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 |
|---|---|---|---|
| 2avi | BTN | Avidin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2avi | BTN | Avidin | / | 1.000 | |
| 1avd | BTN | Avidin | / | 0.607 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.596 | |
| 2c4i | BTN | Avidin | / | 0.579 | |
| 2uyw | BTN | Avd protein | / | 0.578 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.531 | |
| 1mk5 | BTN | Streptavidin | / | 0.520 | |
| 2izk | GLL | Streptavidin | / | 0.520 | |
| 1stp | BTN | Streptavidin | / | 0.515 | |
| 2izh | BTN | Streptavidin | / | 0.514 | |
| 3vgw | NVZ | Avidin | / | 0.514 | |
| 2rtf | BTN | Streptavidin | / | 0.510 | |
| 2y3f | BTN | Streptavidin | / | 0.506 | |
| 4bx7 | B4F | Streptavidin | / | 0.506 | |
| 2uz2 | BTN | Avd protein | / | 0.505 | |
| 3vhh | VHH | Avidin | / | 0.504 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.502 | |
| 3ry2 | BTN | Streptavidin | / | 0.502 | |
| 4dne | DTB | Streptavidin | / | 0.501 | |
| 2rtn | IMI | Streptavidin | / | 0.500 | |
| 2rto | IMI | Streptavidin | / | 0.498 | |
| 2izl | IMI | Streptavidin | / | 0.497 | |
| 4gda | BTN | Streptavidin | / | 0.495 | |
| 3wyq | BTN | Streptavidin | / | 0.492 | |
| 4z28 | BTN | Hoefavidin | / | 0.490 | |
| 1lcw | SHM | Streptavidin | / | 0.488 | |
| 1rxh | BNI | Streptavidin | / | 0.488 | |
| 4bj8 | BTN | Avidin | / | 0.488 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.487 | |
| 2rti | GLL | Streptavidin | / | 0.487 | |
| 1swt | BTN | Streptavidin | / | 0.486 | |
| 2rtg | BTN | Streptavidin | / | 0.486 | |
| 2rtd | BTN | Streptavidin | / | 0.485 | |
| 2izf | BTN | Streptavidin | / | 0.482 | |
| 2rte | BTN | Streptavidin | / | 0.482 | |
| 1sre | HAB | Streptavidin | / | 0.480 | |
| 1srg | MHB | Streptavidin | / | 0.480 | |
| 2izg | BTN | Streptavidin | / | 0.480 | |
| 2rtk | GLL | Streptavidin | / | 0.479 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.479 | |
| 1swp | BTQ | Streptavidin | / | 0.478 | |
| 3wzn | BTN | Streptavidin | / | 0.477 | |
| 3sp9 | IL2 | Peroxisome proliferator-activated receptor delta | / | 0.476 | |
| 1sri | DMB | Streptavidin | / | 0.475 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.474 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.473 | |
| 2rtr | IMI | Streptavidin | / | 0.473 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.473 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.472 | |
| 1i9h | BNI | Streptavidin | / | 0.471 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.469 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.466 | |
| 1swn | BTN | Streptavidin | / | 0.464 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.464 | |
| 2trt | TAC | Tetracycline repressor protein class D | / | 0.463 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.463 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.461 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.461 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.460 | |
| 1luq | BTN | Streptavidin | / | 0.459 | |
| 2rtq | IMI | Streptavidin | / | 0.459 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.458 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.457 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.457 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.456 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.455 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.454 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.454 | |
| 5cfn | 2BA | Stimulator of interferon genes protein | / | 0.454 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.453 | |
| 3ew2 | BTN | Hypothetical conserved protein | / | 0.453 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.452 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.452 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.452 | |
| 1lcz | BH7 | Streptavidin | / | 0.451 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2rtp | IMI | Streptavidin | / | 0.451 | |
| 2xw7 | NDP | Dihydrofolate reductase | / | 0.451 | |
| 3wyp | BSO | Streptavidin | / | 0.451 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1ddu | CB3 | Thymidylate synthase | / | 0.450 | |
| 1df8 | BTN | Streptavidin | / | 0.450 | |
| 1nc9 | IMI | Streptavidin | / | 0.450 | |
| 1srf | MTB | Streptavidin | / | 0.450 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4u9y | COA | Alpha-tubulin N-acetyltransferase 1 | / | 0.450 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 1lqa | NDP | Protein tas | / | 0.449 | |
| 1zdw | FLV | Prenyltransferase | / | 0.449 | |
| 2hcd | BIV | Vitamin D3 receptor A | / | 0.449 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.449 | |
| 3up3 | XCA | aceDAF-12 | / | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.448 | |
| 1mep | BTN | Streptavidin | / | 0.448 | |
| 2oa7 | GTX | Glutathione S-transferase P 1 | 2.5.1.18 | 0.448 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.448 | |
| 3vfq | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.448 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.448 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 5a3b | APR | SIR2 family protein | / | 0.447 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2izj | BTN | Streptavidin | / | 0.446 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.446 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.446 | |
| 3arv | SAU | Chitinase A | / | 0.446 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 2j07 | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.445 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.445 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.444 | |
| 1srh | MOB | Streptavidin | / | 0.444 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.444 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.444 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.444 | |
| 2rtm | IMI | Streptavidin | / | 0.443 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.443 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.443 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.443 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 4fox | D16 | Thymidylate synthase ThyA | / | 0.442 | |
| 4jsr | 1NQ | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.442 | |
| 4ydd | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.442 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.441 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.441 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2xi4 | AFT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.441 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.441 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2h3w | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.440 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.440 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.440 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.440 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.440 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 | |
| 4kwh | NAP | Reductase homolog | / | 0.440 | |
| 4l4x | NDP | AmphI | / | 0.440 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 |