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 |
|---|---|---|---|
| 2vmy | FFO | Serine hydroxymethyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 1.000 | |
| 1dfo | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.609 | |
| 1eqb | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.597 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.532 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.530 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.490 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.483 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.481 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.477 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.476 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.474 | |
| 1fml | RTL | Retinol dehydratase | / | 0.472 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.470 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.468 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.468 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.467 | |
| 4l8u | 9AZ | Serum albumin | / | 0.467 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.465 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.464 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.463 | |
| 1nqm | BTN | Streptavidin | / | 0.463 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.461 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.461 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.461 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.461 | |
| 4l4x | NDP | AmphI | / | 0.461 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.460 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.459 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.459 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.459 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.458 | |
| 4k9p | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 4pd6 | URI | Nucleoside permease | / | 0.458 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.457 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.457 | |
| 3vwe | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.457 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.457 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.456 | |
| 1mcz | TDP | Benzoylformate decarboxylase | 4.1.1.7 | 0.456 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.456 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.456 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.456 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.455 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.455 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.454 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.453 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.453 | |
| 3cd3 | STU | Tyrosine-protein kinase Fes/Fps | 2.7.10.2 | 0.453 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.453 | |
| 4ktf | 1TM | Cytochrome P450 | / | 0.453 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.453 | |
| 1hvy | D16 | Thymidylate synthase | 2.1.1.45 | 0.452 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.452 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.452 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 1men | GAR | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.451 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.451 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 3w0i | O11 | Vitamin D3 receptor | / | 0.451 | |
| 4br0 | AU1 | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.451 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.450 | |
| 4gg5 | 0J3 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.450 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.450 | |
| 1flm | FMN | FMN-binding protein | / | 0.449 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.449 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.449 | |
| 2r5n | TPP | Transketolase 1 | / | 0.449 | |
| 3oey | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 4bmp | FMN | Protein NrdI | / | 0.449 | |
| 4wxg | 2BO | Serine hydroxymethyltransferase | / | 0.449 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.448 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.448 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.448 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.448 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 3zuy | TCH | Transporter | / | 0.448 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4deg | 0JJ | Hepatocyte growth factor receptor | 2.7.10.1 | 0.448 | |
| 1aj2 | 2PH | Dihydropteroate synthase | / | 0.447 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.447 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.447 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.447 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2wgj | VGH | Hepatocyte growth factor receptor | 2.7.10.1 | 0.447 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.447 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 4pan | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.447 | |
| 1eio | GCH | Gastrotropin | / | 0.446 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.446 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.446 | |
| 1py5 | PY1 | TGF-beta receptor type-1 | 2.7.11.30 | 0.446 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.446 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.446 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.446 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 4iah | 1DX | Alr2278 protein | / | 0.446 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.446 | |
| 1njf | AGS | DNA polymerase III subunit tau | 2.7.7.7 | 0.445 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.445 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.445 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4bdc | ODH | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.445 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.445 | |
| 1db1 | VDX | Vitamin D3 receptor | / | 0.444 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.444 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.444 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.444 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.444 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.443 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.443 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.443 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.443 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.443 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.443 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.443 | |
| 4u7w | NDP | MxaA | / | 0.443 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.442 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.442 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.442 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.442 | |
| 2pmd | GNP | Translation initiation factor 2 subunit gamma | / | 0.442 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.442 | |
| 3zc5 | W9Z | Hepatocyte growth factor receptor | 2.7.10.1 | 0.442 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.442 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.442 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.441 | |
| 1guy | NAD | Malate dehydrogenase | / | 0.441 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.441 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2e9v | 85A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 2hb8 | MVD | Vitamin D3 receptor | / | 0.441 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.441 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.441 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.441 | |
| 3daa | PDD | D-alanine aminotransferase | 2.6.1.21 | 0.441 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.441 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.441 | |
| 4kq2 | 1S3 | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.441 | |
| 4u9z | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.441 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.440 | |
| 1nvq | UCN | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 1rbq | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.440 | |
| 1u2d | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.440 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.440 | |
| 2p5c | SAH | Diphthine synthase | / | 0.440 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.440 | |
| 3bgi | SAH | Thiopurine S-methyltransferase | 2.1.1.67 | 0.440 | |
| 3epo | MP5 | Phosphomethylpyrimidine synthase | / | 0.440 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.440 | |
| 4aoi | 4K0 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 4kq2 | U5P | Glycogen [starch] synthase isoform 2 | 2.4.1.11 | 0.440 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.440 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |