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 |
|---|---|---|---|
| 2ddy | MDW | Matrilysin | 3.4.24.23 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ddy | MDW | Matrilysin | 3.4.24.23 | 1.000 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.511 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.495 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.492 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.487 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.487 | |
| 4x5f | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.486 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.483 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.478 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.476 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.470 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.469 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.469 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.466 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 3eku | CY9 | Actin-5C | / | 0.466 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.464 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.464 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.462 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.462 | |
| 2pa7 | TYD | TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase | 5.3.2.3 | 0.461 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.461 | |
| 4e2d | FMN | Dehydrogenase | / | 0.460 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.459 | |
| 3bgs | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.459 | |
| 4j7g | TRH | PCZA361.3 | / | 0.459 | |
| 1ix1 | BB2 | Peptide deformylase | / | 0.458 | |
| 2xtn | GTP | GTPase IMAP family member 2 | / | 0.458 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.458 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.458 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.458 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.458 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.458 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.458 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.457 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.457 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.456 | |
| 2emu | SAH | Diphthine synthase | / | 0.456 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.456 | |
| 3v2u | ATP | Protein GAL3 | / | 0.456 | |
| 2cmo | M1L | Glutamate receptor 2 | / | 0.455 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.455 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.455 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.454 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.453 | |
| 2ab8 | MTP | Adenosine kinase | 2.7.1.20 | 0.453 | |
| 2owf | SAH | Diphthine synthase | / | 0.453 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.453 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.453 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.452 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.452 | |
| 2a5k | AZP | Replicase polyprotein 1ab | 3.4.22 | 0.452 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.452 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.452 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.452 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.452 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2y3p | SM8 | DNA gyrase subunit A | / | 0.451 | |
| 4lb2 | DM5 | Serum albumin | / | 0.451 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.451 | |
| 1ra2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.450 | |
| 2en5 | SAH | Diphthine synthase | / | 0.450 | |
| 2fr0 | NDP | 6-deoxyerythronolide-B synthase EryA1, modules 1 and 2 | / | 0.450 | |
| 2vhq | ATP | NTPase P4 | / | 0.450 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.450 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.450 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.450 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.449 | |
| 2o12 | FMN | Chorismate synthase | / | 0.449 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.449 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2j4k | U5P | Uridylate kinase | 2.7.4.22 | 0.448 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.448 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.448 | |
| 2x7t | WZB | Carbonic anhydrase 2 | 4.2.1.1 | 0.448 | |
| 3lfm | 3DT | Alpha-ketoglutarate-dependent dioxygenase FTO | / | 0.448 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.448 | |
| 5bnw | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.448 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.447 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.447 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.447 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.446 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.446 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.446 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.446 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.446 | |
| 3sqz | COA | Putative hydroxymethylglutaryl-CoA synthase | / | 0.446 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 4i1n | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.445 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1til | ATP | Anti-sigma F factor | / | 0.445 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.445 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.445 | |
| 6gsu | GPS | Glutathione S-transferase Mu 1 | 2.5.1.18 | 0.445 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.444 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.444 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.444 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3a6q | FMN | FMN-binding protein | / | 0.444 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.444 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.444 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.444 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.444 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.443 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.443 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.443 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2weo | FBW | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.443 | |
| 3eks | CY9 | Actin-5C | / | 0.443 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.443 | |
| 3qi4 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.443 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.443 | |
| 4ge5 | A89 | Tyrosine-protein phosphatase non-receptor type 9 | 3.1.3.48 | 0.443 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4xr9 | NAD | CalS8 | / | 0.443 | |
| 1ezv | UQ6 | Cytochrome b | / | 0.442 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2c2a | ADP | Sensor histidine kinase | / | 0.442 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.442 | |
| 2q3e | NAI | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.442 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.442 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4rp8 | ASC | Ascorbate-specific PTS system EIIC component | / | 0.442 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.441 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.441 | |
| 1tow | CRZ | Fatty acid-binding protein, adipocyte | / | 0.441 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.441 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.441 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3b9l | AZZ | Serum albumin | / | 0.441 | |
| 3co9 | 3MS | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3o3p | GDD | Glycosyl transferase, family 2 | / | 0.441 | |
| 4qx5 | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.441 | |
| 1kfb | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.440 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.440 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.440 | |
| 2npx | NAD | NADH peroxidase | 1.11.1.1 | 0.440 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.440 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.440 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.440 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.440 |