		 ? GO:0003677 ... P0ACJ8 11724532
    1662 1o3r:A
    (3.0)    		 BS02 >1o3r:C (identical to 1o3s:C)
    ctagatcgcattttt
    		 ? GO:0003677 ... P0ACJ8 11724532
    1663 1o3s:A
    (3.0)    		 BS01 >1o3s:B (identical to 1o3r:B)
    aaaaatgcgat
    		 ? GO:0003677 ... P0ACJ8 11724533 PDBbind: Kd=14pM
    1664 1o3s:A
    (3.0)    		 BS02 >1o3s:C (identical to 1o3r:C)
    ctagatcgcattttt
    		 ? GO:0003677 ... P0ACJ8 11724533 PDBbind: Kd=14pM
    1665 1o3t:A
    (2.8)    		 BS01 >1o3t:C (identical to 1o3t:F)
    gcgaaaaatgcgat
    		 ? GO:0003677 ... P0ACJ8 11724532
    1666 1o3t:A
    (2.8)    		 BS02 >1o3t:D (identical to 1o3t:E)
    ctagatcgcatttttcg
    		 ? GO:0003677 ... P0ACJ8 11724532
    1667 1o3t:B
    (2.8)    		 BS01 >1o3t:E (identical to 1o3t:D)
    ctagatcgcatttttcg
    		 ? GO:0003677 ... P0ACJ8 11724532
    1668 1o3t:B
    (2.8)    		 BS02 >1o3t:F (identical to 1o3t:C)
    gcgaaaaatgcgat
    		 ? GO:0003677 ... P0ACJ8 11724532
    1669 1o4x:A
    (-1.00)    		 BS01 >1o4x:C
    tgtctttgtcatgctaatg
    		 ? GO:0000981 ... P14859 14559893
    1670 1o4x:A
    (-1.00)    		 BS02 >1o4x:D
    cattagcatgacaaagaca
    		 ? GO:0000981 ... P14859 14559893
    1671 1o4x:B
    (-1.00)    		 BS01 >1o4x:C
    tgtctttgtcatgctaatg
    		 ? N/A P48431 14559893
    1672 1o4x:B
    (-1.00)    		 BS02 >1o4x:D
    cattagcatgacaaagaca
    		 ? N/A P48431 14559893
    1673 1oct:C
    (3.0)    		 BS01 >1oct:A (identical to 1cqt:M)
    tgtatgcaaataagg
    		 ? GO:0000981 ... P14859 8156594
    1674 1oct:C
    (3.0)    		 BS02 >1oct:B (identical to 1cqt:N)
    accttatttgcatac
    		 ? GO:0000981 ... P14859 8156594
    1675 1odg:A
    (2.8)    		 BS01 >1odg:F (identical to 1odg:W)
    taggcctggatc
    		 3.1.-.- GO:0004519 ... P09184 12626704
    1676 1odg:A
    (2.8)    		 BS02 >1odg:W (identical to 1odg:F)
    taggcctggatc
    		 3.1.-.- GO:0004519 ... P09184 12626704
    1677 1odh:A
    (2.85)    		 BS01 >1odh:C
    cgatgcgggtgca
    		 ? GO:0001228 ... P70348 12682016
    1678 1odh:A
    (2.85)    		 BS02 >1odh:D
    tgcacccgcatcg
    		 ? GO:0001228 ... P70348 12682016
    1679 1oe4:A
    (2.0)    		 BS01 >1oe4:E (identical to 1oe5:E, 1oe6:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1680 1oe4:A
    (2.0)    		 BS02 >1oe4:F (identical to 1oe6:F, 2ofi:B)
    cggactcacggg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1681 1oe4:B
    (2.0)    		 BS01 >1oe4:E (identical to 1oe5:E, 1oe6:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1682 1oe5:A
    (2.3)    		 BS01 >1oe5:E (identical to 1oe4:E, 1oe6:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1683 1oe5:A
    (2.3)    		 BS02 >1oe5:F
    ccggactcacggg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1684 1oe5:B
    (2.3)    		 BS01 >1oe5:E (identical to 1oe4:E, 1oe6:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1685 1oe6:A
    (2.65)    		 BS01 >1oe6:E (identical to 1oe4:E, 1oe5:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1686 1oe6:A
    (2.65)    		 BS02 >1oe6:F (identical to 1oe4:F, 2ofi:B)
    cggactcacggg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1687 1oe6:B
    (2.65)    		 BS01 >1oe6:E (identical to 1oe4:E, 1oe5:E)
    cccgtgagtccg
    		 3.2.2.- GO:0006284 ... Q9YGN6 12820976
    1688 1oh5:A
    (2.9)    		 BS01 >1oh5:E
    agctgccacgcaccagtg
    		 ? GO:0000018 ... P23909 12907723
    1689 1oh5:A
    (2.9)    		 BS02 >1oh5:F
    actggtgcatggcagct
    		 ? GO:0000018 ... P23909 12907723
    1690 1oh5:B
    (2.9)    		 BS01 >1oh5:E
    agctgccacgcaccagtg
    		 ? GO:0000018 ... P23909 12907723
    1691 1oh6:A
    (2.4)    		 BS01 >1oh6:E (identical to 2wtu:E)
    agctgccaagcaccag
    		 ? GO:0000018 ... P23909 12907723
    1692 1oh6:A
    (2.4)    		 BS02 >1oh6:F (identical to 2wtu:F)
    ctggtgcatggcagct
    		 ? GO:0000018 ... P23909 12907723
    1693 1oh6:B
    (2.4)    		 BS01 >1oh6:E (identical to 2wtu:E)
    agctgccaagcaccag
    		 ? GO:0000018 ... P23909 12907723
    1694 1oh6:B
    (2.4)    		 BS02 >1oh6:F (identical to 2wtu:F)
    ctggtgcatggcagct
    		 ? GO:0000018 ... P23909 12907723
    1695 1oh7:A
    (2.5)    		 BS01 >1oh7:E (identical to 1e3m:E, 3k0s:E, 1ng9:E, 1w7a:E, 1wb9:E, 1wbb:E, 1wbd:E)
    agctgccaggcaccagtg
    		 ? GO:0000018 ... P23909 12907723
    1696 1oh7:A
    (2.5)    		 BS02 >1oh7:F
    actggtgcgtggcagct
    		 ? GO:0000018 ... P23909 12907723
    1697 1oh7:B
    (2.5)    		 BS01 >1oh7:E (identical to 1e3m:E, 3k0s:E, 1ng9:E, 1w7a:E, 1wb9:E, 1wbb:E, 1wbd:E)
    agctgccaggcaccagtg
    		 ? GO:0000018 ... P23909 12907723
    1698 1oh7:B
    (2.5)    		 BS02 >1oh7:F
    actggtgcgtggcagct
    		 ? GO:0000018 ... P23909 12907723
    1699 1oh8:A
    (2.9)    		 BS01 >1oh8:E
    agctgccaggcacc
    		 ? GO:0000018 ... P23909 12907723
    1700 1oh8:A
    (2.9)    		 BS02 >1oh8:F
    gtgccttggcagct
    		 ? GO:0000018 ... P23909 12907723
    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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