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 |
|---|---|---|---|
| 3lbf | SAH | Protein-L-isoaspartate O-methyltransferase | 2.1.1.77 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3lbf | SAH | Protein-L-isoaspartate O-methyltransferase | 2.1.1.77 | 1.000 | |
| 4o29 | SAH | Protein-L-isoaspartate O-methyltransferase | / | 0.547 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.478 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.478 | |
| 3enk | UPG | UDP-glucose 4-epimerase | / | 0.473 | |
| 2wot | ZZG | TGF-beta receptor type-1 | 2.7.11.30 | 0.469 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.467 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.466 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.466 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.466 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.466 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.465 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 2qrq | S13 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.463 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.462 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.462 | |
| 1jol | FFO | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.461 | |
| 3i5z | Z48 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.461 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.461 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.460 | |
| 3ut5 | LOC | Tubulin beta chain | / | 0.460 | |
| 4c3f | 7KW | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.460 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.460 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.459 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.459 | |
| 1nv9 | SAH | Release factor glutamine methyltransferase | 2.1.1.297 | 0.458 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.458 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.457 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.457 | |
| 1kr5 | SAH | Protein-L-isoaspartate(D-aspartate) O-methyltransferase | 2.1.1.77 | 0.456 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.456 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.456 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.456 | |
| 4g47 | TZF | Mycocyclosin synthase | 1.14.21.9 | 0.456 | |
| 1h74 | AGS | Homoserine kinase | 2.7.1.39 | 0.455 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 2xhd | 7T9 | Glutamate receptor 2 | / | 0.455 | |
| 3fzn | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.454 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.453 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 5bxy | SAH | Putative RNA methylase family UPF0020 | / | 0.453 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.452 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.452 | |
| 3t7s | SAM | Uncharacterized protein | / | 0.452 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.451 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.451 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.451 | |
| 5hs1 | VOR | Lanosterol 14-alpha demethylase | / | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.450 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.450 | |
| 2gr1 | FAD | Ferredoxin reductase | / | 0.450 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.450 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.450 | |
| 4g6h | NAI | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.450 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.448 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.448 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.448 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.448 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.447 | |
| 1sg9 | SAM | Release factor glutamine methyltransferase | 2.1.1.297 | 0.447 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.447 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3onw | GDP | Guanine nucleotide-binding protein G(i) subunit alpha-1 | / | 0.447 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.447 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.447 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1h6v | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.446 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.446 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.446 | |
| 2b8t | THM | Thymidine kinase | / | 0.446 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.446 | |
| 3up3 | XCA | aceDAF-12 | / | 0.446 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.445 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.445 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.445 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 4hzf | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.445 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.445 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.445 | |
| 4z54 | GDP | Neuronal-specific septin-3 | / | 0.445 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.444 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.444 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.444 | |
| 3rou | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.444 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.443 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.443 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.443 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.443 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.442 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 1p0h | ACO | Mycothiol acetyltransferase | 2.3.1.189 | 0.442 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.442 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.442 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.442 | |
| 2z3l | PHE_ARG_TYR_LEU_GLY | Leucyl/phenylalanyl-tRNA--protein transferase | 2.3.2.6 | 0.442 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 3awh | FMN | FMN-binding protein | / | 0.442 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.442 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.441 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.441 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.441 | |
| 2vr1 | ATF | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.441 | |
| 3myk | BIT | Myosin-2 heavy chain | / | 0.441 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.441 | |
| 4kvz | SAH | PtnL protein | / | 0.441 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.441 | |
| 4l8u | 9AZ | Serum albumin | / | 0.441 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.440 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.440 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.440 | |
| 2en5 | SAH | Diphthine synthase | / | 0.440 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.440 | |
| 2hj3 | FAD | FAD-linked sulfhydryl oxidase ERV1 | / | 0.440 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.440 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.440 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.440 | |
| 2p2x | SAH | Diphthine synthase | / | 0.440 | |
| 3elm | 24F | Collagenase 3 | 3.4.24 | 0.440 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.440 | |
| 3ty3 | GGG | Homoisocitrate dehydrogenase | 1.1.1.87 | 0.440 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.440 | |
| 4lj6 | ACP | Chaperone protein ClpB | / | 0.440 |