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 |
|---|---|---|---|
| 3kdi | A8S | Abscisic acid receptor PYL2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 1.000 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.629 | |
| 4oic | A8S | Bet v I allergen-like | / | 0.621 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.611 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.606 | |
| 3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.604 | |
| 4ds8 | A8S | Abscisic acid receptor PYL3 | / | 0.590 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.587 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.582 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.566 | |
| 3k3k | A8S | Abscisic acid receptor PYR1 | / | 0.560 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.555 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.551 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.550 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.550 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.545 | |
| 3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.544 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.543 | |
| 3qn1 | A8S | Abscisic acid receptor PYR1 | / | 0.535 | |
| 3nef | PYV | Abscisic acid receptor PYL1 | / | 0.532 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.528 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.525 | |
| 3nmv | PYV | Abscisic acid receptor PYL2 | / | 0.524 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.521 | |
| 3r6p | A8S | Abscisic acid receptor PYL10 | / | 0.518 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.512 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.507 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.505 | |
| 4dsb | A8S | Abscisic acid receptor PYL3 | / | 0.495 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.493 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.489 | |
| 3c3d | FO1 | 2-phospho-L-lactate transferase | / | 0.488 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.486 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.484 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.480 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.475 | |
| 4dp3 | MMV | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.472 | |
| 4ia3 | BIV | Vitamin D3 receptor A | / | 0.471 | |
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 0.470 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.470 | |
| 1fpq | SAM | Isoliquiritigenin 2'-O-methyltransferase | / | 0.469 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.468 | |
| 2oz6 | CMP | Cyclic AMP receptor-like protein | / | 0.467 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.463 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.463 | |
| 4ia7 | BIV | Vitamin D3 receptor A | / | 0.463 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.461 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 2itq | ITQ | Epidermal growth factor receptor | 2.7.10.1 | 0.460 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.460 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.460 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.459 | |
| 4h96 | 14Q | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1fdt | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 2blc | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.458 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.458 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.458 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.458 | |
| 3qfx | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.458 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.458 | |
| 5d7p | OCZ | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.458 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.457 | |
| 3pre | 3RE | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 4oac | ADP | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.456 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2cda | NAP | Glucose 1-dehydrogenase | / | 0.455 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.455 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.455 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.455 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.455 | |
| 4m2x | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4xe6 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 1ie8 | KH1 | Vitamin D3 receptor | / | 0.454 | |
| 4ajw | VWN | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform | 2.7.1.153 | 0.454 | |
| 4g8z | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.454 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.453 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.453 | |
| 1klk | PMD | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.452 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.452 | |
| 4ia2 | BIV | Vitamin D3 receptor A | / | 0.452 | |
| 4ig3 | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.452 | |
| 4n6h | EJ4 | Delta-type opioid receptor | / | 0.452 | |
| 1e3k | R18 | Progesterone receptor | / | 0.451 | |
| 1y2c | 3DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.451 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.451 | |
| 1e8x | ATP | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 2vss | ACO | Hydroxycinnamoyl-CoA hydratase-lyase | 4.1.2.41 | 0.450 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.450 | |
| 2yx6 | ADP | Uncharacterized protein | / | 0.450 | |
| 3w0h | W12 | Vitamin D3 receptor | / | 0.450 | |
| 3zw3 | ZW3 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.450 | |
| 4l7s | G7K | Tyrosine-protein kinase ITK/TSK | 2.7.10.2 | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.449 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.449 | |
| 1s1w | UC1 | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 1s4d | SAH | Uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | 0.449 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.449 | |
| 1xdu | SFG | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.449 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.449 | |
| 4gk3 | L87 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 4pda | CTN | Nucleoside permease | / | 0.449 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1ia1 | TQ3 | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2of4 | 979 | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.448 | |
| 3eek | 53S | Uncharacterized protein | / | 0.448 | |
| 3eem | 53V | Uncharacterized protein | / | 0.448 | |
| 3neg | PYV | Abscisic acid receptor PYL1 | / | 0.448 | |
| 4ajf | F03 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.448 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.447 | |
| 1rkh | VD2 | Vitamin D3 receptor | / | 0.447 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.447 | |
| 2vwp | NDP | Glucose 1-dehydrogenase | / | 0.447 | |
| 3cse | N22 | Uncharacterized protein | / | 0.447 | |
| 4h95 | 06U | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1drb | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1mc5 | AHE | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 2b5v | NAP | Glucose 1-dehydrogenase | / | 0.446 | |
| 2blb | CP7 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 2zaw | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 3eva | SAH | Genome polyprotein | 2.1.1.56 | 0.446 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.446 | |
| 3mee | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 3w0r | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.446 | |
| 4ruj | VDX | Vitamin D3 receptor A | / | 0.446 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1j3j | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.445 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.445 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.445 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.445 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.445 | |
| 4n70 | 2HX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.445 | |
| 5ccc | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.444 | |
| 1rt5 | UC2 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 2bl9 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 2bla | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 2x7g | PVB | SRSF protein kinase 2 | 2.7.11.1 | 0.444 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.444 | |
| 3d8v | UD1 | Bifunctional protein GlmU | / | 0.444 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.444 | |
| 3inv | C50 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.444 | |
| 4at2 | ASD | Possible succinate dehydrogenase | / | 0.444 | |
| 4i1r | LZU | Mucosa-associated lymphoid tissue lymphoma translocation protein 1 | 3.4.22 | 0.444 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4qmx | H8H | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 4zs2 | FLU | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.444 | |
| 5cyq | T27 | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 1cjv | FOK | Adenylate cyclase type 2 | / | 0.443 | |
| 1cjv | FOK | Adenylate cyclase type 5 | / | 0.443 | |
| 1j3i | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.443 | |
| 1k74 | 9CR | Retinoic acid receptor RXR-alpha | / | 0.443 | |
| 1m8h | 6NI | Nitric oxide synthase, inducible | 1.14.13.39 | 0.443 | |
| 1v0p | PVB | Cell division control protein 2 homolog | 2.7.11.22 | 0.443 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2phk | ATP | Phosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform | 2.7.11.19 | 0.443 | |
| 2tsc | CB3 | Thymidylate synthase | / | 0.443 | |
| 3w5t | LHP | Vitamin D3 receptor | / | 0.443 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 5d7q | 4I5 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.443 | |
| 1ivr | CBA | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.442 | |
| 2hc4 | VDX | Vitamin D3 receptor A | / | 0.442 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.442 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.442 | |
| 3nun | JMZ | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.442 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.442 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.442 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.442 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 4ogr | ADN | Cyclin-dependent kinase 9 | 2.7.11.22 | 0.442 | |
| 4rup | H97 | Vitamin D3 receptor A | / | 0.442 | |
| 1l2i | ETC | Estrogen receptor | / | 0.441 | |
| 1qpj | STU | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.441 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1yim | CM4 | Estrogen receptor | / | 0.441 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.441 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3qrt | X14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3vjo | ANP | Epidermal growth factor receptor | 2.7.10.1 | 0.441 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.441 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4k18 | 1OB | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.441 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 3uzc | T4E | Adenosine receptor A2a | / | 0.441 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.440 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.440 | |
| 1s19 | MC9 | Vitamin D3 receptor | / | 0.440 | |
| 1txi | TX5 | Vitamin D3 receptor | / | 0.440 | |
| 1uy8 | PU5 | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.440 | |
| 2hw2 | RFP | Rifampin ADP-ribosyl transferase | / | 0.440 | |
| 2rkv | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.440 | |
| 3gi3 | B10 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.440 | |
| 4g21 | 0VP | Vitamin D3 receptor A | / | 0.440 | |
| 4gg7 | 0J8 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.440 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.440 | |
| 4i2p | G73 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.440 | |
| 4l49 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4qq3 | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.440 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.440 | |
| 4xdm | GDM | Heat shock cognate 90 kDa protein | / | 0.440 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.440 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.440 |