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BioLiP
Download all results in tab-seperated text for 713946 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
    29201 1nkw:C (3.1) BS01 rna ? GO:0003735 ... Q9RXK1 11733066
    29202 1nkw:D (3.1) BS01 rna ? GO:0000049 ... Q9RXJ0 11733066
    29203 1nkw:I (3.1) BS01 rna ? GO:0003735 ... Q9RXJ2 11733066
    29204 1nkw:J (3.1) BS01 rna ? GO:0003735 ... Q9RSK9 11733066
    29205 1nkw:K (3.1) BS01 rna ? GO:0000049 ... Q9RXJ5 11733066
    29206 1nkw:L (3.1) BS01 rna ? GO:0003735 ... Q9RSJ5 11733066
    29207 1nkw:O (3.1) BS01 rna ? GO:0000027 ... Q9RSW7 11733066
    29208 1nkw:Q (3.1) BS01 rna ? GO:0003735 ... Q9RXJ7 11733066
    29209 1nkw:X (3.1) BS01 rna ? GO:0003735 ... Q9RSL0 11733066
    29210 1nkw:Y (3.1) BS01 rna ? GO:0000049 ... Q9RW44 11733066
    29211 1nkw:Z (3.1) BS01 rna ? GO:0003735 ... P49228 11733066
    29212 1nkz:A (2.0) BS01 BCL ? GO:0005886 ... P26789 12595263
    29213 1nkz:A (2.0) BS02 BCL ? GO:0005886 ... P26789 12595263
    29214 1nkz:A (2.0) BS03 BCL ? GO:0005886 ... P26789 12595263
    29215 1nkz:B (2.0) BS01 BCL ? GO:0005886 ... P26790 12595263
    29216 1nkz:B (2.0) BS02 BCL ? GO:0005886 ... P26790 12595263
    29217 1nkz:B (2.0) BS03 BCL ? GO:0005886 ... P26790 12595263
    29218 1nkz:C (2.0) BS01 BCL ? GO:0005886 ... P26789 12595263
    29219 1nkz:C (2.0) BS02 BCL ? GO:0005886 ... P26789 12595263
    29220 1nkz:C (2.0) BS03 BCL ? GO:0005886 ... P26789 12595263
    29221 1nkz:C (2.0) BS04 BCL ? GO:0005886 ... P26789 12595263
    29222 1nkz:D (2.0) BS01 BCL ? GO:0005886 ... P26790 12595263
    29223 1nkz:D (2.0) BS02 BCL ? GO:0005886 ... P26790 12595263
    29224 1nkz:D (2.0) BS03 BCL ? GO:0005886 ... P26790 12595263
    29225 1nkz:E (2.0) BS01 BCL ? GO:0005886 ... P26789 12595263
    29226 1nkz:E (2.0) BS02 BCL ? GO:0005886 ... P26789 12595263
    29227 1nkz:E (2.0) BS03 BCL ? GO:0005886 ... P26789 12595263
    29228 1nkz:E (2.0) BS04 BCL ? GO:0005886 ... P26789 12595263
    29229 1nkz:F (2.0) BS01 BCL ? GO:0005886 ... P26790 12595263
    29230 1nkz:F (2.0) BS02 BCL ? GO:0005886 ... P26790 12595263
    29231 1nkz:F (2.0) BS03 BCL ? GO:0005886 ... P26790 12595263
    29232 1nl4:B (2.7) BS01 ZN 2.5.1.58 GO:0003824 ... Q02293 12657284
    29233 1nl4:B (2.7) BS02 HFP 2.5.1.58 GO:0003824 ... Q02293 12657284
    29234 1nl4:B (2.7) BS03 FTL 2.5.1.58 GO:0003824 ... Q02293 12657284 PDBbind: -logKd/Ki=9.41, IC50=0.39nM
    29235 1nl5:A (2.1) BS01 GLC ? GO:0005515 ... P0AEX9 12794084
    29236 1nl5:A (2.1) BS02 GLC ? GO:0005515 ... P0AEX9 12794084
    29237 1nl6:A (2.8) BS01 750 3.4.22.38 GO:0006508 ... P43235 11311061 PDBbind: -logKd/Ki=11.32, Ki=4.8pM
    BindingDB: IC50=30nM, Ki=0.0048nM
    29238 1nl6:B (2.8) BS01 750 3.4.22.38 GO:0006508 ... P43235 11311061 BindingDB: IC50=30nM, Ki=0.0048nM
    29239 1nl7:A (1.903) BS01 COA 2.3.1.9 GO:0003985 ... P07097 N/A
    29240 1nl7:B (1.903) BS01 COA 2.3.1.9 GO:0003985 ... P07097 N/A
    29241 1nl9:A (2.4) BS01 989 3.1.3.48 GO:0004725 ... P18031 12670229 PDBbind: -logKd/Ki=5.96, Ki=1.1uM
    BindingDB: Ki=631nM
    29242 1nlf:B (1.95) BS01 SO4 ? GO:0005524 ... P20356 12777796
    29243 1nli:A (1.93) BS01 ADE 3.2.2.22 GO:0006952 ... P09989 12676436 MOAD: Kd=260uM
    PDBbind: -logKd/Ki=3.59, Kd=260uM
    29244 1nlj:A (2.4) BS01 2CA 3.4.22.38 GO:0006508 ... P43235 11311061 PDBbind: -logKd/Ki=9.80, Ki=0.16nM
    BindingDB: Ki=0.16nM, IC50=70nM
    29245 1nlj:B (2.4) BS01 2CA 3.4.22.38 GO:0006508 ... P43235 11311061 BindingDB: Ki=0.16nM, IC50=70nM
    29246 1nlk:L (2.0) BS01 ADP 2.7.4.6 GO:0004550 ... P15266 8263923
    29247 1nlk:R (2.0) BS01 ADP 2.7.4.6 GO:0004550 ... P15266 8263923
    29248 1nlm:A (2.5) BS01 UD1 2.4.1.227 GO:0005515 ... P17443 12538870
    29249 1nlm:B (2.5) BS01 UD1 2.4.1.227 GO:0005515 ... P17443 12538870
    29250 1nln:A (1.6) BS01 peptide 3.4.22.39 GO:0003677 ... P03252 12758141
    29251 1nlo:C (-1.00) BS01 peptide 2.7.10.2 GO:0006897 ... P00523 8807900
    29252 1nlp:C (-1.00) BS01 peptide 2.7.10.2 GO:0006897 ... P00523 8807900
    29253 1nlt:A (2.7) BS01 peptide ? GO:0006457 ... P25491 14656432
    29254 1nlt:A (2.7) BS02 ZN ? GO:0006457 ... P25491 14656432
    29255 1nlt:A (2.7) BS03 ZN ? GO:0006457 ... P25491 14656432
    29256 1nlu:A (1.3) BS01 peptide 3.4.21.100 GO:0004252 ... P42790 14733955
    29257 1nlu:A (1.3) BS02 peptide 3.4.21.100 GO:0004252 ... P42790 14733955
    29258 1nlu:A (1.3) BS03 CA 3.4.21.100 GO:0004252 ... P42790 14733955
    29259 1nlv:A (1.8) BS01 ATP 3.6.4.- GO:0000281 ... P07830 12732734
    29260 1nlw:A (2.0) BS01 dna ? GO:0000122 ... Q05195 12553908
    29261 1nlw:A (2.0) BS02 dna ? GO:0000122 ... Q05195 12553908
    29262 1nlw:D (2.0) BS01 dna ? GO:0000122 ... Q05195 12553908
    29263 1nlw:D (2.0) BS02 dna ? GO:0000122 ... Q05195 12553908
    29264 1nly:A (2.8) BS01 AGS ? GO:0000166 ... Q7BK04 12727865
    29265 1nly:B (2.8) BS01 AGS ? GO:0000166 ... Q7BK04 12727865
    29266 1nm0:A (2.3) BS01 SO4 1.11.1.6 GO:0004096 ... P42321 14646074
    29267 1nm0:A (2.3) BS02 SO4 1.11.1.6 GO:0004096 ... P42321 14646074
    29268 1nm0:A (2.3) BS03 HEM 1.11.1.6 GO:0004096 ... P42321 14646074
    29269 1nm0:A (2.3) BS04 FMT 1.11.1.6 GO:0004096 ... P42321 14646074
    29270 1nm0:A (2.3) BS05 GOL 1.11.1.6 GO:0004096 ... P42321 14646074
    29271 1nm1:A (1.8) BS01 ATP 3.6.4.- GO:0000281 ... P07830 12732734
    29272 1nm5:A (2.4) BS01 NAD 7.1.1.1 GO:0000166 ... Q2RSB2 12564924 MOAD: Kd=20uM
    29273 1nm5:B (2.4) BS01 NAD 7.1.1.1 GO:0000166 ... Q2RSB2 12564924 MOAD: Kd=20uM
    29274 1nm6:A (1.8) BS01 peptide 3.4.21.5 GO:0004252 ... P00734 12873514
    29275 1nm6:A (1.8) BS02 L86 3.4.21.5 GO:0004252 ... P00734 12873514 MOAD: Ki=0.09nM
    PDBbind: -logKd/Ki=10.05, Ki=0.09nM
    BindingDB: Ki=0.090000nM
    29276 1nm9:A (2.1) BS01 GLC 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29277 1nm9:A (2.1) BS02 AGL 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29278 1nm9:A (2.1) BS03 GLC 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29279 1nm9:A (2.1) BS04 AGL 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29280 1nm9:A (2.1) BS05 HMC 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29281 1nm9:A (2.1) BS06 CA 3.2.1.1 GO:0003824 ... P0DUB6 15182367
    29282 1nma:N (3.0) BS01 MAN 3.2.1.18 GO:0004308 ... P05803 7517697
    29283 1nmb:N (2.2) BS01 BMA 3.2.1.18 GO:0004308 ... P05803 7994573
    29284 1nmb:N (2.2) BS02 MAN 3.2.1.18 GO:0004308 ... P05803 7994573
    29285 1nmb:N (2.2) BS03 MAN 3.2.1.18 GO:0004308 ... P05803 7994573
    29286 1nmb:N (2.2) BS04 MAN 3.2.1.18 GO:0004308 ... P05803 7994573
    29287 1nmb:N (2.2) BS05 CA 3.2.1.18 GO:0004308 ... P05803 7994573
    29288 1nmc:A (2.5) BS01 CA 3.2.1.18 GO:0004308 ... P03472 9642070
    29289 1nmc:N (2.5) BS01 CA 3.2.1.18 GO:0004308 ... P03472 9642070
    29290 1nmd:A (1.9) BS01 ATP 3.6.4.- GO:0000281 ... P07830 12732734
    29291 1nme:A (1.6) BS01 158 3.4.22.56 GO:0004197 ... P42574 12563278
    29292 1nme:B (1.6) BS01 158 3.4.22.56 GO:0004197 ... P42574 12563278
    29293 1nme:B (1.6) BS02 159 3.4.22.56 GO:0004197 ... P42574 12563278
    29294 1nmi:A (-1.00) BS01 HEC ? GO:0005515 ... P00044 N/A
    29295 1nmk:A (2.1) BS01 SFM 5.2.1.8 GO:0000413 ... P62937 12656618 MOAD: ic50=5.7nM
    PDBbind: -logKd/Ki=8.24, IC50=5.7nM
    29296 1nmk:B (2.1) BS01 SFM 5.2.1.8 GO:0000413 ... P62937 12656618 MOAD: ic50=5.7nM
    29297 1nml:A (2.2) BS01 HEC 1.11.1.5 GO:0004130 ... P83787 15274917
    29298 1nml:A (2.2) BS02 HEC 1.11.1.5 GO:0004130 ... P83787 15274917
    29299 1nmm:A (2.0) BS01 CA ? GO:0004461 ... P29752 11485999
    29300 1nmm:C (2.0) BS01 CA ? GO:0004461 ... P29752 11485999
    29301 1nmo:A (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29302 1nmo:A (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29303 1nmo:B (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29304 1nmo:B (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29305 1nmo:C (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29306 1nmo:C (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29307 1nmo:D (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29308 1nmo:D (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29309 1nmo:E (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29310 1nmo:E (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29311 1nmo:F (2.2) BS01 FE ? GO:0005737 ... P0AFP6 14519207
    29312 1nmo:F (2.2) BS02 FE ? GO:0005737 ... P0AFP6 14519207
    29313 1nmp:A (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29314 1nmp:A (2.2) BS02 MG ? GO:0005737 ... P0AFP6 14519207
    29315 1nmp:B (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29316 1nmp:C (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29317 1nmp:C (2.2) BS02 MG ? GO:0005737 ... P0AFP6 14519207
    29318 1nmp:D (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29319 1nmp:D (2.2) BS02 MG ? GO:0005737 ... P0AFP6 14519207
    29320 1nmp:E (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29321 1nmp:E (2.2) BS02 MG ? GO:0005737 ... P0AFP6 14519207
    29322 1nmp:F (2.2) BS01 MG ? GO:0005737 ... P0AFP6 14519207
    29323 1nmp:F (2.2) BS02 MG ? GO:0005737 ... P0AFP6 14519207
    29324 1nmq:A (2.4) BS01 160 3.4.22.56 GO:0001554 ... P42574 12563278
    29325 1nmq:B (2.4) BS01 160 3.4.22.56 GO:0001554 ... P42574 12563278
    29326 1nms:A (1.7) BS01 161 3.4.22.56 GO:0001554 ... P42574 12563278
    29327 1nms:B (1.7) BS01 161 3.4.22.56 GO:0001554 ... P42574 12563278
    29328 1nmu:A (2.31) BS01 GLC ? GO:0005515 ... P0AEX9 12589748
    29329 1nmu:A (2.31) BS02 GLC ? GO:0005515 ... P0AEX9 12589748
    29330 1nmu:A (2.31) BS03 GLC ? GO:0005515 ... P0AEX9 12589748
    29331 1nmu:A (2.31) BS04 GLC ? GO:0005515 ... P0AEX9 12589748
    29332 1nmu:C (2.31) BS01 GLC ? GO:0005515 ... P0AEX9 12589748
    29333 1nmu:C (2.31) BS02 GLC ? GO:0005515 ... P0AEX9 12589748
    29334 1nmu:C (2.31) BS03 GLC ? GO:0005515 ... P0AEX9 12589748
    29335 1nmu:C (2.31) BS04 GLC ? GO:0005515 ... P0AEX9 12589748
    29336 1nmx:A (1.7) BS01 FDM 2.7.4.9 GO:0004550 ... P23919 12614151
    29337 1nmx:A (1.7) BS02 ADP 2.7.4.9 GO:0004550 ... P23919 12614151
    29338 1nmy:A (1.6) BS01 FDM 2.7.4.9 GO:0004550 ... P23919 12614151
    29339 1nmy:A (1.6) BS02 ADP 2.7.4.9 GO:0004550 ... P23919 12614151
    29340 1nmy:A (1.6) BS03 ANP 2.7.4.9 GO:0004550 ... P23919 12614151
    29341 1nmz:A (1.75) BS01 NYM 2.7.4.9 GO:0004550 ... P23919 12614151
    29342 1nmz:A (1.75) BS02 ANP 2.7.4.9 GO:0004550 ... P23919 12614151
    29343 1nn0:A (1.6) BS01 2DT 2.7.4.9 GO:0004550 ... P23919 12614151
    29344 1nn0:A (1.6) BS02 ADP 2.7.4.9 GO:0004550 ... P23919 12614151
    29345 1nn1:A (1.9) BS01 2DT 2.7.4.9 GO:0004550 ... P23919 12614151
    29346 1nn1:A (1.9) BS02 ANP 2.7.4.9 GO:0004550 ... P23919 12614151
    29347 1nn2:A (2.2) BS01 CA 3.2.1.18 GO:0004308 ... P06820 1920428
    29348 1nn3:A (1.55) BS01 2DT 2.7.4.9 GO:0004550 ... P23919 12614151
    29349 1nn3:A (1.55) BS02 ADP 2.7.4.9 GO:0004550 ... P23919 12614151
    29350 1nn5:A (1.5) BS01 2DT 2.7.4.9 GO:0004550 ... P23919 12614151
    29351 1nn5:A (1.5) BS02 ANP 2.7.4.9 GO:0004550 ... P23919 12614151
    29352 1nn7:A (2.1) BS01 ZN ? GO:0005249 ... Q63881 12835418
    29353 1nna:A (2.5) BS01 CA 3.2.1.18 GO:0004308 ... P03472 8371267
    29354 1nnb:A (2.8) BS01 CA 3.2.1.18 GO:0004308 ... P03472 8371267
    29355 1nnb:A (2.8) BS02 DAN 3.2.1.18 GO:0004308 ... P03472 8371267 PDBbind: -logKd/Ki=5.00, Ki=10uM
    BindingDB: IC50=13000nM
    29356 1nnc:A (1.8) BS01 CA 3.2.1.18 GO:0004308 ... P03472 7549872
    29357 1nnc:A (1.8) BS02 ZMR 3.2.1.18 GO:0004308 ... P03472 7549872
    29358 1nne:A (3.11) BS01 dna ? GO:0003677 ... Q56215 12582174
    29359 1nne:A (3.11) BS02 dna ? GO:0003677 ... Q56215 12582174
    29360 1nne:A (3.11) BS03 BEF ? GO:0003677 ... Q56215 12582174
    29361 1nne:A (3.11) BS04 ADP ? GO:0003677 ... Q56215 12582174
    29362 1nne:B (3.11) BS01 dna ? GO:0003677 ... Q56215 12582174
    29363 1nne:B (3.11) BS02 dna ? GO:0003677 ... Q56215 12582174
    29364 1nne:B (3.11) BS03 BEF ? GO:0003677 ... Q56215 12582174
    29365 1nne:B (3.11) BS04 ADP ? GO:0003677 ... Q56215 12582174
    29366 1nnf:A (1.1) BS01 FE ? GO:0006826 ... P35755 12533539
    29367 1nnf:A (1.1) BS02 EDT ? GO:0006826 ... P35755 12533539
    29368 1nnj:A (1.9) BS01 dna 3.2.2.23
    4.2.99.18
    GO:0003676 ... P42371 16243784 PDBbind: Kd=6nM
    29369 1nnj:A (1.9) BS02 dna 3.2.2.23
    4.2.99.18
    GO:0003676 ... P42371 16243784 PDBbind: Kd=6nM
    29370 1nnj:A (1.9) BS03 ZN 3.2.2.23
    4.2.99.18
    GO:0003676 ... P42371 16243784
    29371 1nnl:A (1.53) BS01 CA 3.1.3.3 GO:0000287 ... P78330 12777757
    29372 1nnl:B (1.53) BS01 CA 3.1.3.3 GO:0000287 ... P78330 12777757
    29373 1nnr:A (2.25) BS01 MN 2.5.1.18 GO:0004364 ... Q9I4K6 15504029
    29374 1nnr:B (2.25) BS01 MN 2.5.1.18 GO:0004364 ... Q9I4K6 15504029
    29375 1nns:A (1.95) BS01 ASP 3.5.1.1 GO:0004067 ... P00805 12595697
    29376 1nns:B (1.95) BS01 ASP 3.5.1.1 GO:0004067 ... P00805 12595697
    29377 1nnu:A (2.5) BS01 NAD 1.3.1.9 GO:0004318 ... Q9BH77 11792710
    29378 1nnu:A (2.5) BS02 TCT 1.3.1.9 GO:0004318 ... Q9BH77 11792710 MOAD: Ki=0.15uM
    PDBbind: -logKd/Ki=6.82, Ki=0.15uM
    29379 1nnu:B (2.5) BS01 NAD 1.3.1.9 GO:0004318 ... Q9BH77 11792710
    29380 1nnu:B (2.5) BS02 TCT 1.3.1.9 GO:0004318 ... Q9BH77 11792710 MOAD: Ki=0.15uM
    29381 1nny:A (2.4) BS01 515 3.1.3.48 GO:0004725 ... P18031 12670229 PDBbind: -logKd/Ki=7.66, Ki=22nM
    BindingDB: Ki=20nM
    29382 1no3:A (2.15) BS01 FE 1.13.11.58 GO:0005737 ... P09186 14993710
    29383 1no3:A (2.15) BS02 4NC 1.13.11.58 GO:0005737 ... P09186 14993710
    29384 1no6:A (2.4) BS01 794 3.1.3.48 GO:0004725 ... P18031 12670229 PDBbind: -logKd/Ki=4.41, Ki=39uM
    BindingDB: Ki=39000nM, Kd=26000nM
    29385 1no9:H (1.9) BS01 peptide 3.4.21.5 GO:0004252 ... P00734 12885234
    29386 1no9:H (1.9) BS02 4ND 3.4.21.5 GO:0004252 ... P00734 12885234 PDBbind: -logKd/Ki=7.62, Ki=24nM
    29387 1noc:A (2.6) BS01 HEM 1.14.13.39 GO:0004517 ... P29477 9334294
    29388 1noc:A (2.6) BS02 IMD 1.14.13.39 GO:0004517 ... P29477 9334294
    29389 1nod:A (2.6) BS01 ARG 1.14.13.39 GO:0004517 ... P29477 9516116
    29390 1nod:A (2.6) BS02 HEM 1.14.13.39 GO:0004517 ... P29477 9516116
    29391 1nod:A (2.6) BS03 H4B 1.14.13.39 GO:0004517 ... P29477 9516116
    29392 1nod:B (2.6) BS01 ARG 1.14.13.39 GO:0004517 ... P29477 9516116
    29393 1nod:B (2.6) BS02 HEM 1.14.13.39 GO:0004517 ... P29477 9516116
    29394 1nod:B (2.6) BS03 H4B 1.14.13.39 GO:0004517 ... P29477 9516116
    29395 1noe:A (-1.00) BS01 SF4 ? GO:0009055 ... P00260 8639555
    29396 1noi:A (2.5) BS01 PO4 2.4.1.1 GO:0000166 ... P00489 8652510
    29397 1noi:A (2.5) BS02 PLP 2.4.1.1 GO:0000166 ... P00489 8652510
    29398 1noi:A (2.5) BS03 NTZ 2.4.1.1 GO:0000166 ... P00489 8652510 MOAD: Ki=700uM
    PDBbind: -logKd/Ki=3.15, Ki=700uM
    29399 1noi:B (2.5) BS01 PO4 2.4.1.1 GO:0000166 ... P00489 8652510
    29400 1noi:B (2.5) BS02 PLP 2.4.1.1 GO:0000166 ... P00489 8652510

    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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