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 |
|---|---|---|---|
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4tqg | NDP | Putative dTDP-d-glucose 4 6-dehydratase | / | 1.000 | |
| 4fiz | CUE | 17beta-hydroxysteroid dehydrogenase | / | 0.507 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.495 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.492 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.486 | |
| 4oqy | NDP | (S)-imine reductase | / | 0.484 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.483 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.477 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.476 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.476 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.476 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.472 | |
| 2bgm | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.472 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.471 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.470 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.470 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.469 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.469 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.467 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.467 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.466 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.464 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.464 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.463 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.462 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.462 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.462 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.461 | |
| 3zuy | TCH | Transporter | / | 0.461 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.460 | |
| 3fwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.460 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.460 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.459 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.459 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.457 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.457 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.457 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.457 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.457 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.457 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.456 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1ri4 | SAM | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.456 | |
| 4jic | FMN | GTN Reductase | / | 0.456 | |
| 1fk8 | NAD | 3-alpha-hydroxysteroid dehydrogenase/carbonyl reductase | 1.1.1.50 | 0.455 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.455 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.455 | |
| 1qr6 | NAD | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.455 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.455 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.455 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.455 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.455 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.455 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.454 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.453 | |
| 2y3r | TRK | TamL | / | 0.453 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.453 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.452 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.452 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.452 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 4qec | NAP | ElxO | / | 0.452 | |
| 1l5s | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.451 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.451 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.451 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.451 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.450 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.450 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.450 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.450 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.450 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.450 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.450 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.450 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.450 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.450 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.450 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.449 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.449 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.449 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.449 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.449 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.449 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.449 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.449 | |
| 2ddo | ATP | Pyridoxine/pyridoxal/pyridoxamine kinase | / | 0.448 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.448 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.448 | |
| 3w2u | ROU | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.448 | |
| 4e2d | FMN | Dehydrogenase | / | 0.448 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.448 | |
| 4y0k | NAP | AntE | / | 0.448 | |
| 1udc | UFM | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2xfs | J01 | Uncharacterized protein | / | 0.447 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.447 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.447 | |
| 3sj7 | NDP | 3-oxoacyl-(Acyl-carrier-protein) reductase, putative | / | 0.447 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.446 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.446 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.446 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.446 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.446 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.446 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 1hdr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.445 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.445 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.444 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.444 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.444 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.444 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.444 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.444 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.444 | |
| 2y4g | TIR | TamL | / | 0.444 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.444 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.444 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4wxf | PLG | Serine hydroxymethyltransferase | / | 0.444 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.443 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.443 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.443 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.443 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 4u7w | NDP | MxaA | / | 0.443 | |
| 5c8w | PCG | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.443 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.442 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.442 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.442 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.442 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.442 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.442 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.441 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.441 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.441 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.441 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.441 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.441 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.440 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.440 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.440 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.440 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3gon | ANP | Phosphomevalonate kinase | / | 0.440 | |
| 3gvi | ADP | Malate dehydrogenase | / | 0.440 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.440 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.440 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3s87 | ADP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.440 | |
| 3w1t | WRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.440 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.440 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.440 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.440 |