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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
    63201 1xzc:A (1.75) BS01 PMB 3.1.1.74 GO:0005576 ... P00590 N/A
    63202 1xzk:A (2.01) BS01 DFP 3.1.1.74 GO:0005576 ... P00590 8990497
    63203 1xzk:B (2.01) BS01 DFP 3.1.1.74 GO:0005576 ... P00590 8990497
    63204 1xzl:A (1.69) BS01 HEE 3.1.1.74 GO:0005576 ... P00590 8990497
    63205 1xzm:A (1.75) BS01 DPE 3.1.1.74 GO:0005576 ... P00590 8990497
    63206 1xzn:A (2.27) BS01 MG 2.4.2.9 GO:0003723 ... P41007 15716449
    63207 1xzn:B (2.27) BS01 MG 2.4.2.9 GO:0003723 ... P41007 15716449
    63208 1xzo:A (1.702) BS01 CA ? GO:0005886 ... P54178 15723536
    63209 1xzo:A (1.702) BS02 CA ? GO:0005886 ... P54178 15723536
    63210 1xzo:A (1.702) BS03 CA ? GO:0005886 ... P54178 15723536
    63211 1xzo:B (1.702) BS01 CA ? GO:0005886 ... P54178 15723536
    63212 1xzo:B (1.702) BS02 CA ? GO:0005886 ... P54178 15723536
    63213 1xzo:B (1.702) BS03 CA ? GO:0005886 ... P54178 15723536
    63214 1xzq:A (2.9) BS01 FON 3.6.5.- GO:0002098 ... Q9WYA4 15616586
    63215 1xzq:A (2.9) BS02 FON 3.6.5.- GO:0002098 ... Q9WYA4 15616586
    63216 1xzq:B (2.9) BS01 FON 3.6.5.- N/A Q9WYA4 15616586
    63217 1xzq:B (2.9) BS02 FON 3.6.5.- N/A Q9WYA4 15616586
    63218 1xzu:A (2.16) BS01 HEM ? GO:0004601 ... P69905 15835899
    63219 1xzu:B (2.16) BS01 HEM ? GO:0004601 ... P68871 15835899
    63220 1xzu:C (2.16) BS01 HEM ? GO:0004601 ... P69905 15835899
    63221 1xzu:D (2.16) BS01 HEM ? GO:0004601 ... P68871 15835899
    63222 1xzv:A (2.11) BS01 HEM ? GO:0004601 ... P69905 15835899
    63223 1xzv:B (2.11) BS01 HEM ? GO:0004601 ... P68871 15835899
    63224 1xzv:C (2.11) BS01 HEM ? GO:0004601 ... P69905 15835899
    63225 1xzv:D (2.11) BS01 HEM ? GO:0004601 ... P68871 15835899
    63226 1xzw:A (2.5) BS01 FE 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63227 1xzw:A (2.5) BS02 MN 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63228 1xzw:A (2.5) BS03 PO4 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63229 1xzw:A (2.5) BS04 PO4 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63230 1xzw:B (2.5) BS01 FE 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63231 1xzw:B (2.5) BS02 MN 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63232 1xzw:B (2.5) BS03 PO4 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63233 1xzw:B (2.5) BS04 PO4 3.1.3.2 GO:0003993 ... Q9SE00 15625111
    63234 1xzx:X (2.5) BS01 T3 ? GO:0003677 ... P10828 15466465 MOAD: Kd=0.06nM
    PDBbind: -logKd/Ki=10.22, Kd=0.06nM
    63235 1y01:B (2.8) BS01 HEM ? GO:0004601 ... P69905 15550245
    63236 1y01:B (2.8) BS02 CHK ? GO:0004601 ... P69905 15550245
    63237 1y02:A (1.8) BS01 ZN 2.3.2.27 N/A Q8WZ73 15576038
    63238 1y02:A (1.8) BS02 ZN 2.3.2.27 N/A Q8WZ73 15576038
    63239 1y07:A (1.55) BS01 FE 1.15.1.2 GO:0005506 ... O83795 16791639
    63240 1y07:B (1.55) BS01 FE 1.15.1.2 GO:0005506 ... O83795 16791639
    63241 1y07:C (1.55) BS01 FE 1.15.1.2 GO:0005506 ... O83795 16791639
    63242 1y07:D (1.55) BS01 FE 1.15.1.2 GO:0005506 ... O83795 16791639
    63243 1y09:A (2.25) BS01 HEM ? GO:0004601 ... P69905 15835899
    63244 1y09:B (2.25) BS01 HEM ? GO:0004601 ... P68871 15835899
    63245 1y09:C (2.25) BS01 HEM ? GO:0004601 ... P69905 15835899
    63246 1y09:D (2.25) BS01 HEM ? GO:0004601 ... P68871 15835899
    63247 1y0a:A (2.22) BS01 HEM ? GO:0004601 ... P69905 15835899
    63248 1y0a:B (2.22) BS01 HEM ? GO:0004601 ... P68871 15835899
    63249 1y0a:C (2.22) BS01 HEM ? GO:0004601 ... P69905 15835899
    63250 1y0a:D (2.22) BS01 HEM ? GO:0004601 ... P68871 15835899
    63251 1y0b:A (1.8) BS01 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63252 1y0b:A (1.8) BS02 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63253 1y0b:B (1.8) BS01 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63254 1y0b:B (1.8) BS02 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63255 1y0b:C (1.8) BS01 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63256 1y0b:C (1.8) BS02 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63257 1y0b:D (1.8) BS01 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63258 1y0b:D (1.8) BS02 G4P 2.4.2.22 GO:0000310 ... P42085 N/A
    63259 1y0c:A (2.3) BS01 HEM ? GO:0004601 ... P69905 15835899
    63260 1y0c:B (2.3) BS01 HEM ? GO:0004601 ... P68871 15835899
    63261 1y0c:C (2.3) BS01 HEM ? GO:0004601 ... P69905 15835899
    63262 1y0c:D (2.3) BS01 HEM ? GO:0004601 ... P68871 15835899
    63263 1y0d:A (2.1) BS01 HEM ? GO:0004601 ... P69905 15835899
    63264 1y0d:B (2.1) BS01 HEM ? GO:0004601 ... P68871 15835899
    63265 1y0d:C (2.1) BS01 HEM ? GO:0004601 ... P69905 15835899
    63266 1y0d:D (2.1) BS01 HEM ? GO:0004601 ... P68871 15835899
    63267 1y0g:A (2.2) BS01 8PP ? N/A P0A8X2 N/A
    63268 1y0g:B (2.2) BS01 8PP ? N/A P0A8X2 N/A
    63269 1y0g:C (2.2) BS01 8PP ? N/A P0A8X2 N/A
    63270 1y0g:D (2.2) BS01 8PP ? N/A P0A8X2 N/A
    63271 1y0j:A (-1.00) BS01 ZN ? GO:0003700 ... P17679 15644435
    63272 1y0j:B (-1.00) BS01 ZN ? GO:0006357 ... Q9VPQ6 15644435
    63273 1y0l:A (2.5) BS01 HAN N/A N/A N/A 15788533 MOAD: Kd~1nM
    63274 1y0l:B (2.5) BS01 HAN N/A N/A N/A 15788533
    63275 1y0l:C (2.5) BS01 HAN N/A N/A N/A 15788533
    63276 1y0l:D (2.5) BS01 HAN N/A N/A N/A 15788533 MOAD: Kd~1nM
    63277 1y0l:F (2.5) BS01 HAN N/A N/A N/A 15788533 MOAD: Kd~1nM
    63278 1y0l:H (2.5) BS01 HAN N/A N/A N/A 15788533 MOAD: Kd~1nM
    PDBbind: -logKd/Ki=9.00, Kd=1nM
    63279 1y0l:L (2.5) BS01 HAN N/A N/A N/A 15788533 PDBbind: -logKd/Ki=9.00, Kd=1nM
    63280 1y0p:A (1.5) BS01 HEM 1.3.2.4 GO:0008202 ... P0C278 N/A
    63281 1y0p:A (1.5) BS02 HEM 1.3.2.4 GO:0008202 ... P0C278 N/A
    63282 1y0p:A (1.5) BS03 HEM 1.3.2.4 GO:0008202 ... P0C278 N/A
    63283 1y0p:A (1.5) BS04 HEM 1.3.2.4 GO:0008202 ... P0C278 N/A
    63284 1y0p:A (1.5) BS05 FAD 1.3.2.4 GO:0008202 ... P0C278 N/A
    63285 1y0p:A (1.5) BS06 MEZ 1.3.2.4 GO:0008202 ... P0C278 N/A
    63286 1y0r:A (1.75) BS01 ZN 3.4.11.- GO:0004177 ... O59196 15713475
    63287 1y0r:A (1.75) BS02 ZN 3.4.11.- GO:0004177 ... O59196 15713475
    63288 1y0s:A (2.65) BS01 331 ? GO:0003677 ... Q03181 10809235
    63289 1y0s:A (2.65) BS02 B7G ? GO:0003677 ... Q03181 10809235
    63290 1y0s:B (2.65) BS01 331 ? GO:0003677 ... Q03181 10809235
    63291 1y0s:B (2.65) BS02 B7G ? GO:0003677 ... Q03181 10809235
    63292 1y0t:A (2.14) BS01 HEM ? GO:0004601 ... P69905 15835899
    63293 1y0t:B (2.14) BS01 HEM ? GO:0004601 ... P68871 15835899
    63294 1y0t:C (2.14) BS01 HEM ? GO:0004601 ... P69905 15835899
    63295 1y0t:D (2.14) BS01 HEM ? GO:0004601 ... P68871 15835899
    63296 1y0v:A (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63297 1y0v:A (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63298 1y0v:B (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63299 1y0v:B (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63300 1y0v:C (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63301 1y0v:C (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63302 1y0v:D (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63303 1y0v:D (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63304 1y0v:E (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63305 1y0v:E (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63306 1y0v:F (3.6) BS01 MG 4.6.1.1 GO:0003824 ... P40136 15719022
    63307 1y0v:F (3.6) BS02 POP 4.6.1.1 GO:0003824 ... P40136 15719022
    63308 1y0v:H (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63309 1y0v:H (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63310 1y0v:H (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63311 1y0v:I (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63312 1y0v:I (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63313 1y0v:I (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63314 1y0v:J (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63315 1y0v:J (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63316 1y0v:J (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63317 1y0v:K (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63318 1y0v:K (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63319 1y0v:K (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63320 1y0v:L (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63321 1y0v:L (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63322 1y0v:L (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63323 1y0v:M (3.6) BS01 CA ? GO:0005102 ... P0DP33 15719022
    63324 1y0v:M (3.6) BS02 CA ? GO:0005102 ... P0DP33 15719022
    63325 1y0v:M (3.6) BS03 CA ? GO:0005102 ... P0DP33 15719022
    63326 1y0w:A (2.14) BS01 HEM ? GO:0004601 ... P69905 15835899
    63327 1y0w:B (2.14) BS01 HEM ? GO:0004601 ... P68871 15835899
    63328 1y0w:C (2.14) BS01 HEM ? GO:0004601 ... P69905 15835899
    63329 1y0w:D (2.14) BS01 HEM ? GO:0004601 ... P68871 15835899
    63330 1y0x:X (3.1) BS01 T44 ? GO:0003677 ... P10828 15466465 PDBbind: -logKd/Ki=8.70, Kd=2nM
    BindingDB: EC50=240nM
    63331 1y0y:A (1.6) BS01 peptide 3.4.11.- GO:0004177 ... O59196 15713475
    63332 1y0y:A (1.6) BS02 ZN 3.4.11.- GO:0004177 ... O59196 15713475
    63333 1y0y:A (1.6) BS03 ZN 3.4.11.- GO:0004177 ... O59196 15713475
    63334 1y0z:A (2.4) BS01 FE2 1.-.-.- GO:0005634 ... Q9LIG0 16511070
    63335 1y0z:B (2.4) BS01 FE2 1.-.-.- GO:0005634 ... Q9LIG0 16511070
    63336 1y10:A (2.3) BS01 CA 4.6.1.1 GO:0004016 ... P9WMU9 15890882
    63337 1y10:B (2.3) BS01 CA 4.6.1.1 GO:0004016 ... P9WMU9 15890882
    63338 1y10:C (2.3) BS01 CA 4.6.1.1 GO:0004016 ... P9WMU9 15890882
    63339 1y10:D (2.3) BS01 CA 4.6.1.1 GO:0004016 ... P9WMU9 15890882
    63340 1y13:A (2.2) BS01 ZN 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63341 1y13:A (2.2) BS02 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63342 1y13:A (2.2) BS03 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63343 1y13:B (2.2) BS01 ZN 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63344 1y13:B (2.2) BS02 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63345 1y13:B (2.2) BS03 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63346 1y13:C (2.2) BS01 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63347 1y13:C (2.2) BS02 ZN 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63348 1y13:C (2.2) BS03 BIO 4.2.3.12 GO:0003874 ... C6KTB6 N/A
    63349 1y17:A (2.4) BS01 CA ? GO:0005576 ... Q9DEF9 N/A
    63350 1y17:B (2.4) BS01 CA ? GO:0005576 ... Q9DEF8 N/A
    63351 1y18:A (2.8) BS01 HAN N/A N/A N/A 15788533
    63352 1y18:B (2.8) BS01 HAN N/A N/A N/A 15788533
    63353 1y18:C (2.8) BS01 HAN N/A N/A N/A 15788533
    63354 1y18:D (2.8) BS01 HAN N/A N/A N/A 15788533
    63355 1y18:E (2.8) BS01 HAN N/A N/A N/A 15788533
    63356 1y18:H (2.8) BS01 HAN N/A N/A N/A 15788533
    63357 1y18:L (2.8) BS01 HAN N/A N/A N/A 15788533
    63358 1y19:B (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63359 1y19:B (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63360 1y19:D (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63361 1y19:D (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63362 1y19:F (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63363 1y19:F (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63364 1y19:H (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63365 1y19:H (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63366 1y19:J (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63367 1y19:J (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63368 1y19:L (2.6) BS01 peptide ? GO:0005856 ... P26039 15623515
    63369 1y19:L (2.6) BS02 peptide ? GO:0005856 ... P26039 15623515
    63370 1y1a:A (2.3) BS01 CA ? GO:0000287 ... Q99828 15840829
    63371 1y1a:A (2.3) BS02 CA ? GO:0000287 ... Q99828 15840829
    63372 1y1a:A (2.3) BS03 CA ? GO:0000287 ... Q99828 15840829
    63373 1y1a:B (2.3) BS01 CA ? GO:0000287 ... Q99828 15840829
    63374 1y1a:B (2.3) BS02 CA ? GO:0000287 ... Q99828 15840829
    63375 1y1a:B (2.3) BS03 CA ? GO:0000287 ... Q99828 15840829
    63376 1y1a:B (2.3) BS04 GSH ? GO:0000287 ... Q99828 15840829
    63377 1y1d:A (1.7) BS01 FHI ? GO:0005179 ... P02766 15689188 BindingDB: Kd=320nM
    63378 1y1e:X (1.73) BS01 CA 1.8.3.7 N/A Q8NBK3 15907468
    63379 1y1e:X (1.73) BS02 CA 1.8.3.7 N/A Q8NBK3 15907468
    63380 1y1f:X (1.8) BS01 CA 1.8.3.7 N/A Q8NBK3 15907468
    63381 1y1f:X (1.8) BS02 CA 1.8.3.7 N/A Q8NBK3 15907468
    63382 1y1g:X (1.67) BS01 CA 1.8.3.7 N/A Q8NBK3 15907468
    63383 1y1g:X (1.67) BS02 CA 1.8.3.7 N/A Q8NBK3 15907468
    63384 1y1i:X (2.61) BS01 CA 1.8.3.7 N/A Q8NBK3 15907468
    63385 1y1i:X (2.61) BS02 CA 1.8.3.7 N/A Q8NBK3 15907468
    63386 1y1j:X (1.55) BS01 CA 1.8.3.7 N/A Q8NBK3 15907468
    63387 1y1j:X (1.55) BS02 CA 1.8.3.7 N/A Q8NBK3 15907468
    63388 1y1k:E (1.56) BS01 CA 3.4.21.62 GO:0004252 ... P00782 15865427
    63389 1y1m:A (1.8) BS01 AC5 ? GO:0015276 ... P35439 15996549 MOAD: Ki=15.3mM
    PDBbind: -logKd/Ki=1.82, Ki=15.3mM
    63390 1y1m:B (1.8) BS01 AC5 ? GO:0015276 ... P35439 15996549 MOAD: Ki=15.3mM
    63391 1y1p:A (1.6) BS01 NMN 1.1.1.2 GO:0008106 ... Q9UUN9 16095619
    63392 1y1p:A (1.6) BS02 AMP 1.1.1.2 GO:0008106 ... Q9UUN9 16095619
    63393 1y1p:B (1.6) BS01 NMN 1.1.1.2 GO:0008106 ... Q9UUN9 16095619
    63394 1y1p:B (1.6) BS02 AMP 1.1.1.2 GO:0008106 ... Q9UUN9 16095619
    63395 1y1q:C (2.35) BS01 U 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    63396 1y1r:B (2.11) BS01 BJE 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    63397 1y1r:D (2.11) BS01 BJE 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    63398 1y1r:D (2.11) BS02 BJE 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    63399 1y1s:A (2.55) BS01 URA 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    63400 1y1s:B (2.55) BS01 URA 2.4.2.3 GO:0003824 ... P0A1F6 N/A
    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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