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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.
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    # PDB
    (Resolution Å)     		Site # Ligand EC number GO terms UniProt PubMed Binding
    affinity
    42401 1z9j:A (4.5) BS04 U10 ? GO:0009772 ... P0C0Y8 15895982
    42402 1z9j:A (4.5) BS05 FE ? GO:0009772 ... P0C0Y8 15895982
    42403 1z9j:A (4.5) BS06 BCL ? GO:0009772 ... P0C0Y8 15895982
    42404 1z9j:A (4.5) BS07 BPH ? GO:0009772 ... P0C0Y8 15895982
    42405 1z9j:A (4.5) BS08 U10 ? GO:0009772 ... P0C0Y8 15895982
    42406 1z9j:B (4.5) BS01 BCL ? GO:0009772 ... P0C0Y9 15895982
    42407 1z9j:B (4.5) BS02 BPH ? GO:0009772 ... P0C0Y9 15895982
    42408 1z9j:B (4.5) BS03 FE ? GO:0009772 ... P0C0Y9 15895982
    42409 1z9j:B (4.5) BS04 MN ? GO:0009772 ... P0C0Y9 15895982
    42410 1z9j:B (4.5) BS05 BCL ? GO:0009772 ... P0C0Y9 15895982
    42411 1z9j:B (4.5) BS06 BCL ? GO:0009772 ... P0C0Y9 15895982
    42412 1z9j:B (4.5) BS07 BPH ? GO:0009772 ... P0C0Y9 15895982
    42413 1z9j:B (4.5) BS08 U10 ? GO:0009772 ... P0C0Y9 15895982
    42414 1z9k:A (4.6) BS01 BCL ? GO:0009772 ... P0C0Y8 15895982
    42415 1z9k:A (4.6) BS02 BCL ? GO:0009772 ... P0C0Y8 15895982
    42416 1z9k:A (4.6) BS03 BPH ? GO:0009772 ... P0C0Y8 15895982
    42417 1z9k:A (4.6) BS04 U10 ? GO:0009772 ... P0C0Y8 15895982
    42418 1z9k:A (4.6) BS05 FE ? GO:0009772 ... P0C0Y8 15895982
    42419 1z9k:A (4.6) BS06 BCL ? GO:0009772 ... P0C0Y8 15895982
    42420 1z9k:A (4.6) BS07 BPH ? GO:0009772 ... P0C0Y8 15895982
    42421 1z9k:B (4.6) BS01 BPH ? GO:0009772 ... P0C0Y9 15895982
    42422 1z9k:B (4.6) BS02 FE ? GO:0009772 ... P0C0Y9 15895982
    42423 1z9k:B (4.6) BS03 BCL ? GO:0009772 ... P0C0Y9 15895982
    42424 1z9k:B (4.6) BS04 BCL ? GO:0009772 ... P0C0Y9 15895982
    42425 1z9k:B (4.6) BS05 BPH ? GO:0009772 ... P0C0Y9 15895982
    42426 1z9k:B (4.6) BS06 U10 ? GO:0009772 ... P0C0Y9 15895982
    42427 1z9n:A (1.5) BS01 CU 1.15.1.1 GO:0004784 ... Q59452 19103206
    42428 1z9n:A (1.5) BS02 ZN 1.15.1.1 GO:0004784 ... Q59452 19103206
    42429 1z9n:A (1.5) BS03 HEM 1.15.1.1 GO:0004784 ... Q59452 19103206
    42430 1z9n:B (1.5) BS01 HEM 1.15.1.1 GO:0004784 ... Q59452 19103206
    42431 1z9n:B (1.5) BS02 CU 1.15.1.1 GO:0004784 ... Q59452 19103206
    42432 1z9n:B (1.5) BS03 ZN 1.15.1.1 GO:0004784 ... Q59452 19103206
    42433 1z9n:C (1.5) BS01 CU 1.15.1.1 GO:0004784 ... Q59452 19103206
    42434 1z9n:C (1.5) BS02 ZN 1.15.1.1 GO:0004784 ... Q59452 19103206
    42435 1z9n:C (1.5) BS03 HEM 1.15.1.1 GO:0004784 ... Q59452 19103206
    42436 1z9n:D (1.5) BS01 HEM 1.15.1.1 GO:0004784 ... Q59452 19103206
    42437 1z9n:D (1.5) BS02 CU 1.15.1.1 GO:0004784 ... Q59452 19103206
    42438 1z9n:D (1.5) BS03 ZN 1.15.1.1 GO:0004784 ... Q59452 19103206
    42439 1z9o:A (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42440 1z9o:A (1.9) BS02 peptide ? GO:0005789 ... Q9Z270 16004875
    42441 1z9o:B (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42442 1z9o:B (1.9) BS02 peptide ? GO:0005789 ... Q9Z270 16004875
    42443 1z9o:C (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42444 1z9o:C (1.9) BS02 peptide ? GO:0005789 ... Q9Z270 16004875
    42445 1z9o:D (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42446 1z9o:E (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42447 1z9o:E (1.9) BS02 peptide ? GO:0005789 ... Q9Z270 16004875
    42448 1z9o:F (1.9) BS01 peptide ? GO:0005789 ... Q9Z270 16004875
    42449 1z9y:A (1.66) BS01 ZN 4.2.1.1
    4.2.1.69    		 GO:0002009 ... P00918 N/A
    42450 1z9y:A (1.66) BS02 FUN 4.2.1.1
    4.2.1.69    		 GO:0002009 ... P00918 N/A PDBbind: -logKd/Ki=7.19, Ki=65nM
    BindingDB: Ki=6.5e+4nM
    42451 1za0:A (2.0) BS01 MN 1.14.19.- GO:0005515 ... P9WNZ5 15929999
    42452 1za1:B (2.2) BS01 ZN 2.1.3.2 GO:0005515 ... P0A7F3 15951418
    42453 1za1:B (2.2) BS02 CTP 2.1.3.2 GO:0005515 ... P0A7F3 15951418
    42454 1za1:D (2.2) BS01 ZN 2.1.3.2 GO:0005515 ... P0A7F3 15951418
    42455 1za1:D (2.2) BS02 CTP 2.1.3.2 GO:0005515 ... P0A7F3 15951418
    42456 1za2:A (2.5) BS01 CP 2.1.3.2 GO:0004070 ... P0A786 15951418
    42457 1za2:A (2.5) BS02 CP 2.1.3.2 GO:0004070 ... P0A786 15951418
    42458 1za2:B (2.5) BS01 ZN ? GO:0005515 ... P0A7F3 15951418
    42459 1za2:B (2.5) BS02 CTP ? GO:0005515 ... P0A7F3 15951418
    42460 1za2:C (2.5) BS01 CP 2.1.3.2 GO:0004070 ... P0A786 15951418
    42461 1za2:C (2.5) BS02 CP 2.1.3.2 GO:0004070 ... P0A786 15951418
    42462 1za2:D (2.5) BS01 ZN ? GO:0005515 ... P0A7F3 15951418
    42463 1za2:D (2.5) BS02 CTP ? GO:0005515 ... P0A7F3 15951418
    42464 1za5:A (1.8) BS01 FE 1.15.1.1 GO:0000303 ... P0AGD3 16430211
    42465 1za5:B (1.8) BS01 FE 1.15.1.1 GO:0000303 ... P0AGD3 16430211
    42466 1zab:A (2.36) BS01 ZN 3.5.4.5 GO:0001882 ... P56389 16784234
    42467 1zab:A (2.36) BS02 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42468 1zab:A (2.36) BS03 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42469 1zab:B (2.36) BS01 ZN 3.5.4.5 GO:0001882 ... P56389 16784234
    42470 1zab:B (2.36) BS02 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42471 1zab:B (2.36) BS03 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42472 1zab:C (2.36) BS01 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42473 1zab:C (2.36) BS02 ZN 3.5.4.5 GO:0001882 ... P56389 16784234
    42474 1zab:C (2.36) BS03 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42475 1zab:D (2.36) BS01 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42476 1zab:D (2.36) BS02 ZN 3.5.4.5 GO:0001882 ... P56389 16784234
    42477 1zab:D (2.36) BS03 URD 3.5.4.5 GO:0001882 ... P56389 16784234
    42478 1zai:A (1.76) BS01 2FP 4.1.2.13 GO:0004332 ... P00883 15870069
    42479 1zai:B (1.76) BS01 2FP 4.1.2.13 GO:0004332 ... P00883 15870069
    42480 1zai:C (1.76) BS01 2FP 4.1.2.13 GO:0004332 ... P00883 15870069
    42481 1zai:D (1.76) BS01 2FP 4.1.2.13 GO:0004332 ... P00883 15870069
    42482 1zaj:A (1.89) BS01 M2P 4.1.2.13 GO:0004332 ... P00883 15870069 PDBbind: -logKd/Ki=5.10, IC50=8uM
    BindingDB: IC50=8000nM
    42483 1zaj:B (1.89) BS01 M2P 4.1.2.13 GO:0004332 ... P00883 15870069 BindingDB: IC50=8000nM
    42484 1zaj:C (1.89) BS01 M2P 4.1.2.13 GO:0004332 ... P00883 15870069 BindingDB: IC50=8000nM
    42485 1zaj:D (1.89) BS01 M2P 4.1.2.13 GO:0004332 ... P00883 15870069 BindingDB: IC50=8000nM
    42486 1zak:A (3.5) BS01 AP5 2.7.4.3 GO:0004017 ... P43188 9428681
    42487 1zak:B (3.5) BS01 AP5 2.7.4.3 GO:0004017 ... P43188 9428681
    42488 1zal:A (1.89) BS01 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42489 1zal:A (1.89) BS02 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42490 1zal:B (1.89) BS01 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42491 1zal:B (1.89) BS02 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42492 1zal:C (1.89) BS01 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42493 1zal:C (1.89) BS02 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42494 1zal:D (1.89) BS01 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42495 1zal:D (1.89) BS02 PO4 4.1.2.13 GO:0004332 ... P00883 15870069
    42496 1zao:A (1.84) BS01 MN 2.7.11.1 GO:0004672 ... O30245 15943813
    42497 1zao:A (1.84) BS02 MN 2.7.11.1 GO:0004672 ... O30245 15943813
    42498 1zao:A (1.84) BS03 PO4 2.7.11.1 GO:0004672 ... O30245 15943813
    42499 1zao:A (1.84) BS04 ATP 2.7.11.1 GO:0004672 ... O30245 15943813
    42500 1zap:A (2.5) BS01 A70 3.4.23.24 GO:0004190 ... P0CS83 8845753 MOAD: Ki=0.17nM
    42501 1zar:A (1.75) BS01 MN 2.7.11.1 GO:0004672 ... O30245 15943813
    42502 1zar:A (1.75) BS02 ADP 2.7.11.1 GO:0004672 ... O30245 15943813
    42503 1zav:A (1.9) BS01 peptide ? GO:0003735 ... P29394 15989950
    42504 1zav:A (1.9) BS02 peptide ? GO:0003735 ... P29394 15989950
    42505 1zav:A (1.9) BS03 peptide ? GO:0003735 ... P29394 15989950
    42506 1zav:U (1.9) BS01 peptide ? GO:0003735 ... P29396 15989950
    42507 1zav:W (1.9) BS01 peptide ? GO:0003735 ... P29396 15989950
    42508 1zav:W (1.9) BS02 peptide ? GO:0003735 ... P29396 15989950
    42509 1zaw:A (2.3) BS01 peptide ? GO:0003735 ... P29394 15989950
    42510 1zaw:A (2.3) BS02 peptide ? GO:0003735 ... P29394 15989950
    42511 1zaw:A (2.3) BS03 peptide ? GO:0003735 ... P29394 15989950
    42512 1zaw:U (2.3) BS01 peptide ? GO:0003735 ... P29396 15989950
    42513 1zaw:W (2.3) BS01 peptide ? GO:0003735 ... P29396 15989950
    42514 1zaw:W (2.3) BS02 peptide ? GO:0003735 ... P29396 15989950
    42515 1zax:A (2.1) BS01 peptide ? GO:0003735 ... P29394 15989950
    42516 1zax:A (2.1) BS02 peptide ? GO:0003735 ... P29394 15989950
    42517 1zax:U (2.1) BS01 peptide ? GO:0003735 ... P29396 15989950
    42518 1zax:W (2.1) BS01 peptide ? GO:0003735 ... P29396 15989950
    42519 1zax:W (2.1) BS02 peptide ? GO:0003735 ... P29396 15989950
    42520 1zay:A (2.7) BS01 dna ? GO:0000976 ... P0ACP7 N/A
    42521 1zay:A (2.7) BS02 HPA ? GO:0000976 ... P0ACP7 N/A
    42522 1zbb:A (9.0) BS01 dna ? GO:0000786 ... P84233 16001076
    42523 1zbb:A (9.0) BS02 dna ? GO:0000786 ... P84233 16001076
    42524 1zbb:B (9.0) BS01 dna ? GO:0000786 ... P62799 16001076
    42525 1zbb:B (9.0) BS02 dna ? GO:0000786 ... P62799 16001076
    42526 1zbb:C (9.0) BS01 dna ? GO:0000786 ... P06897 16001076
    42527 1zbb:C (9.0) BS02 dna ? GO:0000786 ... P06897 16001076
    42528 1zbb:D (9.0) BS01 dna ? GO:0000786 ... P02281 16001076
    42529 1zbb:D (9.0) BS02 dna ? GO:0000786 ... P02281 16001076
    42530 1zbb:E (9.0) BS01 dna ? GO:0000786 ... P84233 16001076
    42531 1zbb:E (9.0) BS02 dna ? GO:0000786 ... P84233 16001076
    42532 1zbb:F (9.0) BS01 dna ? GO:0000786 ... P62799 16001076
    42533 1zbb:F (9.0) BS02 dna ? GO:0000786 ... P62799 16001076
    42534 1zbb:G (9.0) BS01 dna ? GO:0000786 ... P06897 16001076
    42535 1zbb:G (9.0) BS02 dna ? GO:0000786 ... P06897 16001076
    42536 1zbb:H (9.0) BS01 dna ? GO:0000786 ... P02281 16001076
    42537 1zbb:H (9.0) BS02 dna ? GO:0000786 ... P02281 16001076
    42538 1zbb:a (9.0) BS01 dna ? GO:0000786 ... P84233 16001076
    42539 1zbb:a (9.0) BS02 dna ? GO:0000786 ... P84233 16001076
    42540 1zbb:b (9.0) BS01 dna ? GO:0000786 ... P62799 16001076
    42541 1zbb:b (9.0) BS02 dna ? GO:0000786 ... P62799 16001076
    42542 1zbb:c (9.0) BS01 dna ? GO:0000786 ... P06897 16001076
    42543 1zbb:c (9.0) BS02 dna ? GO:0000786 ... P06897 16001076
    42544 1zbb:d (9.0) BS01 dna ? GO:0000786 ... P02281 16001076
    42545 1zbb:d (9.0) BS02 dna ? GO:0000786 ... P02281 16001076
    42546 1zbb:e (9.0) BS01 dna ? GO:0000786 ... P84233 16001076
    42547 1zbb:e (9.0) BS02 dna ? GO:0000786 ... P84233 16001076
    42548 1zbb:f (9.0) BS01 dna ? GO:0000786 ... P62799 16001076
    42549 1zbb:f (9.0) BS02 dna ? GO:0000786 ... P62799 16001076
    42550 1zbb:g (9.0) BS01 dna ? GO:0000786 ... P06897 16001076
    42551 1zbb:g (9.0) BS02 dna ? GO:0000786 ... P06897 16001076
    42552 1zbb:h (9.0) BS01 dna ? GO:0000786 ... P02281 16001076
    42553 1zbb:h (9.0) BS02 dna ? GO:0000786 ... P02281 16001076
    42554 1zbc:A (2.29) BS01 peptide ? GO:0004568 ... Q29411 N/A
    42555 1zbd:A (2.6) BS01 MG ? GO:0001669 ... P63012 10025402
    42556 1zbd:A (2.6) BS02 GTP ? GO:0001669 ... P63012 10025402
    42557 1zbk:A (2.9) BS01 peptide ? GO:0005576 ... Q6TMG6 N/A
    42558 1zbu:A (2.998) BS01 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42559 1zbu:A (2.998) BS02 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42560 1zbu:A (2.998) BS03 AMP 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42561 1zbu:B (2.998) BS01 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42562 1zbu:B (2.998) BS02 AMP 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42563 1zbu:C (2.998) BS01 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42564 1zbu:C (2.998) BS02 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42565 1zbu:C (2.998) BS03 AMP 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42566 1zbu:D (2.998) BS01 MG 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42567 1zbu:D (2.998) BS02 AMP 3.1.-.- GO:0000175 ... Q8IV48 N/A
    42568 1zbv:A (3.21) BS01 peptide ? GO:0005576 ... Q8SPQ0 N/A
    42569 1zbw:A (2.8) BS01 peptide ? GO:0005576 ... Q8SPQ0 N/A
    42570 1zc3:A (2.0) BS01 MG 3.6.5.2 GO:0003924 ... P11233 15920473
    42571 1zc3:A (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    42572 1zc3:C (2.0) BS01 MG 3.6.5.2 GO:0003924 ... P11233 15920473
    42573 1zc3:C (2.0) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    42574 1zc4:A (2.5) BS01 MG 3.6.5.2 GO:0003924 ... P11233 15920473
    42575 1zc4:A (2.5) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    42576 1zc4:C (2.5) BS01 MG 3.6.5.2 GO:0003924 ... P11233 15920473
    42577 1zc4:C (2.5) BS02 GNP 3.6.5.2 GO:0003924 ... P11233 15920473
    42578 1zcb:A (2.0) BS01 GDP ? GO:0001525 ... P27601 16388592
    42579 1zcl:A (2.9) BS01 SO4 3.1.3.48 GO:0004721 ... Q78EG7 16142898
    42580 1zcl:B (2.9) BS01 SO4 3.1.3.48 GO:0004721 ... Q78EG7 16142898
    42581 1zcr:B (1.8) BS01 IOD ? GO:0005179 ... P02766 15981995
    42582 1zd2:P (3.0) BS01 MG 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563
    42583 1zd2:P (3.0) BS02 NC3 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563 PDBbind: -logKd/Ki=3.30, IC50>500uM
    BindingDB: IC50=>500000nM
    42584 1zd3:A (2.3) BS01 MG 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563
    42585 1zd3:A (2.3) BS02 NC4 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563 MOAD: ic50>500uM
    PDBbind: -logKd/Ki=3.30, IC50>500uM
    BindingDB: IC50=36000nM
    42586 1zd4:A (2.7) BS01 MG 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563
    42587 1zd4:A (2.7) BS02 NC6 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563 PDBbind: -logKd/Ki=3.60, IC50=253uM
    BindingDB: IC50=>100000nM
    42588 1zd5:A (2.6) BS01 MG 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563
    42589 1zd5:A (2.6) BS02 NC7 3.1.3.76
    3.3.2.10    		 GO:0000287 ... P34913 16322563 PDBbind: -logKd/Ki=4.87, IC50=13.4uM
    42590 1zd9:A (1.7) BS01 GDP ? GO:0003924 ... Q96BM9 N/A
    42591 1zdf:A (2.45) BS01 MN 2.4.1.186 GO:0005737 ... P13280 15849187
    42592 1zdf:A (2.45) BS02 UPG 2.4.1.186 GO:0005737 ... P13280 15849187
    42593 1zdg:A (2.3) BS01 MN 2.4.1.186 GO:0005737 ... P13280 15849187
    42594 1zdg:A (2.3) BS02 UPG 2.4.1.186 GO:0005737 ... P13280 15849187
    42595 1zdh:A (2.7) BS01 rna ? GO:0003723 ... P03612 9245600
    42596 1zdh:C (2.7) BS01 rna ? GO:0003723 ... P03612 9245600
    42597 1zdi:A (2.7) BS01 rna ? GO:0003723 ... P03612 9245600
    42598 1zdi:C (2.7) BS01 rna ? GO:0003723 ... P03612 9245600
    42599 1zdj:A (2.9) BS01 rna ? GO:0003723 ... P03612 9917072
    42600 1zdj:C (2.9) BS01 rna ? GO:0003723 ... P03612 9917072
    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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