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 |
|---|---|---|---|
| 2ag0 | TPP | Benzaldehyde lyase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ag0 | TPP | Benzaldehyde lyase | / | 1.000 | |
| 2uz1 | TPP | Benzaldehyde lyase | / | 0.620 | |
| 2ag1 | TPP | Benzaldehyde lyase | / | 0.577 | |
| 2q5o | PPY | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.524 | |
| 2jla | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.508 | |
| 2q5o | TPW | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.508 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.501 | |
| 2ihv | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.498 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.498 | |
| 4zp1 | TPP | Pyruvate decarboxylase | 4.1.1.1 | 0.491 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.487 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.486 | |
| 2w93 | TPP | Pyruvate decarboxylase isozyme 1 | / | 0.485 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.484 | |
| 3cge | COA | Coenzyme A disulfide reductase | / | 0.482 | |
| 5ahk | TPP | Acetolactate synthase II, large subunit | / | 0.481 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.477 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.474 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.470 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.470 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.467 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.466 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 2bbq | PFG | Thymidylate synthase | / | 0.465 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.465 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 2b7a | IZA | Tyrosine-protein kinase JAK2 | / | 0.464 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.464 | |
| 3iod | A6D | Pantothenate synthetase | 6.3.2.1 | 0.463 | |
| 4jb1 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.463 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.462 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.462 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.462 | |
| 1ovm | TPP | Indole-3-pyruvate decarboxylase | 4.1.1.74 | 0.460 | |
| 1y9d | TPP | Pyruvate oxidase | 1.2.3.3 | 0.460 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.460 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.460 | |
| 1nvs | UCM | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.459 | |
| 1r2j | FAD | FkbI | / | 0.459 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.459 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.459 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.458 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.458 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.458 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.458 | |
| 1orh | SAH | Protein arginine N-methyltransferase 1 | / | 0.457 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2ihu | TP9 | N(2)-(2-carboxyethyl)arginine synthase | / | 0.457 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.457 | |
| 4wud | ANP | DNA gyrase subunit B | / | 0.457 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.457 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.456 | |
| 1n83 | CLR | Nuclear receptor ROR-alpha | / | 0.456 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.456 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.455 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.455 | |
| 2yei | XQI | Heat shock protein HSP 90-alpha | / | 0.455 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 4ach | KDI | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.455 | |
| 4juf | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.455 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.454 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.454 | |
| 3eya | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.454 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.454 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit alpha | / | 0.454 | |
| 5c4i | TPP | Oxalate oxidoreductase subunit beta | / | 0.454 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.453 | |
| 3cgb | COA | Coenzyme A disulfide reductase | / | 0.453 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.453 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.453 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.452 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.452 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2c3y | HTL | Pyruvate synthase | / | 0.451 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3mdm | FJZ | Cholesterol 24-hydroxylase | / | 0.451 | |
| 1kek | HTL | Pyruvate synthase | / | 0.450 | |
| 2bxm | IMN | Serum albumin | / | 0.450 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.450 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.450 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.450 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.449 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.449 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.449 | |
| 2pvn | P63 | Casein kinase II subunit alpha | 2.7.11.1 | 0.449 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.449 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.448 | |
| 1mma | ADP | Myosin-2 heavy chain | / | 0.448 | |
| 2c42 | TPP | Pyruvate synthase | / | 0.448 | |
| 2egl | SAH | Diphthine synthase | / | 0.448 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 2pan | TDP | Glyoxylate carboligase | 4.1.1.47 | 0.448 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.447 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.447 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.447 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.447 | |
| 3w0p | ADP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.447 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.446 | |
| 2p8u | COA | Hydroxymethylglutaryl-CoA synthase, cytoplasmic | 2.3.3.10 | 0.446 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.446 | |
| 3kb6 | NAD | D-lactate dehydrogenase | / | 0.446 | |
| 3pft | FMN | Flavin reductase | / | 0.446 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1l4m | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.445 | |
| 1upa | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.445 | |
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.445 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.445 | |
| 4prv | ADP | DNA gyrase subunit B | / | 0.445 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.444 | |
| 2yn8 | STU | Ephrin type-B receptor 4 | 2.7.10.1 | 0.444 | |
| 3mjh | GTP | Ras-related protein Rab-5A | / | 0.444 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.444 | |
| 3nta | COA | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.444 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.444 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.444 | |
| 5a3c | NAD | SIR2 family protein | / | 0.444 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.444 | |
| 2clq | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.443 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.443 | |
| 2kce | D16 | Thymidylate synthase | / | 0.443 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.443 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3inx | JZC | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.443 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.443 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.442 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.442 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.442 | |
| 3anl | SYC | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 0.442 | |
| 3owj | 1EL | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.442 | |
| 3pce | 3HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.442 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.442 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.442 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 4nvk | 2NY | Peroxidase | / | 0.442 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.441 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.441 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.441 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3pld | F90 | Endothiapepsin | 3.4.23.22 | 0.441 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.441 | |
| 4pzd | NAD | 3-Hydroxyacyl-CoA dehydrogenase | / | 0.441 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1iqe | XMB | Coagulation factor X | 3.4.21.6 | 0.440 | |
| 1l4k | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.440 | |
| 1m2r | MNY | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.440 | |
| 2iht | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.440 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.440 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.440 | |
| 3h06 | VBP | Glutamate receptor 2 | / | 0.440 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3ijo | B4D | Glutamate receptor 2 | / | 0.440 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.440 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.440 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.440 |