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 |
|---|---|---|---|
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1eir | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 1.000 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.853 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.791 | |
| 1kwc | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.782 | |
| 1kw8 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.678 | |
| 1lgt | BP3 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.600 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.561 | |
| 1kmy | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.506 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.492 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.483 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.483 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.477 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.477 | |
| 1s36 | CEI | Obelin | / | 0.470 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.468 | |
| 1yw9 | A84 | Methionine aminopeptidase 2 | / | 0.465 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.465 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.465 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.464 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.462 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.461 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.461 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.460 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1tys | TMP | Thymidylate synthase | / | 0.458 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.457 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.457 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.457 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.456 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.456 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.454 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.454 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.454 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.453 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.453 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.453 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.452 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.451 | |
| 4ap1 | NAP | Steroid monooxygenase | / | 0.451 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.450 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.450 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1tkb | N1T | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 1tys | DHF | Thymidylate synthase | / | 0.449 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.449 | |
| 4kxj | P34 | Nucleoprotein | / | 0.449 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.448 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.448 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.448 | |
| 2oaz | I96 | Methionine aminopeptidase 2 | / | 0.448 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 1e2n | RCA | Thymidine kinase | / | 0.447 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.446 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.445 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.445 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.444 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.444 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.444 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.443 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.442 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.442 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 1h66 | RH1 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.441 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.441 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.441 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2y88 | 2ER | Phosphoribosyl isomerase A | 5.3.1.16 | 0.440 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.440 |