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 |
|---|---|---|---|
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3o0q | ADN | Vitamin B12-dependent ribonucleotide reductase | / | 1.000 | |
| 3o0o | 5AD | Vitamin B12-dependent ribonucleotide reductase | / | 0.631 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.491 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.488 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.482 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.481 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.481 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.480 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.478 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.477 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.476 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.476 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.476 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.474 | |
| 1kp3 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.473 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.473 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.471 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.470 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.469 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.469 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.469 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.469 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.467 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.467 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.466 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.465 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.465 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.465 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.465 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.465 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.464 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.464 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.464 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.463 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.463 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.462 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.461 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.461 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.461 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.461 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.460 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.458 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.458 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.458 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.458 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1c9k | 5GP | Bifunctional adenosylcobalamin biosynthesis protein CobU | / | 0.457 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.457 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.457 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.457 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2b53 | D23 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.456 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.456 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.456 | |
| 4u0m | ATP | Cyclic GMP-AMP synthase | / | 0.456 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.456 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.456 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.455 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.455 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.455 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.455 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.454 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.454 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.454 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.454 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.454 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.453 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.453 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.452 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.452 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.452 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.451 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.451 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.450 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.450 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.449 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.449 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4bls | APC | NTPase P4 | / | 0.449 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.449 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.448 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.448 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.448 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1tys | DHF | Thymidylate synthase | / | 0.447 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.446 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.446 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.446 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 2dgn | DOI | Adenylosuccinate synthetase isozyme 1 | / | 0.445 | |
| 2drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.445 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.445 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.445 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.444 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.444 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.444 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.444 | |
| 3nbv | ANP | Ketohexokinase | / | 0.444 | |
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.444 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.444 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.444 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.443 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.443 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.443 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.443 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.443 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.443 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1i6k | TYM | Tryptophan--tRNA ligase | 6.1.1.2 | 0.442 | |
| 1jil | 485 | Tyrosine--tRNA ligase | / | 0.442 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.442 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.442 | |
| 3w6h | AZM | Carbonic anhydrase 1 | 4.2.1.1 | 0.442 | |
| 4f5y | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.442 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.441 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.441 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.441 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.440 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.440 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.440 | |
| 4nvk | 2NY | Peroxidase | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.440 |