sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3f8k | COA | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3f8k | COA | Uncharacterized protein | / | 1.000 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.576 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.554 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.553 | |
| 4jwp | ACO | GCN5-related N-acetyltransferase | / | 0.531 | |
| 1ghe | ACO | Acetyltransferase | 2.3.1 | 0.529 | |
| 4kub | COA | Uncharacterized protein | / | 0.528 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.525 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.524 | |
| 2bei | ACO | Diamine acetyltransferase 2 | 2.3.1.57 | 0.520 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.509 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.508 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.507 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.502 | |
| 1qsm | ACO | Histone acetyltransferase HPA2 | / | 0.501 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.500 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.500 | |
| 4oae | CLM | Uncharacterized protein | / | 0.500 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.497 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.495 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.495 | |
| 2prb | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.494 | |
| 3av7 | KYN | Uncharacterized protein | / | 0.493 | |
| 4kvm | SER_ALA_SER_GLU_1XE | N-terminal acetyltransferase A complex catalytic subunit ard1 | 2.3.1.88 | 0.491 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.489 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.489 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.485 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.484 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.484 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.484 | |
| 4kvx | ACO | N-terminal acetyltransferase A complex catalytic subunit ard1 | 2.3.1.88 | 0.484 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.482 | |
| 4r3k | COA | N-alpha-acetyltransferase | 2.3.1 | 0.480 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.479 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.479 | |
| 3vgl | ANP | Glucokinase | / | 0.478 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.475 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.475 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.474 | |
| 4fgr | ADP | Phosphoribosylaminoimidazole-succinocarboxamide synthase | 6.3.2.6 | 0.474 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.473 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.473 | |
| 4l8u | 9AZ | Serum albumin | / | 0.473 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.472 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.472 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.472 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.471 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.471 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.470 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.469 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.469 | |
| 2cns | ACO | Ribosomal-protein-alanine acetyltransferase | / | 0.468 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.468 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.467 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.467 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.467 | |
| 1v0c | ACO | AAC(6')-Ib | / | 0.466 | |
| 2fxf | ACO | Diamine acetyltransferase 1 | / | 0.466 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 4oad | CLM | Uncharacterized protein | / | 0.465 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.465 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.464 | |
| 1yon | A2R | 2-dehydropantoate 2-reductase | 1.1.1.169 | 0.463 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.463 | |
| 4r87 | COA | Spermidine N(1)-acetyltransferase | / | 0.463 | |
| 1ict | T44 | Transthyretin | / | 0.461 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.461 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.460 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.460 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.460 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.460 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.460 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.459 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.459 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.458 | |
| 4jxr | ACO | Acetyltransferase | / | 0.458 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.458 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.457 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.457 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.457 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.457 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.457 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.456 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.456 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.456 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.456 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.456 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.454 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.454 | |
| 4l9k | EHF | Serum albumin | / | 0.454 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1i7g | AZ2 | Peroxisome proliferator-activated receptor alpha | / | 0.453 | |
| 2c6d | ANP | Aurora kinase A | 2.7.11.1 | 0.453 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.453 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.453 | |
| 3ln1 | CEL | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.453 | |
| 3lu8 | IQX | Serum albumin | / | 0.453 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.453 | |
| 4oag | ADP | Mitochondrial dynamics protein MID51 | / | 0.453 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.452 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.452 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.452 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.452 | |
| 5c88 | COA | N-alpha-acetyltransferase | / | 0.452 | |
| 1kgj | FL8 | Transthyretin | / | 0.451 | |
| 1yre | COA | Uncharacterized protein | / | 0.451 | |
| 3zuy | TCH | Transporter | / | 0.451 | |
| 4xld | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 2ad5 | ADP | CTP synthase | / | 0.450 | |
| 5fkn | TDC | Tetracycline repressor protein class D | / | 0.450 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.450 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.450 | |
| 1wlv | COA | Phenylacetic acid degradation protein PaaI | / | 0.449 | |
| 3i59 | N6S | CRP-like cAMP-activated global transcriptional regulator | / | 0.449 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.448 | |
| 1osv | CHC | Bile acid receptor | / | 0.448 | |
| 2bue | COA | AAC(6')-Ib | / | 0.448 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.448 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.448 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.448 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 1knu | YPA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.447 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.447 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 3two | NDP | Mannitol dehydrogenase | / | 0.447 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.446 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.446 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 5fkl | TDC | Tetracycline repressor protein class D | / | 0.446 | |
| 1byg | STU | Tyrosine-protein kinase CSK | / | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.445 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1r2j | FAD | FkbI | / | 0.445 | |
| 1s7l | COA | Acetyl transferase | / | 0.445 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.445 | |
| 3h0s | B38 | Acetyl-CoA carboxylase | / | 0.445 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.445 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3vsp | EK8 | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 4hgs | 15G | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.445 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.445 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.445 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.444 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.444 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.444 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.444 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.444 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.444 | |
| 3vs7 | KS1 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.444 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.444 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.444 | |
| 4qvt | ACO | Acetyltransferase YpeA | 2.3.1 | 0.444 | |
| 5csh | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.444 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.443 | |
| 3gxl | QIG | TGF-beta receptor type-1 | 2.7.11.30 | 0.443 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.443 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.442 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.442 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.442 | |
| 2am2 | 2LG | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.442 | |
| 2d8a | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.442 | |
| 3ac3 | KSH | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.442 | |
| 3gbk | 2PQ | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.442 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.442 | |
| 4jq8 | KJ8 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1gqt | ACP | Ribokinase | / | 0.441 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.441 | |
| 1pnv | TYD | dTDP-epi-vancosaminyltransferase | 2.4.1.311 | 0.441 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 2wpx | ACO | Orf14 | / | 0.441 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 3sjz | GNP | Translation initiation factor 2 subunit gamma | / | 0.441 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.441 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.441 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.441 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.441 | |
| 4mfp | COA | Uncharacterized protein | / | 0.441 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1bob | ACO | Histone acetyltransferase type B catalytic subunit | / | 0.440 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 1zgy | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.440 | |
| 2d4v | NAD | Isocitrate dehydrogenase [NADP] | / | 0.440 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.440 | |
| 2pob | GW4 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.440 | |
| 3dr8 | ACO | L-methionine sulfoximine/L-methionine sulfone acetyltransferase | / | 0.440 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.440 |