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 |
|---|---|---|---|
| 1qd1 | FON | Formimidoyltransferase-cyclodeaminase | 2.1.2.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1qd1 | FON | Formimidoyltransferase-cyclodeaminase | 2.1.2.5 | 1.000 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.502 | |
| 3gwd | FAD | Cyclohexanone monooxygenase | / | 0.483 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.481 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 3o26 | NDP | Salutaridine reductase | / | 0.479 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.478 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.464 | |
| 4hxy | NDP | Plm1 | / | 0.464 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.464 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.462 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.461 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.460 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.460 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.459 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.459 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.458 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.458 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.458 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.458 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.457 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.456 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.456 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.456 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 5ch7 | MD1 | DMSO reductase family type II enzyme, molybdopterin subunit | / | 0.456 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.454 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.454 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 2qir | COA | Aminoglycoside 6-N-acetyltransferase type Ib11 | / | 0.453 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.452 | |
| 2e8t | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.452 | |
| 4l4x | NDP | AmphI | / | 0.452 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.452 | |
| 4s1h | ADP | Pyridoxal kinase, putative | / | 0.452 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.451 | |
| 5fm7 | ADP | RuvB-like helicase | / | 0.451 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.450 | |
| 2iea | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.450 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.450 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.449 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.449 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.448 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.448 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.448 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.448 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.448 | |
| 2bgl | NAJ | Secoisolariciresinol dehydrogenase | 1.1.1.331 | 0.447 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.447 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.447 | |
| 2qtc | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.447 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.447 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.447 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.446 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.446 | |
| 1il0 | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.445 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.444 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.444 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.444 | |
| 4f0e | 0RU | Poly [ADP-ribose] polymerase 15 | 2.4.2.30 | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 4mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.443 | |
| 1g8o | U5P | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.442 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.442 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 5aga | ANP | DNA polymerase theta | / | 0.442 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.441 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2gyu | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.441 | |
| 4i4z | 2NE | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.441 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 5iot | UMP | Flavin-dependent thymidylate synthase | 2.1.1.148 | 0.441 | |
| 1mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.440 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.440 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.440 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.440 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.440 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.440 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.440 |