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 |
|---|---|---|---|
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 1.000 | |
| 1ml3 | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.572 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.569 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.567 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.562 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.562 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.561 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.556 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.556 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.553 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.552 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.551 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.546 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.545 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.544 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.536 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.535 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.535 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.534 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.532 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.532 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.530 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.529 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.527 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.526 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.523 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.521 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.519 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.516 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.515 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.513 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.510 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.510 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.510 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.510 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.499 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.497 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.497 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.496 | |
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.494 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.494 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.494 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.489 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.488 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.485 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.484 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.479 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.478 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.476 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.474 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.474 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.472 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.467 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.466 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.466 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.462 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.461 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.460 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.460 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 4jic | FMN | GTN Reductase | / | 0.458 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.457 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.456 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.454 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.453 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 2rhg | IGP | Tryptophan synthase alpha chain | / | 0.452 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.451 | |
| 2hma | SAM | tRNA-specific 2-thiouridylase MnmA | / | 0.450 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.450 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.450 | |
| 3ieu | GDP | GTPase Era | / | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 3zuy | TCH | Transporter | / | 0.449 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.449 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.449 | |
| 1gae | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.448 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.448 | |
| 1beu | IPL | Tryptophan synthase alpha chain | / | 0.447 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.446 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.446 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.445 | |
| 3img | BZ3 | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.445 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.444 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.444 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.444 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.444 | |
| 4hbg | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.444 | |
| 4l4x | NDP | AmphI | / | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.443 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.442 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.442 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.441 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.440 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.440 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 | |
| 4dan | 2FA | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.440 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.440 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 |