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 |
|---|---|---|---|
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 1.000 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.629 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.623 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.622 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.621 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.619 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.613 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.605 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.602 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.601 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.596 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.596 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.588 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.586 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.585 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.584 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.582 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.582 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.581 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.580 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.577 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.574 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.573 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.571 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.566 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.562 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.561 | |
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.561 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.561 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.556 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.553 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.550 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.549 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.547 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.545 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.543 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.541 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.541 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.540 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.539 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.536 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.534 | |
| 1a7k | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.530 | |
| 1gae | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.527 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.526 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.525 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.517 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.505 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.492 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.463 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.463 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.455 | |
| 5a3b | APR | SIR2 family protein | / | 0.453 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.452 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.449 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.448 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.447 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.442 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.441 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.441 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.441 |