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 |
|---|---|---|---|
| 2oth | NIM | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2oth | NIM | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 1.000 | |
| 2oli | IOP | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.702 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.636 | |
| 3fo7 | IMN | Phospholipase A2 VRV-PL-VIIIa | / | 0.594 | |
| 1skg | VAL_ALA_PHE_ARG_SER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.571 | |
| 1th6 | OIN | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.567 | |
| 2oyf | IAC | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.550 | |
| 4hmb | PZZ | Phospholipase A2 VRV-PL-VIIIa | / | 0.548 | |
| 5p2p | DHG | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.546 | |
| 1dcy | I3N | Phospholipase A2, membrane associated | / | 0.536 | |
| 4qer | STL | Phospholipase A2 VRV-PL-VIIIa | / | 0.531 | |
| 1db5 | 6IN | Phospholipase A2, membrane associated | / | 0.526 | |
| 3u8d | U8D | Phospholipase A2, membrane associated | / | 0.526 | |
| 2qvd | BER | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.524 | |
| 4eix | NIM | Phospholipase A2 VRV-PL-VIIIa | / | 0.513 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.503 | |
| 1db4 | 8IN | Phospholipase A2, membrane associated | / | 0.494 | |
| 1kvo | OAP | Phospholipase A2, membrane associated | / | 0.486 | |
| 1fx9 | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.483 | |
| 2pws | IBP | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.482 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.481 | |
| 2z7g | EH9 | Adenosine deaminase | 3.5.4.4 | 0.477 | |
| 1v79 | FR7 | Adenosine deaminase | 3.5.4.4 | 0.473 | |
| 1y6o | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.471 | |
| 4b1f | KRH | Glutamate racemase | / | 0.471 | |
| 4zvm | DM2 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.468 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.467 | |
| 4jlt | 8PR | Cytochrome P450 2B4 | 1.14.14.1 | 0.467 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.466 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.465 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.463 | |
| 1y4l | SVR | Basic phospholipase A2 homolog 2 | / | 0.463 | |
| 4qf7 | C0R | Phospholipase A2 VRV-PL-VIIIa | / | 0.462 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.461 | |
| 1wxy | FRK | Adenosine deaminase | 3.5.4.4 | 0.460 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.460 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.460 | |
| 2qhw | PZZ | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.459 | |
| 1mcz | RMN | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 1uml | FR4 | Adenosine deaminase | 3.5.4.4 | 0.458 | |
| 5c8d | 5AD | Probable transcriptional regulator | / | 0.457 | |
| 1qxl | FR8 | Adenosine deaminase | 3.5.4.4 | 0.456 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 5c8a | 5AD | Probable transcriptional regulator | / | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 4iah | 1DX | Alr2278 protein | / | 0.453 | |
| 1al8 | DHP | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.452 | |
| 2v19 | FMN | Dodecin | / | 0.452 | |
| 1v7a | FRC | Adenosine deaminase | 3.5.4.4 | 0.451 | |
| 2ph5 | NAD | Homospermidine synthase | / | 0.451 | |
| 3fco | IIG | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3ctj | 320 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.449 | |
| 3new | 3NE | Mitogen-activated protein kinase 14 | / | 0.449 | |
| 7cat | NDP | Catalase | 1.11.1.6 | 0.449 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.448 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.448 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.447 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.447 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.447 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.446 | |
| 4o4e | ATP | Kinase | / | 0.446 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.444 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.444 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.444 | |
| 3tub | FPU | Tyrosine-protein kinase SYK | 2.7.10.2 | 0.444 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.444 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.443 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.443 | |
| 2wcg | MT5 | Glucosylceramidase | 3.2.1.45 | 0.443 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.443 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.443 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.442 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.442 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.442 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.442 | |
| 2z50 | 028 | Geranylgeranyl pyrophosphate synthase | / | 0.441 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.441 | |
| 3jt8 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.441 | |
| 4gqk | ADP | Actin cross-linking toxin VgrG1 | / | 0.441 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.441 | |
| 1kru | IPT | Galactoside O-acetyltransferase | 2.3.1.18 | 0.440 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.440 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.440 |