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 |
|---|---|---|---|
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2x7b | COA | N-alpha-acetyltransferase | 2.3.1 | 1.000 | |
| 4lx9 | ACO | N-alpha-acetyltransferase | 2.3.1 | 0.655 | |
| 5c88 | COA | N-alpha-acetyltransferase | / | 0.599 | |
| 4r3k | COA | N-alpha-acetyltransferase | 2.3.1 | 0.552 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.531 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.527 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.526 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.524 | |
| 4b5o | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.521 | |
| 3f8k | COA | Uncharacterized protein | / | 0.518 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.517 | |
| 2cns | ACO | Ribosomal-protein-alanine acetyltransferase | / | 0.512 | |
| 4hkf | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.508 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.508 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.505 | |
| 2c27 | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.504 | |
| 2wpw | ACO | Orf14 | / | 0.504 | |
| 2ob0 | ACO | N-alpha-acetyltransferase 50 | / | 0.502 | |
| 4mxe | ACO | N-acetyltransferase ESCO1 | 2.3.1 | 0.497 | |
| 3vwd | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.496 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.495 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.494 | |
| 3mgd | ACO | Predicted acetyltransferase | / | 0.493 | |
| 2f1k | NAP | Prephenate dehydrogenase | / | 0.491 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.487 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.487 | |
| 4gs4 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.482 | |
| 4u9v | ACO | N-alpha-acetyltransferase 40 | 2.3.1 | 0.482 | |
| 4if5 | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.481 | |
| 4ag7 | COA | Glucosamine 6-phosphate N-acetyltransferase | / | 0.479 | |
| 4crz | ACO | PanD regulatory factor | / | 0.478 | |
| 4kvx | ACO | N-terminal acetyltransferase A complex catalytic subunit ard1 | 2.3.1.88 | 0.477 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.475 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.475 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.474 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.471 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.470 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 4h6z | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.470 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.468 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.468 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.468 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.467 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.467 | |
| 3lu8 | IQX | Serum albumin | / | 0.466 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.465 | |
| 2cy2 | ACO | Probable acetyltransferase | / | 0.464 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.464 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.464 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.463 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.462 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.461 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.461 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.461 | |
| 1s7n | COA | Acetyl transferase | / | 0.461 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.461 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.461 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.460 | |
| 4cs0 | ACO | PanD regulatory factor | / | 0.460 | |
| 4h6u | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.460 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.459 | |
| 2q4v | ACO | Diamine acetyltransferase 2 | 2.3.1.57 | 0.458 | |
| 3oq6 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.458 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.457 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.457 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.456 | |
| 1s5k | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.456 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.456 | |
| 2zdt | 46C | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.456 | |
| 4xd2 | NAI | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.455 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.455 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.455 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.454 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.454 | |
| 3pgp | ACO | Uncharacterized protein | / | 0.454 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.453 | |
| 2qr1 | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.453 | |
| 2yww | ATP | Aspartate carbamoyltransferase regulatory chain | / | 0.453 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.453 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.453 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.453 | |
| 5kcp | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.452 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.452 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.452 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.452 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.452 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.452 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.452 | |
| 6adh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.451 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.451 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.451 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 4cry | ACO | PanD regulatory factor | / | 0.451 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.450 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 1bwf | ATF | Glycerol kinase | / | 0.449 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.449 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.449 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 2exc | JNK | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.448 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.448 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.448 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.448 | |
| 2e9z | UTP | Genome polyprotein | / | 0.447 | |
| 3k9u | ACO | Spermidine N(1)-acetyltransferase | / | 0.447 | |
| 4kub | COA | Uncharacterized protein | / | 0.447 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.447 | |
| 1j39 | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.446 | |
| 2o12 | FMN | Chorismate synthase | / | 0.446 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3mdv | CL6 | Cholesterol 24-hydroxylase | / | 0.446 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.446 | |
| 5kje | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 5kjf | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2a4n | COA | Aac(6')-Ii protein | / | 0.445 | |
| 2hbh | XE4 | Vitamin D3 receptor A | / | 0.445 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 2nv6 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.445 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.445 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4f9f | GDP | Putative glycosyltransferase | / | 0.445 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1qsm | ACO | Histone acetyltransferase HPA2 | / | 0.444 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 2c6d | ANP | Aurora kinase A | 2.7.11.1 | 0.444 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 2jdc | CAO | Probable acetyltransferase | / | 0.444 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.444 | |
| 2y9q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.444 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.444 | |
| 4e73 | 0NR | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.444 | |
| 4g2f | C07 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 1n71 | COA | Aac(6')-Ii protein | / | 0.443 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.443 | |
| 4hyu | 1BK | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.443 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.442 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.442 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1o8c | NDP | Probable acrylyl-CoA reductase AcuI | 1.3.1.84 | 0.441 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4c4f | 7CE | Dual specificity protein kinase TTK | 2.7.12.1 | 0.441 | |
| 4fuy | EK2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.441 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 4ma6 | 28E | Ara h 8 allergen | / | 0.441 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.441 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.440 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.440 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.440 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.440 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.440 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.440 | |
| 5ebu | FMN | Lactate oxidase | / | 0.440 |