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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
    64201 1yds:E (2.2) BS02 IQS 2.7.11.11 GO:0001669 ... P00517 8824261 MOAD: Ki=1.2uM
    PDBbind: -logKd/Ki=5.92, Ki=1.2uM
    BindingDB: IC50=5300nM
    64202 1ydt:E (2.3) BS01 peptide 2.7.11.11 GO:0001669 ... P00517 8824261
    64203 1ydt:E (2.3) BS02 IQB 2.7.11.11 GO:0001669 ... P00517 8824261 MOAD: Ki=48nM
    PDBbind: -logKd/Ki=7.32, Ki=48nM
    BindingDB: IC50=73nM
    64204 1ydy:A (1.7) BS01 CA 3.1.4.46 GO:0006629 ... P09394 N/A
    64205 1ydy:B (1.7) BS01 CA 3.1.4.46 GO:0006629 ... P09394 N/A
    64206 1ydz:A (3.3) BS01 HEM ? GO:0004601 ... P69905 15835899
    64207 1ydz:B (3.3) BS01 HEM ? GO:0004601 ... P68871 15835899
    64208 1ydz:B (3.3) BS02 OXY ? GO:0004601 ... P68871 15835899
    64209 1ydz:C (3.3) BS01 HEM ? GO:0004601 ... P69905 15835899
    64210 1ydz:D (3.3) BS01 HEM ? GO:0004601 ... P68871 15835899
    64211 1ydz:D (3.3) BS02 OXY ? GO:0004601 ... P68871 15835899
    64212 1ye0:A (2.5) BS01 HEM ? GO:0004601 ... P69905 15835899
    64213 1ye0:B (2.5) BS01 HEM ? GO:0004601 ... P68871 15835899
    64214 1ye0:B (2.5) BS02 OXY ? GO:0004601 ... P68871 15835899
    64215 1ye0:C (2.5) BS01 HEM ? GO:0004601 ... P69905 15835899
    64216 1ye0:C (2.5) BS02 OXY ? GO:0004601 ... P69905 15835899
    64217 1ye0:D (2.5) BS01 HEM ? GO:0004601 ... P68871 15835899
    64218 1ye0:D (2.5) BS02 OXY ? GO:0004601 ... P68871 15835899
    64219 1ye1:A (4.5) BS01 HEM ? GO:0004601 ... P69905 15835899
    64220 1ye1:B (4.5) BS01 HEM ? GO:0004601 ... P68871 15835899
    64221 1ye1:C (4.5) BS01 HEM ? GO:0004601 ... P69905 15835899
    64222 1ye1:D (4.5) BS01 HEM ? GO:0004601 ... P68871 15835899
    64223 1ye2:A (1.8) BS01 HEM ? GO:0004601 ... P69905 15835899
    64224 1ye2:B (1.8) BS01 HEM ? GO:0004601 ... P68871 15835899
    64225 1ye2:B (1.8) BS02 OXY ? GO:0004601 ... P68871 15835899
    64226 1ye2:C (1.8) BS01 HEM ? GO:0004601 ... P69905 15835899
    64227 1ye2:C (1.8) BS02 OXY ? GO:0004601 ... P69905 15835899
    64228 1ye2:D (1.8) BS01 HEM ? GO:0004601 ... P68871 15835899
    64229 1ye2:D (1.8) BS02 OXY ? GO:0004601 ... P68871 15835899
    64230 1ye3:A (1.59) BS01 ZN 1.1.1.1 GO:0004022 ... P00327 N/A
    64231 1ye3:A (1.59) BS02 ZN 1.1.1.1 GO:0004022 ... P00327 N/A
    64232 1ye4:A (2.4) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64233 1ye4:B (2.4) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64234 1ye4:C (2.4) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64235 1ye4:D (2.4) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64236 1ye6:A (2.3) BS01 NAP 1.1.1.307 GO:0004032 ... O74237 15670843
    64237 1ye6:B (2.3) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64238 1ye6:C (2.3) BS01 NAP 1.1.1.307 GO:0004032 ... O74237 15670843
    64239 1ye6:D (2.3) BS01 NAD 1.1.1.307 GO:0004032 ... O74237 15670843
    64240 1ye9:A (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64241 1ye9:B (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64242 1ye9:C (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64243 1ye9:D (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64244 1ye9:E (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64245 1ye9:F (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64246 1ye9:G (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64247 1ye9:H (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64248 1ye9:I (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64249 1ye9:J (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64250 1ye9:K (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64251 1ye9:L (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64252 1ye9:M (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64253 1ye9:N (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64254 1ye9:O (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64255 1ye9:P (2.8) BS01 HDD 1.11.1.6 GO:0004096 ... P21179 15823018
    64256 1yea:A (1.9) BS01 HEC ? GO:0005739 ... P00045 1326054
    64257 1yeb:A (1.95) BS01 HEC ? GO:0005739 ... P00045 1326054
    64258 1yec:H (1.9) BS01 PNB ? N/A P01863 9027317
    64259 1yec:L (1.9) BS01 ZN N/A N/A N/A 9027317
    64260 1yec:L (1.9) BS02 PNB N/A N/A N/A 9027317
    64261 1yed:A (3.1) BS01 PNB N/A N/A N/A 9027317
    64262 1yed:B (3.1) BS01 PNB ? N/A P01868 9027317
    64263 1yed:H (3.1) BS01 PNB ? N/A P01868 9027317
    64264 1yed:L (3.1) BS01 PNB N/A N/A N/A 9027317
    64265 1yee:H (2.2) BS01 PNB ? N/A P01865 9027317
    64266 1yee:L (2.2) BS01 PNB N/A N/A N/A 9027317
    64267 1yef:H (2.0) BS01 PNC ? N/A P01863 9223277
    64268 1yef:L (2.0) BS01 ZN N/A N/A N/A 9223277
    64269 1yef:L (2.0) BS02 PNC N/A N/A N/A 9223277
    64270 1yeg:H (2.0) BS01 BPN ? N/A P01863 9223277
    64271 1yeg:L (2.0) BS01 ZN N/A N/A N/A 9223277
    64272 1yeg:L (2.0) BS02 BPN N/A N/A N/A 9223277
    64273 1yeh:L (2.55) BS01 ZN N/A N/A N/A 9223277
    64274 1yei:H (1.9) BS01 PGG N/A N/A N/A 9826512 PDBbind: -logKd/Ki=7.46, Kd=35nM
    64275 1yei:L (1.9) BS01 ZN ? GO:0046872 ... Q58EU8 9826512
    64276 1yei:L (1.9) BS02 PGG ? GO:0046872 ... Q58EU8 9826512 MOAD: Kd=35nM
    PDBbind: -logKd/Ki=7.46, Kd=35nM
    64277 1yej:H (1.85) BS01 PNF N/A N/A N/A 9826512 PDBbind: -logKd/Ki=7.46, Kd=35nM
    64278 1yej:L (1.85) BS01 ZN ? GO:0046872 ... Q58EU8 9826512
    64279 1yej:L (1.85) BS02 ZN ? GO:0046872 ... Q58EU8 9826512
    64280 1yej:L (1.85) BS03 PNF ? GO:0046872 ... Q58EU8 9826512 MOAD: Kd=35nM
    PDBbind: -logKd/Ki=7.46, Kd=35nM
    64281 1yek:H (2.1) BS01 NPO ? N/A P01863 9826512
    64282 1yek:L (2.1) BS01 ZN ? GO:0046872 ... Q58EU8 9826512
    64283 1yek:L (2.1) BS02 NPO ? GO:0046872 ... Q58EU8 9826512
    64284 1yen:A (2.8) BS01 HEM ? GO:0004601 ... P69905 15835899
    64285 1yen:B (2.8) BS01 HEM ? GO:0004601 ... P68871 15835899
    64286 1yen:B (2.8) BS02 OXY ? GO:0004601 ... P68871 15835899
    64287 1yen:C (2.8) BS01 HEM ? GO:0004601 ... P69905 15835899
    64288 1yen:D (2.8) BS01 HEM ? GO:0004601 ... P68871 15835899
    64289 1yen:D (2.8) BS02 OXY ? GO:0004601 ... P68871 15835899
    64290 1yeo:A (2.22) BS01 HEM ? GO:0004601 ... P69905 15835899
    64291 1yeo:B (2.22) BS01 HEM ? GO:0004601 ... P68871 15835899
    64292 1yeo:B (2.22) BS02 OXY ? GO:0004601 ... P68871 15835899
    64293 1yeo:C (2.22) BS01 HEM ? GO:0004601 ... P69905 15835899
    64294 1yeo:C (2.22) BS02 OXY ? GO:0004601 ... P69905 15835899
    64295 1yeo:D (2.22) BS01 HEM ? GO:0004601 ... P68871 15835899
    64296 1yeo:D (2.22) BS02 OXY ? GO:0004601 ... P68871 15835899
    64297 1yeq:A (2.75) BS01 HEM ? GO:0004601 ... P69905 15835899
    64298 1yeq:B (2.75) BS01 HEM ? GO:0004601 ... P68871 15835899
    64299 1yeq:B (2.75) BS02 OXY ? GO:0004601 ... P68871 15835899
    64300 1yeq:C (2.75) BS01 HEM ? GO:0004601 ... P69905 15835899
    64301 1yeq:C (2.75) BS02 OXY ? GO:0004601 ... P69905 15835899
    64302 1yeq:D (2.75) BS01 HEM ? GO:0004601 ... P68871 15835899
    64303 1yet:A (1.9) BS01 GDM 3.6.4.10 GO:0005524 ... P07900 9108479 PDBbind: -logKd/Ki=5.92, Kd=1.2uM
    BindingDB: IC50=42nM, Kd=714nM
    64304 1yeu:A (2.12) BS01 HEM ? GO:0004601 ... P69905 15835899
    64305 1yeu:B (2.12) BS01 HEM ? GO:0004601 ... P68871 15835899
    64306 1yeu:B (2.12) BS02 OXY ? GO:0004601 ... P68871 15835899
    64307 1yeu:C (2.12) BS01 HEM ? GO:0004601 ... P69905 15835899
    64308 1yeu:D (2.12) BS01 HEM ? GO:0004601 ... P68871 15835899
    64309 1yeu:D (2.12) BS02 OXY ? GO:0004601 ... P68871 15835899
    64310 1yev:A (2.11) BS01 HEM ? GO:0004601 ... P69905 15835899
    64311 1yev:B (2.11) BS01 HEM ? GO:0004601 ... P68871 15835899
    64312 1yev:B (2.11) BS02 OXY ? GO:0004601 ... P68871 15835899
    64313 1yev:C (2.11) BS01 HEM ? GO:0004601 ... P69905 15835899
    64314 1yev:C (2.11) BS02 OXY ? GO:0004601 ... P69905 15835899
    64315 1yev:D (2.11) BS01 HEM ? GO:0004601 ... P68871 15835899
    64316 1yev:D (2.11) BS02 OXY ? GO:0004601 ... P68871 15835899
    64317 1yew:A (2.801) BS01 CU 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64318 1yew:A (2.801) BS02 CUA 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64319 1yew:C (2.801) BS01 ZN ? GO:0004497 ... O05111 15674245
    64320 1yew:E (2.801) BS01 CU 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64321 1yew:E (2.801) BS02 ZN 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64322 1yew:E (2.801) BS03 CUA 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64323 1yew:G (2.801) BS01 ZN ? GO:0004497 ... O05111 15674245
    64324 1yew:I (2.801) BS01 CU 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64325 1yew:I (2.801) BS02 CUA 1.14.18.3 GO:0004497 ... G1UBD1 15674245
    64326 1yew:K (2.801) BS01 ZN ? GO:0004497 ... O05111 15674245
    64327 1yey:A (2.34) BS01 MG 4.2.1.68 GO:0000287 ... Q8P3K2 N/A
    64328 1yey:B (2.34) BS01 MG 4.2.1.68 GO:0000287 ... Q8P3K2 N/A
    64329 1yey:C (2.34) BS01 MG 4.2.1.68 GO:0000287 ... Q8P3K2 N/A
    64330 1yey:D (2.34) BS01 MG 4.2.1.68 GO:0000287 ... Q8P3K2 N/A
    64331 1yf3:A (2.29) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64332 1yf3:A (2.29) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64333 1yf3:A (2.29) BS03 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64334 1yf3:B (2.29) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64335 1yf3:B (2.29) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64336 1yf3:B (2.29) BS03 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64337 1yf4:A (1.98) BS01 peptide 3.4.21.4 GO:0004252 ... P00761 15854654
    64338 1yf4:A (1.98) BS02 CA 3.4.21.4 GO:0004252 ... P00761 15854654
    64339 1yf6:L (2.25) BS01 BCL ? GO:0009772 ... P0C0Y8 15865437
    64340 1yf6:L (2.25) BS02 BCL ? GO:0009772 ... P0C0Y8 15865437
    64341 1yf6:L (2.25) BS03 BPH ? GO:0009772 ... P0C0Y8 15865437
    64342 1yf6:L (2.25) BS04 U10 ? GO:0009772 ... P0C0Y8 15865437
    64343 1yf6:L (2.25) BS05 U10 ? GO:0009772 ... P0C0Y8 15865437
    64344 1yf6:L (2.25) BS06 FE2 ? GO:0009772 ... P0C0Y8 15865437
    64345 1yf6:L (2.25) BS07 BCL ? GO:0009772 ... P0C0Y8 15865437
    64346 1yf6:L (2.25) BS08 BCL ? GO:0009772 ... P0C0Y8 15865437
    64347 1yf6:M (2.25) BS01 BCL ? GO:0009772 ... P0C0Y9 15865437
    64348 1yf6:M (2.25) BS02 BPH ? GO:0009772 ... P0C0Y9 15865437
    64349 1yf6:M (2.25) BS03 FE2 ? GO:0009772 ... P0C0Y9 15865437
    64350 1yf6:M (2.25) BS04 BCL ? GO:0009772 ... P0C0Y9 15865437
    64351 1yf6:M (2.25) BS05 BCL ? GO:0009772 ... P0C0Y9 15865437
    64352 1yf6:M (2.25) BS06 BCL ? GO:0009772 ... P0C0Y9 15865437
    64353 1yf6:M (2.25) BS07 U10 ? GO:0009772 ... P0C0Y9 15865437
    64354 1yf6:M (2.25) BS08 SPO ? GO:0009772 ... P0C0Y9 15865437
    64355 1yf8:A (2.8) BS01 P6C 3.2.2.22 GO:0017148 ... Q6ITZ3 15774467
    64356 1yf8:B (2.8) BS01 GAL 3.2.2.22 N/A Q6ITZ3 15774467
    64357 1yf8:B (2.8) BS02 GAL 3.2.2.22 N/A Q6ITZ3 15774467
    64358 1yf8:B (2.8) BS03 GAL 3.2.2.22 N/A Q6ITZ3 15774467
    64359 1yfc:A (-1.00) BS01 HEC ? GO:0005515 ... P00044 8901521
    64360 1yfd:A (1.9) BS01 FEO 1.17.4.1 GO:0004748 ... P69924 15634667
    64361 1yfd:B (1.9) BS01 FEO 1.17.4.1 GO:0004748 ... P69924 15634667
    64362 1yff:A (2.4) BS01 HEM ? GO:0004601 ... P69905 N/A
    64363 1yff:B (2.4) BS01 HEM ? GO:0004601 ... P68871 N/A
    64364 1yff:C (2.4) BS01 HEM ? GO:0004601 ... P69905 N/A
    64365 1yff:D (2.4) BS01 HEM ? GO:0004601 ... P68871 N/A
    64366 1yff:E (2.4) BS01 HEM ? GO:0004601 ... P69905 N/A
    64367 1yff:F (2.4) BS01 HEM ? GO:0004601 ... P68871 N/A
    64368 1yff:G (2.4) BS01 HEM ? GO:0004601 ... P69905 N/A
    64369 1yff:H (2.4) BS01 HEM ? GO:0004601 ... P68871 N/A
    64370 1yfh:A (3.01) BS01 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64371 1yfh:A (3.01) BS02 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64372 1yfh:A (3.01) BS03 ZN 2.1.1.63 GO:0003824 ... P16455 15964013
    64373 1yfh:B (3.01) BS01 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64374 1yfh:B (3.01) BS02 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64375 1yfh:B (3.01) BS03 ZN 2.1.1.63 GO:0003824 ... P16455 15964013
    64376 1yfh:C (3.01) BS01 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64377 1yfh:C (3.01) BS02 dna 2.1.1.63 GO:0003824 ... P16455 15964013 PDBbind: Kd=0.8uM
    64378 1yfh:C (3.01) BS03 ZN 2.1.1.63 GO:0003824 ... P16455 15964013
    64379 1yfi:A (2.7) BS01 dna 3.1.21.4 GO:0003677 ... P11405 16195548
    64380 1yfi:A (2.7) BS02 dna 3.1.21.4 GO:0003677 ... P11405 16195548
    64381 1yfi:A (2.7) BS03 dna 3.1.21.4 GO:0003677 ... P11405 16195548
    64382 1yfi:B (2.7) BS01 dna 3.1.21.4 GO:0003677 ... P11405 16195548
    64383 1yfi:B (2.7) BS02 dna 3.1.21.4 GO:0003677 ... P11405 16195548
    64384 1yfj:A (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64385 1yfj:A (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64386 1yfj:A (2.69) BS03 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64387 1yfj:A (2.69) BS04 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64388 1yfj:B (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64389 1yfj:B (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64390 1yfj:B (2.69) BS03 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64391 1yfj:B (2.69) BS04 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64392 1yfj:B (2.69) BS05 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64393 1yfj:C (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64394 1yfj:C (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64395 1yfj:C (2.69) BS03 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64396 1yfj:C (2.69) BS04 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64397 1yfj:C (2.69) BS05 SAH 2.1.1.72 GO:0003676 ... P04392 15882618
    64398 1yfj:D (2.69) BS01 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64399 1yfj:D (2.69) BS02 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    64400 1yfj:D (2.69) BS03 dna 2.1.1.72 GO:0003676 ... P04392 15882618
    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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