sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3f8k | COA | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3f8k | COA | Uncharacterized protein | / | 1.000 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.568 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.554 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.543 | |
| 4oae | CLM | Uncharacterized protein | / | 0.528 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.525 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.521 | |
| 2bei | ACO | Diamine acetyltransferase 2 | 2.3.1.57 | 0.520 | |
| 4kub | COA | Uncharacterized protein | / | 0.520 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.505 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.501 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.501 | |
| 2vbq | BSJ | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.500 | |
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 0.500 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.500 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.495 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.492 | |
| 4oad | CLM | Uncharacterized protein | / | 0.490 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.486 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.482 | |
| 1j4j | ACO | Acetyltransferase | 2.3.1 | 0.480 | |
| 4r3k | COA | N-alpha-acetyltransferase | 2.3.1 | 0.480 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.479 | |
| 1qsm | ACO | Histone acetyltransferase HPA2 | / | 0.479 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.478 | |
| 4kvm | SER_ALA_SER_GLU_1XE | N-terminal acetyltransferase A complex catalytic subunit ard1 | 2.3.1.88 | 0.477 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.476 | |
| 5kgh | ACO | Predicted acetyltransferase | / | 0.475 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.474 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.471 | |
| 1ot7 | IU5 | Bile acid receptor | / | 0.470 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.470 | |
| 3vgl | ANP | Glucokinase | / | 0.470 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.469 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.468 | |
| 4l8u | 9AZ | Serum albumin | / | 0.468 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.467 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.467 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.466 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.465 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.463 | |
| 2yww | ATP | Aspartate carbamoyltransferase regulatory chain | / | 0.463 | |
| 4kos | 4KO | Uncharacterized protein | / | 0.463 | |
| 2e2q | ADP | ATP-dependent hexokinase | / | 0.462 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.462 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.462 | |
| 5kgp | ACO | Predicted acetyltransferase | / | 0.462 | |
| 2cns | ACO | Ribosomal-protein-alanine acetyltransferase | / | 0.461 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.460 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.460 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.459 | |
| 2j7t | 274 | Serine/threonine-protein kinase 10 | 2.7.11.1 | 0.459 | |
| 1rdt | 570 | Peroxisome proliferator-activated receptor gamma | / | 0.457 | |
| 1zp9 | ATP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.457 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.457 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.457 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.457 | |
| 4lb2 | DM5 | Serum albumin | / | 0.457 | |
| 4r87 | COA | Spermidine N(1)-acetyltransferase | / | 0.457 | |
| 5kf1 | ACO | Predicted acetyltransferase | / | 0.457 | |
| 3av7 | KYN | Uncharacterized protein | / | 0.456 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.456 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.455 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.455 | |
| 1ict | T44 | Transthyretin | / | 0.455 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.455 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.455 | |
| 1ozp | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.454 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.454 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.454 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.454 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 2c6d | ANP | Aurora kinase A | 2.7.11.1 | 0.453 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.453 | |
| 4jxr | ACO | Acetyltransferase | / | 0.453 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.453 | |
| 2xpw | OTC | Tetracycline repressor protein class D | / | 0.452 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.452 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.452 | |
| 5c88 | COA | N-alpha-acetyltransferase | / | 0.452 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.451 | |
| 1kgj | FL8 | Transthyretin | / | 0.451 | |
| 1qxo | FMN | Chorismate synthase | / | 0.451 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.451 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.451 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.451 | |
| 2cgp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.450 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.450 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 5kf8 | ACO | Predicted acetyltransferase | / | 0.450 | |
| 5kf9 | ACO | Predicted acetyltransferase | / | 0.450 | |
| 1fnn | ADP | ORC1-type DNA replication protein | / | 0.449 | |
| 1gp2 | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.449 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 2xcl | ANP | Phosphoribosylamine--glycine ligase | / | 0.449 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3gxl | QIG | TGF-beta receptor type-1 | 2.7.11.30 | 0.449 | |
| 3uqd | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.449 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.448 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2bue | COA | AAC(6')-Ib | / | 0.448 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.448 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.448 | |
| 2om9 | AJA | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.448 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.448 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.447 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.447 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2q5p | 241 | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2qo4 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.447 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.447 | |
| 3zuy | TCH | Transporter | / | 0.447 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.447 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.446 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.446 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.446 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.446 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.446 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.446 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.446 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.445 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.445 | |
| 1os1 | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.445 | |
| 1osv | CHC | Bile acid receptor | / | 0.445 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.445 | |
| 3okx | SAM | S-adenosyl-L-methionine-binding protein RPA0152 | / | 0.445 | |
| 4j1t | NAD | NAD/NADP transhydrogenase alpha subunit 1 | / | 0.445 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.445 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.444 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 2gmv | PEP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.444 | |
| 2hen | ADP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.444 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.444 | |
| 3fre | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.444 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.444 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.444 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.444 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.444 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1nhg | TCL | Enoyl-ACP reductase | / | 0.443 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.443 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3r88 | 14F | Anthranilate phosphoribosyltransferase | / | 0.443 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 3vjh | J35 | Peroxisome proliferator-activated receptor gamma | / | 0.443 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.442 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.442 | |
| 2ql6 | ADP | Nicotinamide riboside kinase 1 | / | 0.442 | |
| 3ac3 | KSH | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.442 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.442 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4kov | KOV | Uncharacterized protein | / | 0.442 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.442 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.442 | |
| 1g69 | TZP | Thiamine-phosphate synthase | / | 0.441 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2itp | AEE | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 3i59 | N6R | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 3iel | U5P | Ribonuclease TTHA0252 | 3.1 | 0.441 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.441 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.441 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.441 | |
| 3zh8 | C58 | Protein kinase C iota type | 2.7.11.13 | 0.441 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.441 | |
| 4qvt | ACO | Acetyltransferase YpeA | 2.3.1 | 0.441 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1rk3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 1u26 | IHS | Myo-inositol hexaphosphate phosphohydrolase | / | 0.440 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.440 | |
| 2xgs | 44P | Uncharacterized protein | / | 0.440 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.440 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.440 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.440 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.440 | |
| 3vs7 | KS1 | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.440 | |
| 4a61 | ANP | Plasmid segregation protein ParM | / | 0.440 | |
| 4f9m | FCM | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4o8f | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.440 | |
| 4rph | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.440 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.440 |