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 |
|---|---|---|---|
| 3v0t | ATR | Perakine reductase | 1.1.1.317 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3v0t | ATR | Perakine reductase | 1.1.1.317 | 1.000 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.507 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.501 | |
| 1osv | CHC | Bile acid receptor | / | 0.496 | |
| 1lqa | NDP | Protein tas | / | 0.494 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.494 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.491 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.491 | |
| 2clp | NDP | Aflatoxin B1 aldehyde reductase member 3 | / | 0.488 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.486 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.483 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.480 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.480 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 4ejn | 0R4 | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.480 | |
| 1s1p | NAP | Aldo-keto reductase family 1 member C3 | / | 0.478 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.477 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.477 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.477 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.476 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.476 | |
| 4aub | NAP | L-glyceraldehyde 3-phosphate reductase | 1.1.1 | 0.475 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.475 | |
| 1ah4 | NAP | Aldose reductase | 1.1.1.21 | 0.474 | |
| 1zgd | NAP | Chalcone reductase | / | 0.474 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 1jkx | 138 | Phosphoribosylglycinamide formyltransferase | / | 0.473 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.473 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.472 | |
| 2c91 | NAP | Aflatoxin B1 aldehyde reductase member 2 | / | 0.471 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.471 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 1k8c | NAP | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.469 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.469 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.469 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.469 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.467 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.467 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 2nnh | REA | Cytochrome P450 2C8 | / | 0.466 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.466 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.465 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.464 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.463 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.462 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.462 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.462 | |
| 3lnm | NAP | Voltage-gated potassium channel subunit beta-2 | / | 0.461 | |
| 3o3r | NAP | Aldose reductase-related protein 1 | 1.1.1.21 | 0.461 | |
| 4rfl | NDP | Glycerol-1-phosphate dehydrogenase [NAD(P)+] | / | 0.461 | |
| 2p5n | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.460 | |
| 1mi3 | NAD | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.459 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.459 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.459 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.459 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.458 | |
| 4irn | FAD | AnaB | / | 0.458 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.458 | |
| 5dp2 | NAP | CurF | / | 0.458 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.458 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2vdg | NDP | Aldose reductase | 1.1.1.21 | 0.457 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.457 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.457 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.457 | |
| 4jtc | NAP | Voltage-gated potassium channel subunit beta-2 | / | 0.457 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.456 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.456 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.456 | |
| 4d04 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.456 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.455 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4xzm | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.455 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.454 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.454 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.454 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.453 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.453 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.453 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.453 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.453 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.453 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.453 | |
| 4nxu | ADP | Mitochondrial dynamics protein MID51 | / | 0.453 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.453 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.452 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.452 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.452 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 1ads | NAP | Aldose reductase | 1.1.1.21 | 0.451 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.451 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.451 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 1kqo | DND | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.450 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 4jtd | NAP | Voltage-gated potassium channel subunit beta-2 | / | 0.450 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.450 | |
| 1a80 | NDP | 2,5-diketo-D-gluconic acid reductase A | 1.1.1.346 | 0.449 | |
| 1gia | GSP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.449 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2fvl | NAP | Aldo-keto reductase family 1 member C4 | 1.1.1.225 | 0.449 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.449 | |
| 3utg | FDA | UDP-galactopyranose mutase | / | 0.449 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 4c77 | N01 | Phenylacetone monooxygenase | 1.14.13.92 | 0.449 | |
| 4nxx | GDP | Mitochondrial dynamics protein MID51 | / | 0.449 | |
| 4oze | 24G | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.449 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 2acu | NAP | Aldose reductase | 1.1.1.21 | 0.448 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.448 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.448 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.448 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1ppj | ANY | Cytochrome b | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.447 | |
| 2r9r | NAP | Voltage-gated potassium channel subunit beta-2 | / | 0.447 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.447 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.447 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.446 | |
| 2oby | NAP | Quinone oxidoreductase PIG3 | 1 | 0.446 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3clb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3oy4 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.446 | |
| 4mt9 | 2D6 | Tankyrase-1 | 2.4.2.30 | 0.446 | |
| 5c7h | NDP | Putative oxidoreductase | / | 0.446 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.445 | |
| 3wbw | NDP | Putative 2,5-diketo-D-gluconic acid reductase | / | 0.445 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.445 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.445 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.444 | |
| 1ye4 | NAD | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.444 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.444 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.444 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.444 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.444 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 5hws | NAP | 2-dehydropantoate 2-reductase | / | 0.444 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.443 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.443 | |
| 1ye6 | NAP | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.443 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 2jd1 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.443 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.443 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.443 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.443 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 1z9a | NAD | NAD(P)H-dependent D-xylose reductase | 1.1.1.307 | 0.442 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.442 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.442 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.442 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4tm1 | FDA | KtzI | / | 0.442 | |
| 4xo7 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.442 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.441 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.441 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.441 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.441 | |
| 2wet | FAD | Tryptophan 5-halogenase | / | 0.441 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 3q67 | NAP | Aldose reductase | 1.1.1.21 | 0.441 | |
| 3ukk | FDA | UDP-galactopyranose mutase | / | 0.441 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4qec | NAP | ElxO | / | 0.441 | |
| 4xzn | NAP | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.441 | |
| 5a3b | APR | SIR2 family protein | / | 0.441 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.440 | |
| 2bel | CBO | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.440 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.440 | |
| 2xc3 | RT8 | Steroid C26-monooxygenase | 1.14.13.141 | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.440 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.440 | |
| 4nte | FAD | DepH | / | 0.440 | |
| 4pd6 | URI | Nucleoside permease | / | 0.440 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.440 |