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 |
|---|---|---|---|
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2v74 | SAH | Histone-arginine methyltransferase CARM1 | / | 1.000 | |
| 5dx1 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.547 | |
| 3b3f | SAH | Histone-arginine methyltransferase CARM1 | / | 0.546 | |
| 2y1w | SFG | Histone-arginine methyltransferase CARM1 | / | 0.517 | |
| 5dxj | SFG | Histone-arginine methyltransferase CARM1 | / | 0.514 | |
| 1f3l | SAH | Protein arginine N-methyltransferase 3 | / | 0.488 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.486 | |
| 5dx8 | SFG | Histone-arginine methyltransferase CARM1 | / | 0.484 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 5dwq | SFG | Histone-arginine methyltransferase CARM1 | / | 0.478 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.476 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.476 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.475 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.474 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.471 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.471 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.469 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.468 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.468 | |
| 5dxa | SFG | Histone-arginine methyltransferase CARM1 | / | 0.468 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.466 | |
| 2y1x | SAH | Histone-arginine methyltransferase CARM1 | / | 0.465 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.465 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.464 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.462 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.462 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.462 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.460 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.458 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.457 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 4jzr | 4JR | Egl nine homolog 1 | / | 0.456 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.455 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.454 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 1p4a | PCP | Pur operon repressor | / | 0.451 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.451 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.451 | |
| 4azw | ATP | O-antigen chain terminator bifunctional methyltransferase/kinase WbdD | / | 0.451 | |
| 4kxj | P34 | Nucleoprotein | / | 0.451 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.451 | |
| 1wl4 | COA | Acetyl-CoA acetyltransferase, cytosolic | 2.3.1.9 | 0.450 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.450 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.450 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 3dzk | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.449 | |
| 4ku7 | PCG | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.449 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 3eq6 | BCO | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.448 | |
| 4yfy | 1YJ | VioF | / | 0.448 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.447 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.447 | |
| 3b9x | NOS | Pyrimidine-specific ribonucleoside hydrolase RihB | 3.2.2.8 | 0.447 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.447 | |
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.446 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.446 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.446 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.446 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 2gvv | DI9 | Diisopropyl-fluorophosphatase | 3.1.8.2 | 0.445 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.445 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2yp0 | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.444 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.443 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.443 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.443 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.443 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3djf | BC3 | Purine nucleoside phosphorylase | / | 0.443 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.443 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.443 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.442 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.441 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.441 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.441 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.441 | |
| 4k36 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.441 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.441 | |
| 4ock | ANP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 1i24 | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.440 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.440 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3pz2 | 3PZ | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 |