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 |
|---|---|---|---|
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2hl2 | SSA | Threonine--tRNA ligase | 6.1.1.3 | 1.000 | |
| 3pd5 | TSB | Threonine--tRNA ligase | 6.1.1.3 | 0.639 | |
| 2hl1 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.622 | |
| 3pd2 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.591 | |
| 3pd3 | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.590 | |
| 3pd4 | A3G | Threonine--tRNA ligase | 6.1.1.3 | 0.581 | |
| 4rrg | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.579 | |
| 4rrh | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.572 | |
| 4rrq | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.569 | |
| 4rrf | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.566 | |
| 4rr7 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.549 | |
| 4rr8 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.545 | |
| 4rrm | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.545 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.544 | |
| 4rrb | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.540 | |
| 4rri | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.540 | |
| 4rra | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.539 | |
| 4rr9 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.536 | |
| 4rrl | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.530 | |
| 4rr6 | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.529 | |
| 4rrd | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.512 | |
| 4rrc | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.508 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.507 | |
| 4rrj | A3S | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.501 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.493 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.484 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.484 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.480 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.479 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.474 | |
| 1rx8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.472 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.471 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.470 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.469 | |
| 2yjx | YJX | Heat shock protein HSP 90-alpha | / | 0.468 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.467 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.466 | |
| 2o65 | MYF | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.465 | |
| 1fml | RTL | Retinol dehydratase | / | 0.464 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.464 | |
| 1uye | PU9 | Heat shock protein HSP 90-alpha | / | 0.462 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.462 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.461 | |
| 3apf | BMW | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.460 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.460 | |
| 4m48 | 21B | Sodium-dependent dopamine transporter | / | 0.459 | |
| 5hbs | RTL | Retinol-binding protein 1 | / | 0.459 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 5h8t | RTL | Retinol-binding protein 1 | / | 0.457 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.457 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.456 | |
| 5c4c | UPG | Histo-blood group ABO system transferase | / | 0.456 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.455 | |
| 1opb | RET | Retinol-binding protein 2 | / | 0.455 | |
| 3i28 | 34N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.455 | |
| 3pbz | F02 | Endothiapepsin | 3.4.23.22 | 0.455 | |
| 4y4j | LNR | Endothiapepsin | 3.4.23.22 | 0.455 | |
| 1g7u | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.454 | |
| 2wgg | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.454 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.454 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 1t8x | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.453 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.453 | |
| 2uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.453 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.453 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.452 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.452 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2abi | 1CA | Mineralocorticoid receptor | / | 0.451 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.451 | |
| 2i0y | 5CN | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.451 | |
| 2w8y | NDR | Progesterone receptor | / | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.450 | |
| 2e9v | 85A | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.450 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4jbt | ASD | Cytochrome P450 monooxygenase | / | 0.450 | |
| 1g2v | TTP | Glucose-1-phosphate thymidylyltransferase | / | 0.449 | |
| 2aa2 | AS4 | Mineralocorticoid receptor | / | 0.449 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.449 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.449 | |
| 3v49 | PK0 | Androgen receptor | / | 0.449 | |
| 4j6b | PLO | Cytochrome P450 monooxygenase | / | 0.449 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.448 | |
| 3elb | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.448 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.448 | |
| 1ia3 | TQ5 | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1tys | TMP | Thymidylate synthase | / | 0.447 | |
| 2a3i | C0R | Mineralocorticoid receptor | / | 0.447 | |
| 2aax | PDN | Mineralocorticoid receptor | / | 0.447 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.447 | |
| 4dfn | 0K1 | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.447 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.447 | |
| 1crb | RTL | Retinol-binding protein 1 | / | 0.446 | |
| 1qnf | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 1syn | F89 | Thymidylate synthase | / | 0.446 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1uy7 | PU4 | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 2wug | HPK | 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase | 3.7.1.17 | 0.446 | |
| 3fr8 | NDP | Ketol-acid reductoisomerase, chloroplastic | 1.1.1.86 | 0.446 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.446 | |
| 4c02 | TAK | Activin receptor type-1 | 2.7.11.30 | 0.446 | |
| 1uyd | PU8 | Heat shock protein HSP 90-alpha | / | 0.445 | |
| 2bf7 | HBI | Pteridine reductase 1 | 1.5.1.33 | 0.445 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.445 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.445 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 3r7e | X88 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.445 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.445 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 5c80 | URI | Uridine phosphorylase | / | 0.445 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.445 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.444 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.444 | |
| 2znq | 401 | Peroxisome proliferator-activated receptor delta | / | 0.444 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.444 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.444 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.444 | |
| 3zze | 6XP | Hepatocyte growth factor receptor | 2.7.10.1 | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4feu | 537 | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.444 | |
| 4zea | IMI | Endothiapepsin | 3.4.23.22 | 0.444 | |
| 5dp2 | NAP | CurF | / | 0.444 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.444 | |
| 3eml | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 1mr9 | ACO | Streptogramin A acetyltransferase | 2.3.1 | 0.443 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.443 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.443 | |
| 3dt1 | P40 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3hz1 | 42C | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.443 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 2ao6 | R18 | Androgen receptor | / | 0.442 | |
| 2d4e | NAD | 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831] | / | 0.442 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.442 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4kwi | 1TJ | Reductase homolog | / | 0.442 | |
| 4l8u | 9AZ | Serum albumin | / | 0.442 | |
| 4qer | STL | Phospholipase A2 VRV-PL-VIIIa | / | 0.442 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.441 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1xq3 | R18 | Androgen receptor | / | 0.441 | |
| 1zid | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.441 | |
| 2h39 | ADQ | ADP-glucose phosphorylase | / | 0.441 | |
| 2h55 | DZ8 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 2i0v | 6C3 | Macrophage colony-stimulating factor 1 receptor | 2.7.10.1 | 0.441 | |
| 2j5s | KTA | Alr4455 protein | / | 0.441 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.441 | |
| 3dh7 | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.441 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3up3 | XCA | aceDAF-12 | / | 0.441 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3zsr | O3N | Integrase | / | 0.441 | |
| 4cez | O3N | Integrase | / | 0.441 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.440 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1ia4 | TQ6 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.440 | |
| 1wnb | NAI | Gamma-aminobutyraldehyde dehydrogenase | 1.2.1.19 | 0.440 | |
| 2avx | HTF | Regulatory protein SdiA | / | 0.440 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.440 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.440 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.440 | |
| 3u8h | BHP | Phospholipase A2, membrane associated | / | 0.440 | |
| 4uda | DEX | Mineralocorticoid receptor | / | 0.440 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.440 | |
| 5ans | RX8 | 7,8-dihydro-8-oxoguanine triphosphatase | 3.6.1.55 | 0.440 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.440 |