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 |
|---|---|---|---|
| 2fhn | BNI | Avidin-related protein 4/5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2fhn | BNI | Avidin-related protein 4/5 | / | 1.000 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.568 | |
| 2avi | BTN | Avidin | / | 0.530 | |
| 1mk5 | BTN | Streptavidin | / | 0.529 | |
| 2uyw | BTN | Avd protein | / | 0.524 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.522 | |
| 2rti | GLL | Streptavidin | / | 0.518 | |
| 1avd | BTN | Avidin | / | 0.515 | |
| 2izh | BTN | Streptavidin | / | 0.511 | |
| 4bx7 | B4F | Streptavidin | / | 0.511 | |
| 2rtf | BTN | Streptavidin | / | 0.501 | |
| 4dne | DTB | Streptavidin | / | 0.500 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.499 | |
| 2uz2 | BTN | Avd protein | / | 0.499 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.493 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.490 | |
| 2rtg | BTN | Streptavidin | / | 0.490 | |
| 3ry2 | BTN | Streptavidin | / | 0.490 | |
| 2rto | IMI | Streptavidin | / | 0.489 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.489 | |
| 1stp | BTN | Streptavidin | / | 0.488 | |
| 2izf | BTN | Streptavidin | / | 0.485 | |
| 2izl | IMI | Streptavidin | / | 0.484 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.483 | |
| 2izg | BTN | Streptavidin | / | 0.483 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.482 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.482 | |
| 2rtq | IMI | Streptavidin | / | 0.482 | |
| 2c4i | BTN | Avidin | / | 0.480 | |
| 3wyq | BTN | Streptavidin | / | 0.480 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.478 | |
| 1srg | MHB | Streptavidin | / | 0.477 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.476 | |
| 1df8 | BTN | Streptavidin | / | 0.474 | |
| 2izk | GLL | Streptavidin | / | 0.474 | |
| 1sre | HAB | Streptavidin | / | 0.473 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.473 | |
| 1swp | BTQ | Streptavidin | / | 0.472 | |
| 3wzn | BTN | Streptavidin | / | 0.472 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.471 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.468 | |
| 1sri | DMB | Streptavidin | / | 0.467 | |
| 3af3 | GCP | Pantothenate kinase | 2.7.1.33 | 0.466 | |
| 2rtr | IMI | Streptavidin | / | 0.465 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.465 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.464 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 4bj8 | BTN | Avidin | / | 0.464 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.463 | |
| 2rtn | IMI | Streptavidin | / | 0.463 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 1srf | MTB | Streptavidin | / | 0.462 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.462 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.461 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.461 | |
| 2pu2 | DK2 | Beta-lactamase | 3.5.2.6 | 0.461 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.461 | |
| 1hzj | UD1 | UDP-glucose 4-epimerase | / | 0.460 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.460 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.460 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.460 | |
| 4z28 | BTN | Hoefavidin | / | 0.460 | |
| 1swt | BTN | Streptavidin | / | 0.459 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.459 | |
| 4gda | BTN | Streptavidin | / | 0.459 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.459 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.459 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.458 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.458 | |
| 4l4x | NDP | AmphI | / | 0.458 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.457 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.457 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 2y3f | BTN | Streptavidin | / | 0.456 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.456 | |
| 4d86 | ADP | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.456 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.455 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.454 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.454 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.454 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.453 | |
| 1rxh | BNI | Streptavidin | / | 0.453 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.452 | |
| 2bfr | ADP | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.452 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.452 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4kz0 | 1UJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 5hwo | HMG | Hydroxymethylglutaryl-CoA synthase | / | 0.452 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.451 | |
| 3w5r | LOA | Vitamin D3 receptor | / | 0.451 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 4die | C5P | Cytidylate kinase | / | 0.451 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.450 | |
| 1luq | BTN | Streptavidin | / | 0.450 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 3pbl | ETQ | D(3) dopamine receptor | / | 0.450 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.449 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.449 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.449 | |
| 2rtd | BTN | Streptavidin | / | 0.449 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.449 | |
| 4x5h | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.449 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.448 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.448 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.448 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.448 | |
| 5a3b | APR | SIR2 family protein | / | 0.448 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.447 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.447 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3gtc | GTC | Beta-lactamase | 3.5.2.6 | 0.447 | |
| 3t8w | DGZ | M17 leucyl aminopeptidase | / | 0.447 | |
| 3vhh | VHH | Avidin | / | 0.447 | |
| 4dja | FAD | (6-4) photolyase | / | 0.447 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.447 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 1i9h | BNI | Streptavidin | / | 0.446 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.446 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2rtm | IMI | Streptavidin | / | 0.446 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 4awp | 99A | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 4kqq | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.445 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.445 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.445 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.445 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.445 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.444 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.444 | |
| 1tj2 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.444 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.444 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.444 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.444 | |
| 2rte | BTN | Streptavidin | / | 0.444 | |
| 2zxu | DST | tRNA dimethylallyltransferase | 2.5.1.75 | 0.444 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.444 | |
| 3vgw | NVZ | Avidin | / | 0.444 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 2gs7 | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.443 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.443 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.443 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.443 | |
| 4e2b | FMN | Dehydrogenase | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 1jgt | APC | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.442 | |
| 1ppj | ANY | Cytochrome b | / | 0.442 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.442 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 2rtk | GLL | Streptavidin | / | 0.442 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.442 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.442 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.442 | |
| 1lcw | SHM | Streptavidin | / | 0.441 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.441 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.441 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.441 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.441 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.441 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.440 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.440 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3q44 | D50 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 3up3 | XCA | aceDAF-12 | / | 0.440 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.440 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4bis | 8HQ | Lysine-specific demethylase 4A | 1.14.11 | 0.440 | |
| 4x5i | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 |