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 |
|---|---|---|---|
| 3fvp | UB2 | Thermolysin | 3.4.24.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3fvp | UB2 | Thermolysin | 3.4.24.27 | 1.000 | |
| 1u4g | HPI | Elastase | 3.4.24.26 | 0.573 | |
| 3fv4 | 1U4 | Thermolysin | 3.4.24.27 | 0.568 | |
| 3f2p | S3B | Thermolysin | 3.4.24.27 | 0.552 | |
| 3f28 | S7B | Thermolysin | 3.4.24.27 | 0.545 | |
| 3fgd | BYA | Thermolysin | 3.4.24.27 | 0.528 | |
| 4cth | RDF | Neprilysin | / | 0.499 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.489 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.488 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.485 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.484 | |
| 4zr5 | RDF | Neprilysin | / | 0.481 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.479 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.478 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.474 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.474 | |
| 2e20 | B4P | Propionate kinase | / | 0.473 | |
| 3zuk | RDF | Endopeptidase, peptidase family M13 | / | 0.472 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.472 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.472 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.471 | |
| 3td7 | FAD | Probable FAD-linked sulfhydryl oxidase R596 | 1.8.3.2 | 0.471 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.471 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.469 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.469 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.469 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.467 | |
| 2y3s | TIR | TamL | / | 0.466 | |
| 4b42 | 942 | Glucose-1-phosphate thymidylyltransferase | / | 0.466 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.465 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.465 | |
| 5cwa | 0GA | Anthranilate synthase component 1 | 4.1.3.27 | 0.465 | |
| 3uzx | AOM | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.464 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.464 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.463 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.463 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.461 | |
| 2e1z | B4P | Propionate kinase | / | 0.461 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.461 | |
| 2yoz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.461 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.461 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.461 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.460 | |
| 4ho6 | UTP | Glucose-1-phosphate thymidylyltransferase | / | 0.460 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 4h6p | FMN | Chromate reductase | / | 0.459 | |
| 1dd6 | MCI | Metallo-beta-lactamase type 2 | / | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.458 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.457 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.457 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 3dwb | RDF | Endothelin-converting enzyme 1 | 3.4.24.71 | 0.457 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3zbs | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.457 | |
| 4ifn | 12O | Kelch-like ECH-associated protein 1 | / | 0.457 | |
| 4kug | NAD | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.457 | |
| 5es7 | FON | Linear gramicidin synthase subunit A | / | 0.457 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.456 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.456 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.456 | |
| 3qvi | K95 | HAP protein | / | 0.456 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.455 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.455 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.455 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.455 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 1nja | DCM | Thymidylate synthase | / | 0.453 | |
| 1r1i | TI1 | Neprilysin | / | 0.453 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.453 | |
| 3bht | MFR | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.453 | |
| 4pnr | G18 | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.452 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.452 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.452 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.452 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.452 | |
| 4b4b | GJB | Glucose-1-phosphate thymidylyltransferase | / | 0.452 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.451 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3m2y | BE0 | Carbonic anhydrase 2 | 4.2.1.1 | 0.451 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4xr9 | NAD | CalS8 | / | 0.451 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.450 | |
| 1r1j | OIR | Neprilysin | / | 0.450 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.450 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.450 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.450 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.450 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.450 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.450 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.449 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.449 | |
| 4xbj | IN5 | Alanine racemase, biosynthetic | / | 0.449 | |
| 1x27 | ASP_ASP_TYR_VAL_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.448 | |
| 2y3r | TRK | TamL | / | 0.448 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.448 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.448 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.448 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.448 | |
| 4lcg | 1WM | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.448 | |
| 4tta | FMC | Purine nucleoside phosphorylase DeoD-type | / | 0.448 | |
| 1ep4 | S11 | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 1lke | DOG | Bilin-binding protein | / | 0.447 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2y05 | RAL | Prostaglandin reductase 1 | / | 0.447 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.447 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.447 | |
| 5bur | ATP | 2-succinylbenzoate--CoA ligase | / | 0.447 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2bmb | PMM | Folic acid synthesis protein FOL1 | / | 0.446 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 3dok | GWJ | Pol protein | / | 0.446 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.446 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.446 | |
| 3n0b | FAD | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.446 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.446 | |
| 3w2e | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.446 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4bqp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 4eh9 | IRG | Mitogen-activated protein kinase 14 | / | 0.446 | |
| 4k97 | ATP | Cyclic GMP-AMP synthase | / | 0.446 | |
| 4o0m | ATP | Circadian clock protein kinase KaiC | 2.7.11.1 | 0.446 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.446 | |
| 1ao0 | 5GP | Amidophosphoribosyltransferase | / | 0.445 | |
| 1fxo | TMP | Glucose-1-phosphate thymidylyltransferase | / | 0.445 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.445 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4lch | 1WN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.445 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.445 | |
| 5a3c | NAD | SIR2 family protein | / | 0.445 | |
| 1f4e | TPR | Thymidylate synthase | / | 0.444 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1pu9 | COA | HAT A1 | / | 0.444 | |
| 1pw6 | FRB | Interleukin-2 | / | 0.444 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.444 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.444 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.444 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.444 | |
| 4aux | XTC | Tetracycline repressor protein class D | / | 0.444 | |
| 4ku2 | MYA | 3-oxoacyl-[ACP] synthase III | / | 0.444 | |
| 4okb | 198 | Androgen receptor | / | 0.444 | |
| 4okx | 198 | Androgen receptor | / | 0.444 | |
| 1b8n | IMG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.443 | |
| 2cht | TSA | Chorismate mutase AroH | 5.4.99.5 | 0.443 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.443 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.443 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3dg8 | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3er9 | 3AT | Poly(A) polymerase catalytic subunit | 2.7.7.19 | 0.443 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4ca6 | 3EF | Angiotensin-converting enzyme | 3.2.1 | 0.443 | |
| 4e5o | UMP | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.443 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.443 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.442 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.442 | |
| 2brb | PFQ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.442 | |
| 2hyd | ADP | Putative multidrug export ATP-binding/permease protein SAV1866 | 3.6.3 | 0.442 | |
| 3mfl | DHY | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.442 | |
| 3mfl | DHY | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.442 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4u3j | GTP | Tubulin beta chain | / | 0.442 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.441 | |
| 1n3r | GTP | GTP cyclohydrolase 1 | 3.5.4.16 | 0.441 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 1w5s | ADP | ORC1-type DNA replication protein 2 | / | 0.441 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.441 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.441 | |
| 2wi5 | ZZ5 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.441 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.441 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.441 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.441 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.441 | |
| 4ho4 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.441 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.441 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.441 | |
| 5a8a | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.441 | |
| 1k6m | AGS | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 1 | 2.7.1.105 | 0.440 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.440 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.440 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.440 | |
| 3pn1 | IVH | DNA ligase | / | 0.440 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.440 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.440 |