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 |
|---|---|---|---|
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 1.000 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.616 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.612 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.610 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.606 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.589 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.586 | |
| 1rr6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.567 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.546 | |
| 1v2h | GUN | Purine nucleoside phosphorylase | 2.4.2.1 | 0.539 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.536 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.517 | |
| 2on6 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.512 | |
| 1v3q | 2DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.510 | |
| 3f8w | ADN | Purine nucleoside phosphorylase | / | 0.493 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.484 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.484 | |
| 1rct | NOS | Purine nucleoside phosphorylase | 2.4.2.1 | 0.482 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.480 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.479 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.476 | |
| 1fxu | GU7 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.475 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.475 | |
| 1a9p | 9DI | Purine nucleoside phosphorylase | 2.4.2.1 | 0.474 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.472 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.471 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.469 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.469 | |
| 5dp2 | NAP | CurF | / | 0.469 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.465 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.465 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.463 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.463 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.463 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 2dsg | SAH | Diphthine synthase | / | 0.462 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.461 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4jic | FMN | GTN Reductase | / | 0.460 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.459 | |
| 1u4o | NDD | L-lactate dehydrogenase | 1.1.1.27 | 0.459 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.459 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.458 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.458 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.457 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.457 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.456 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4bri | UNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.455 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.454 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.453 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.453 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.452 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.451 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.451 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.451 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.450 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.450 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.450 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.449 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.449 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.448 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.448 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4n1g | CEI | Obelin | / | 0.448 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.447 | |
| 1je1 | GMP | Purine nucleoside phosphorylase | / | 0.447 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 1w4l | GL8 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.447 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.446 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.446 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.446 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.446 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.446 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.445 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.445 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.445 | |
| 4iae | 1DX | Alr2278 protein | / | 0.445 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.444 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 4e2b | FMN | Dehydrogenase | / | 0.444 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.443 | |
| 1lvu | 9PP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.443 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.442 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.442 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.442 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.442 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.442 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.442 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.441 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 1aka | PLP | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.440 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1eii | RTL | Retinol-binding protein 2 | / | 0.440 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.440 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.440 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.440 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.440 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.440 | |
| 3ju8 | NAD | N-succinylglutamate 5-semialdehyde dehydrogenase | 1.2.1.71 | 0.440 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3v2u | ATP | Protein GAL3 | / | 0.440 |