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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.
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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
    64401 1yfj:D (2.69) BS04 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64402 1yfj:E (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64403 1yfj:E (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64404 1yfj:E (2.69) BS03 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64405 1yfj:F (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64406 1yfj:F (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64407 1yfj:F (2.69) BS03 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64408 1yfk:A (2.7) BS01 CL 5.4.2.11
    5.4.2.4    		 GO:0003824 ... P18669 15883004
    64409 1yfl:A (3.09) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64410 1yfl:A (3.09) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64411 1yfl:A (3.09) BS03 SFG 2.1.1.72 GO:0003676 ... P04392 15882618
    64412 1yfl:B (3.09) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64413 1yfl:B (3.09) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64414 1yfl:B (3.09) BS03 SFG 2.1.1.72 GO:0003676 ... P04392 15882618
    64415 1yfl:D (3.09) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64416 1yfl:D (3.09) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64417 1yfl:D (3.09) BS03 SFG 2.1.1.72 GO:0003676 ... P04392 15882618
    64418 1yfl:E (3.09) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64419 1yfl:E (3.09) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64420 1yfl:E (3.09) BS03 SFG 2.1.1.72 GO:0003676 ... P04392 15882618
    64421 1yfn:A (1.8) BS01 peptide ? N/A P0AFZ3 15880122
    64422 1yfn:B (1.8) BS01 peptide ? N/A P0AFZ3 15880122
    64423 1yfn:C (1.8) BS01 peptide ? N/A P0AFZ3 15880122
    64424 1yfn:C (1.8) BS02 peptide ? N/A P0AFZ3 15880122
    64425 1yfn:D (1.8) BS01 peptide ? N/A P0AFZ3 15880122
    64426 1yfq:A (1.1) BS01 CA ? GO:0000776 ... P26449 15644329
    64427 1yfq:A (1.1) BS02 CA ? GO:0000776 ... P26449 15644329
    64428 1yfr:A (2.15) BS01 MG 6.1.1.7 GO:0000166 ... O67323 15657145
    64429 1yfr:A (2.15) BS02 ATP 6.1.1.7 GO:0000166 ... O67323 15657145
    64430 1yfr:B (2.15) BS01 MG 6.1.1.7 GO:0000166 ... O67323 15657145
    64431 1yfr:B (2.15) BS02 MG 6.1.1.7 GO:0000166 ... O67323 15657145
    64432 1yfr:B (2.15) BS03 ATP 6.1.1.7 GO:0000166 ... O67323 15657145
    64433 1yfs:A (2.08) BS01 ALA 6.1.1.7 GO:0000166 ... O67323 15657145
    64434 1yfs:B (2.08) BS01 ALA 6.1.1.7 GO:0000166 ... O67323 15657145
    64435 1yfu:A (1.9) BS01 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64436 1yfu:A (1.9) BS02 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64437 1yfw:A (2.0) BS01 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64438 1yfw:A (2.0) BS02 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64439 1yfw:A (2.0) BS03 OXY 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64440 1yfw:A (2.0) BS04 4AA 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64441 1yfx:A (2.0) BS01 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64442 1yfx:A (2.0) BS02 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64443 1yfx:A (2.0) BS03 NO 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64444 1yfx:A (2.0) BS04 4AA 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64445 1yfy:A (3.2) BS01 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64446 1yfy:A (3.2) BS02 FE 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64447 1yfy:A (3.2) BS03 3HA 1.13.11.6 GO:0000334 ... Q1LCS4 15909978
    64448 1yfz:A (2.2) BS01 MG 2.4.2.8 GO:0000166 ... Q8R7L0 15854655
    64449 1yfz:A (2.2) BS02 IMP 2.4.2.8 GO:0000166 ... Q8R7L0 15854655 MOAD: Ki=45uM
    PDBbind: -logKd/Ki=4.35, Ki=45uM
    64450 1yfz:B (2.2) BS01 MG 2.4.2.8 GO:0000166 ... Q8R7L0 15854655
    64451 1yfz:B (2.2) BS02 IMP 2.4.2.8 GO:0000166 ... Q8R7L0 15854655 MOAD: Ki=45uM
    64452 1yg5:A (2.7) BS01 HEM ? GO:0004601 ... P69905 15835899
    64453 1yg5:B (2.7) BS01 HEM ? GO:0004601 ... P68871 15835899
    64454 1yg5:B (2.7) BS02 OXY ? GO:0004601 ... P68871 15835899
    64455 1yg5:C (2.7) BS01 HEM ? GO:0004601 ... P69905 15835899
    64456 1yg5:C (2.7) BS02 OXY ? GO:0004601 ... P69905 15835899
    64457 1yg5:D (2.7) BS01 HEM ? GO:0004601 ... P68871 15835899
    64458 1yg5:D (2.7) BS02 OXY ? GO:0004601 ... P68871 15835899
    64459 1yg9:A (1.3) BS01 ZN 3.4.23.- GO:0004190 ... P54958 15811379
    64460 1ygb:A (2.48) BS01 SER 6.1.1.7 GO:0000166 ... O67323 15657145
    64461 1ygc:H (2.0) BS01 CA 3.4.21.21 GO:0004252 ... P08709 15632123
    64462 1ygc:H (2.0) BS02 905 3.4.21.21 GO:0004252 ... P08709 15632123 MOAD: Ki=0.35nM
    BindingDB: Ki=0.35nM
    64463 1ygd:A (2.73) BS01 ZNH ? GO:0004601 ... P69905 15835899
    64464 1ygd:B (2.73) BS01 HEM ? GO:0004601 ... P68871 15835899
    64465 1ygd:B (2.73) BS02 OXY ? GO:0004601 ... P68871 15835899
    64466 1ygd:C (2.73) BS01 ZNH ? GO:0004601 ... P69905 15835899
    64467 1ygd:D (2.73) BS01 HEM ? GO:0004601 ... P68871 15835899
    64468 1ygd:D (2.73) BS02 OXY ? GO:0004601 ... P68871 15835899
    64469 1yge:A (1.4) BS01 FE 1.13.11.12 GO:0005506 ... P08170 8718858
    64470 1ygf:A (2.7) BS01 HEM ? GO:0004601 ... P69905 15835899
    64471 1ygf:A (2.7) BS02 OXY ? GO:0004601 ... P69905 15835899
    64472 1ygf:B (2.7) BS01 HEM ? GO:0004601 ... P68871 15835899
    64473 1ygf:B (2.7) BS02 OXY ? GO:0004601 ... P68871 15835899
    64474 1ygf:C (2.7) BS01 HEM ? GO:0004601 ... P69905 15835899
    64475 1ygf:D (2.7) BS01 HEM ? GO:0004601 ... P68871 15835899
    64476 1ygf:D (2.7) BS02 OXY ? GO:0004601 ... P68871 15835899
    64477 1ygj:A (2.7) BS01 RMC 2.7.1.35 GO:0005524 ... P82197 15985434
    64478 1ygk:A (2.6) BS01 RRC 2.7.1.35 GO:0005524 ... P82197 15985434
    64479 1ygp:A (2.8) BS01 PO4 2.4.1.1 GO:0004645 ... P06738 8703213
    64480 1ygp:A (2.8) BS02 PO4 2.4.1.1 GO:0004645 ... P06738 8703213
    64481 1ygp:A (2.8) BS03 PLP 2.4.1.1 GO:0004645 ... P06738 8703213
    64482 1ygp:B (2.8) BS01 PO4 2.4.1.1 GO:0004645 ... P06738 8703213
    64483 1ygp:B (2.8) BS02 PO4 2.4.1.1 GO:0004645 ... P06738 8703213
    64484 1ygp:B (2.8) BS03 PLP 2.4.1.1 GO:0004645 ... P06738 8703213
    64485 1ygr:A (2.9) BS01 peptide 3.1.3.48 GO:0004725 ... P08575 15684325
    64486 1ygr:B (2.9) BS01 peptide 3.1.3.48 GO:0004725 ... P08575 15684325
    64487 1ygu:A (2.9) BS01 peptide 3.1.3.48 GO:0004725 ... P08575 15684325
    64488 1ygu:B (2.9) BS01 peptide 3.1.3.48 GO:0004725 ... P08575 15684325
    64489 1yh8:A (2.7) BS01 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64490 1yh8:A (2.7) BS02 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64491 1yh8:A (2.7) BS03 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64492 1yh8:B (2.7) BS01 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64493 1yh8:B (2.7) BS02 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64494 1yh9:A (2.2) BS01 HEM ? GO:0004601 ... P69905 15835899
    64495 1yh9:B (2.2) BS01 HEM ? GO:0004601 ... P68871 15835899
    64496 1yh9:B (2.2) BS02 OXY ? GO:0004601 ... P68871 15835899
    64497 1yh9:C (2.2) BS01 HEM ? GO:0004601 ... P69905 15835899
    64498 1yh9:C (2.2) BS02 OXY ? GO:0004601 ... P69905 15835899
    64499 1yh9:D (2.2) BS01 HEM ? GO:0004601 ... P68871 15835899
    64500 1yh9:D (2.2) BS02 OXY ? GO:0004601 ... P68871 15835899
    64501 1yhc:A (2.1) BS01 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64502 1yhc:A (2.1) BS02 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64503 1yhc:A (2.1) BS03 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64504 1yhc:A (2.1) BS04 CAC 3.5.1.108 GO:0006796 ... O67648 15705580
    64505 1yhc:B (2.1) BS01 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64506 1yhc:B (2.1) BS02 ZN 3.5.1.108 GO:0006796 ... O67648 15705580
    64507 1yhc:B (2.1) BS03 CAC 3.5.1.108 GO:0006796 ... O67648 15705580
    64508 1yhe:A (2.1) BS01 HEM ? GO:0004601 ... P69905 15835899
    64509 1yhe:B (2.1) BS01 HEM ? GO:0004601 ... P68871 15835899
    64510 1yhe:B (2.1) BS02 OXY ? GO:0004601 ... P68871 15835899
    64511 1yhe:C (2.1) BS01 HEM ? GO:0004601 ... P69905 15835899
    64512 1yhe:D (2.1) BS01 HEM ? GO:0004601 ... P68871 15835899
    64513 1yhe:D (2.1) BS02 OXY ? GO:0004601 ... P68871 15835899
    64514 1yhj:A (2.8) BS01 R6C 2.7.1.35 GO:0005524 ... P82197 15985434
    64515 1yhl:A (1.95) BS01 MG ? GO:0004659 ... Q8WS26 16288456
    64516 1yhl:A (1.95) BS02 MG ? GO:0004659 ... Q8WS26 16288456
    64517 1yhl:A (1.95) BS03 DMA ? GO:0004659 ... Q8WS26 16288456
    64518 1yhl:A (1.95) BS04 RIS ? GO:0004659 ... Q8WS26 16288456 BindingDB: IC50=27nM
    64519 1yhm:A (2.5) BS01 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64520 1yhm:A (2.5) BS02 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64521 1yhm:A (2.5) BS03 AHD 2.5.1.10 GO:0004659 ... Q8WS26 16288456 MOAD: ic50=147uM
    PDBbind: -logKd/Ki=3.83, IC50=147uM
    64522 1yhm:A (2.5) BS04 IPE 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64523 1yhm:B (2.5) BS01 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64524 1yhm:B (2.5) BS02 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64525 1yhm:B (2.5) BS03 AHD 2.5.1.10 GO:0004659 ... Q8WS26 16288456 MOAD: ic50=147uM
    64526 1yhm:B (2.5) BS04 IPE 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64527 1yhm:C (2.5) BS01 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64528 1yhm:C (2.5) BS02 MG 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64529 1yhm:C (2.5) BS03 AHD 2.5.1.10 GO:0004659 ... Q8WS26 16288456 MOAD: ic50=147uM
    64530 1yhm:C (2.5) BS04 IPE 2.5.1.10 GO:0004659 ... Q8WS26 16288456
    64531 1yhn:A (3.0) BS01 MG 3.6.5.2 GO:0000045 ... P51149 15933719
    64532 1yhn:A (3.0) BS02 GTP 3.6.5.2 GO:0000045 ... P51149 15933719
    64533 1yho:A (-1.00) BS01 NDP 1.5.1.3 GO:0000900 ... P00374 16222560
    64534 1yho:A (-1.00) BS02 TRR 1.5.1.3 GO:0000900 ... P00374 16222560
    64535 1yhq:1 (2.4) BS01 rna ? GO:0003723 ... P32410 15851032
    64536 1yhq:2 (2.4) BS01 rna ? GO:0003735 ... P22452 15851032
    64537 1yhq:3 (2.4) BS01 rna ? GO:0000049 ... P32411 15851032
    64538 1yhq:A (2.4) BS01 rna ? GO:0002181 ... P20276 15851032
    64539 1yhq:A (2.4) BS02 MG ? GO:0002181 ... P20276 15851032
    64540 1yhq:A (2.4) BS03 MG ? GO:0002181 ... P20276 15851032
    64541 1yhq:B (2.4) BS01 rna ? GO:0003723 ... P20279 15851032
    64542 1yhq:C (2.4) BS01 rna ? GO:0003723 ... P12735 15851032
    64543 1yhq:D (2.4) BS01 rna ? GO:0000049 ... P14124 15851032
    64544 1yhq:D (2.4) BS02 rna ? GO:0000049 ... P14124 15851032
    64545 1yhq:E (2.4) BS01 rna ? GO:0002181 ... P14135 15851032
    64546 1yhq:F (2.4) BS01 rna ? GO:0001682 ... P12743 15851032
    64547 1yhq:H (2.4) BS01 rna ? GO:0000027 ... P60617 15851032
    64548 1yhq:I (2.4) BS01 rna ? GO:0003735 ... P14122 15851032
    64549 1yhq:J (2.4) BS01 rna ? GO:0003729 ... P29198 15851032
    64550 1yhq:K (2.4) BS01 rna ? GO:0003735 ... P22450 15851032
    64551 1yhq:L (2.4) BS01 rna ? GO:0003735 ... P12737 15851032
    64552 1yhq:M (2.4) BS01 rna ? GO:0002181 ... P60618 15851032
    64553 1yhq:N (2.4) BS01 rna ? GO:0000027 ... P14123 15851032
    64554 1yhq:N (2.4) BS02 rna ? GO:0000027 ... P14123 15851032
    64555 1yhq:O (2.4) BS01 rna ? GO:0003723 ... P12733 15851032
    64556 1yhq:P (2.4) BS01 rna ? GO:0003723 ... P14119 15851032
    64557 1yhq:Q (2.4) BS01 rna ? GO:0003735 ... P12734 15851032
    64558 1yhq:Q (2.4) BS02 rna ? GO:0003735 ... P12734 15851032
    64559 1yhq:R (2.4) BS01 rna ? GO:0002181 ... P10970 15851032
    64560 1yhq:S (2.4) BS01 rna ? GO:0000027 ... P12732 15851032
    64561 1yhq:T (2.4) BS01 rna ? GO:0002181 ... P10972 15851032
    64562 1yhq:T (2.4) BS02 MG ? GO:0002181 ... P10972 15851032
    64563 1yhq:U (2.4) BS01 rna ? GO:0003735 ... P14116 15851032
    64564 1yhq:V (2.4) BS01 rna ? GO:0003735 ... P10971 15851032
    64565 1yhq:W (2.4) BS01 rna ? GO:0000463 ... P14121 15851032
    64566 1yhq:W (2.4) BS02 rna ? GO:0000463 ... P14121 15851032
    64567 1yhq:X (2.4) BS01 rna ? GO:0002181 ... P18138 15851032
    64568 1yhq:Y (2.4) BS01 rna ? GO:0000166 ... P12736 15851032
    64569 1yhq:Y (2.4) BS02 MG ? GO:0000166 ... P12736 15851032
    64570 1yhq:Z (2.4) BS01 rna ? GO:0003735 ... P60619 15851032
    64571 1yhr:A (2.6) BS01 HEM ? GO:0004601 ... P69905 15835899
    64572 1yhr:B (2.6) BS01 OXY ? GO:0004601 ... P68871 15835899
    64573 1yhr:B (2.6) BS02 HEM ? GO:0004601 ... P68871 15835899
    64574 1yhr:C (2.6) BS01 HEM ? GO:0004601 ... P69905 15835899
    64575 1yhr:D (2.6) BS01 OXY ? GO:0004601 ... P68871 15835899
    64576 1yhr:D (2.6) BS02 HEM ? GO:0004601 ... P68871 15835899
    64577 1yhs:A (2.15) BS01 STU 2.7.11.1 GO:0004672 ... P11309 15657054 MOAD: ic50=0.01uM
    PDBbind: -logKd/Ki=8.00, IC50=0.01uM
    64578 1yht:A (2.0) BS01 GOL 3.2.1.52 GO:0004553 ... Q840G9 15878175
    64579 1yht:A (2.0) BS02 GOL 3.2.1.52 GO:0004553 ... Q840G9 15878175
    64580 1yhu:A (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64581 1yhu:A (3.15) BS02 OXY ? GO:0005344 ... Q8IFK4 15710902
    64582 1yhu:B (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64583 1yhu:B (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    64584 1yhu:B (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64585 1yhu:B (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64586 1yhu:C (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64587 1yhu:C (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64588 1yhu:D (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64589 1yhu:E (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64590 1yhu:E (3.15) BS02 OXY ? GO:0005344 ... Q8IFK4 15710902
    64591 1yhu:F (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64592 1yhu:F (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    64593 1yhu:F (3.15) BS03 HEM ? GO:0001666 ... P80592 15710902
    64594 1yhu:F (3.15) BS04 OXY ? GO:0001666 ... P80592 15710902
    64595 1yhu:G (3.15) BS01 HEM ? GO:0001666 ... Q8IFK2 15710902
    64596 1yhu:G (3.15) BS02 OXY ? GO:0001666 ... Q8IFK2 15710902
    64597 1yhu:H (3.15) BS01 HEM ? GO:0005344 ... Q8IFJ9 15710902
    64598 1yhu:I (3.15) BS01 HEM ? GO:0005344 ... Q8IFK4 15710902
    64599 1yhu:J (3.15) BS01 ZN ? GO:0001666 ... P80592 15710902
    64600 1yhu:J (3.15) BS02 ZN ? GO:0001666 ... P80592 15710902
    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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