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 |
|---|---|---|---|
| 1v8k | ANP | Kinesin-like protein KIF2C |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1v8k | ANP | Kinesin-like protein KIF2C | / | 1.000 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.500 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.481 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.479 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.478 | |
| 4l4x | NDP | AmphI | / | 0.477 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.476 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.473 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.472 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.472 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.471 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.471 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 4yt5 | H4M | H(2)-forming methylenetetrahydromethanopterin dehydrogenase-related protein MJ1338 | / | 0.470 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.468 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.467 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.466 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 5kcz | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 2emu | SAH | Diphthine synthase | / | 0.465 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.463 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.463 | |
| 2ele | SAH | Diphthine synthase | / | 0.462 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.462 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.462 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.462 | |
| 2b69 | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.461 | |
| 2ehl | SAH | Diphthine synthase | / | 0.461 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.461 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.460 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.460 | |
| 1sb8 | UD2 | WbpP | / | 0.459 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.459 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.458 | |
| 2e16 | SAH | Diphthine synthase | / | 0.458 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.458 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.458 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.457 | |
| 2cwf | NDP | Delta(1)-pyrroline-2-carboxylate/Delta(1)-piperideine-2-carboxylate reductase | / | 0.457 | |
| 2dxv | SAH | Diphthine synthase | / | 0.456 | |
| 3l9h | EMQ | Kinesin-like protein KIF11 | / | 0.456 | |
| 3wrb | GDE | Gallate dioxygenase | / | 0.456 | |
| 4xd2 | NAI | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.456 | |
| 1vce | SAH | Diphthine synthase | / | 0.455 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.455 | |
| 3jq3 | ADP | Lombricine kinase | / | 0.455 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.454 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.454 | |
| 2dsg | SAH | Diphthine synthase | / | 0.454 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.454 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.454 | |
| 4xyb | NDP | Formate dehydrogenase | / | 0.454 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.453 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.453 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.453 | |
| 3tqa | NDP | Dihydrofolate reductase | / | 0.453 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.453 | |
| 2p6d | SAH | Diphthine synthase | / | 0.452 | |
| 4bkz | 1WS | Maternal embryonic leucine zipper kinase | 2.7.11.1 | 0.452 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.451 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.451 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.451 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.450 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.450 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.450 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.450 | |
| 1e92 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.449 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.449 | |
| 3up0 | D7S | aceDAF-12 | / | 0.449 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.449 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.448 | |
| 1gqt | ACP | Ribokinase | / | 0.448 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 1xgj | HTC | Beta-lactamase | 3.5.2.6 | 0.448 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.448 | |
| 2pcg | SAH | Diphthine synthase | / | 0.448 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.448 | |
| 1xq6 | NAP | Uncharacterized protein At5g02240 | / | 0.447 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2e8r | SAH | Diphthine synthase | / | 0.447 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2hux | SAH | Diphthine synthase | / | 0.447 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.447 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.447 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.447 | |
| 4z87 | 5GP | Inosine-5'-monophosphate dehydrogenase | / | 0.447 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.446 | |
| 1rrm | APR | Lactaldehyde reductase | 1.1.1.77 | 0.446 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.446 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.446 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.446 | |
| 3p8z | SAH | Genome polyprotein | 2.1.1.56 | 0.446 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.446 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.445 | |
| 2e7r | SAH | Diphthine synthase | / | 0.445 | |
| 2p6k | SAH | Diphthine synthase | / | 0.445 | |
| 2p6l | SAH | Diphthine synthase | / | 0.445 | |
| 2pch | SAH | Diphthine synthase | / | 0.445 | |
| 3qeo | LLT | Deoxycytidine kinase | 2.7.1.74 | 0.445 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.445 | |
| 4l7f | 1V5 | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.445 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 5dp2 | NAP | CurF | / | 0.445 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.444 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.444 | |
| 4hxy | NDP | Plm1 | / | 0.444 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.443 | |
| 2e17 | SAH | Diphthine synthase | / | 0.443 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2nli | FMN | Lactate oxidase | / | 0.443 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 4bzq | ADP | Bifunctional enzyme CysN/CysC | 2.7.1.25 | 0.443 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.443 | |
| 4ipe | ANP | TNF receptor-associated protein 1 | / | 0.443 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 1i6x | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.442 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.442 | |
| 1s60 | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.442 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.442 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.442 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.442 | |
| 2j0v | GDP | Rac-like GTP-binding protein ARAC7 | / | 0.442 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.442 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4itr | GDP | Cell division control protein 42 homolog | / | 0.442 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.442 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 1dxy | NAD | D-2-hydroxyisocaproate dehydrogenase | 1.1.1 | 0.441 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.441 | |
| 1n6l | GTP | Ras-related protein Rab-5A | / | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.441 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.441 | |
| 2qtv | GNP | Small COPII coat GTPase SAR1 | 3.6.5 | 0.441 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4obu | PLP | Pyridoxal-dependent decarboxylase domain protein | / | 0.441 | |
| 4pd6 | URI | Nucleoside permease | / | 0.441 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.441 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1sny | NAP | LD36273p | / | 0.440 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 2eh2 | SAH | Diphthine synthase | / | 0.440 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.440 | |
| 2p5f | SAH | Diphthine synthase | / | 0.440 | |
| 2vmy | FFO | Serine hydroxymethyltransferase | / | 0.440 | |
| 3aut | NAI | Glucose 1-dehydrogenase 4 | 1.1.1.47 | 0.440 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4ehy | ADP | Tetraacyldisaccharide 4'-kinase | / | 0.440 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.440 |