sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 1.000 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.627 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.619 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.610 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.604 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.602 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.599 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.593 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.592 | |
| 1nbo | NAD | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.588 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.587 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.578 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.573 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.573 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.569 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.568 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.560 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.557 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.552 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.552 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.548 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.545 | |
| 2d2i | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.540 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.539 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.537 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.537 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.535 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.535 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.533 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.533 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.528 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.527 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.521 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.521 | |
| 1dss | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.511 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.503 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.503 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.491 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.486 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.483 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.478 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.475 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.470 | |
| 3u9e | COA | Lmo1369 protein | / | 0.464 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.462 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.461 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.460 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.460 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.457 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.456 | |
| 4qec | NAP | ElxO | / | 0.454 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.450 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.448 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.446 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.446 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.445 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.444 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.444 | |
| 3lin | E13 | Protease | / | 0.442 | |
| 4px9 | ADP | ATP-dependent RNA helicase DDX3X | 3.6.4.13 | 0.442 | |
| 2f3k | RO1 | Protease | / | 0.441 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.441 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.441 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.440 |