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 |
|---|---|---|---|
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 1.000 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.698 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.655 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.624 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.622 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.619 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.618 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.617 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.608 | |
| 1a7k | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.605 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.605 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.604 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.604 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.600 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.599 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.598 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.595 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.595 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.595 | |
| 1ml3 | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.594 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.594 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.590 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.588 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.586 | |
| 1nbo | NAD | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.585 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.581 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.580 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.579 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.576 | |
| 1gyp | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.574 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.574 | |
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.572 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.570 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.568 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.568 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.565 | |
| 1nq5 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.563 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.560 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.560 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.558 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.558 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.552 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.546 | |
| 4o59 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.546 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.545 | |
| 2d2i | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.542 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.540 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.537 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.535 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.534 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.527 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.522 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.518 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.513 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.507 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.506 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.503 | |
| 2vyv | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.496 | |
| 1cer | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.491 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.486 | |
| 3oew | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.476 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.471 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.469 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.469 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.468 | |
| 4r21 | STR | Cytochrome P450 family 17 polypeptide 2 | / | 0.467 | |
| 3u9e | COA | Lmo1369 protein | / | 0.465 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.465 | |
| 2fde | 385 | Gag-Pol polyprotein | 3.4.23.16 | 0.462 | |
| 2pr2 | DG1 | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.459 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.459 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.458 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.458 | |
| 4ig0 | 1FG | Gag-Pol polyprotein | 2.7.7.49 | 0.458 | |
| 4r20 | AER | Cytochrome P450 family 17 polypeptide 2 | / | 0.458 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.457 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.454 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.454 | |
| 3o9c | K20 | Pol polyprotein | / | 0.454 | |
| 1bw9 | NAD | Phenylalanine dehydrogenase | / | 0.452 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.452 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 1dss | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.450 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.449 | |
| 2brm | DFZ | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.449 | |
| 4pl4 | ADP | Serine/threonine-protein kinase/endoribonuclease IRE1 | 2.7.11.1 | 0.449 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.448 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.448 | |
| 4dja | FAD | (6-4) photolyase | / | 0.448 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.448 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.447 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.447 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.447 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.446 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.446 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.446 | |
| 3of2 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.446 | |
| 3zia | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.446 | |
| 2aq8 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.445 | |
| 4dre | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 3so9 | 017 | Pol protein | / | 0.444 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.444 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.443 | |
| 1qnf | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 2g82 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 3gob | HXX | DdmC | / | 0.443 | |
| 4djo | MK5 | Pol polyprotein | / | 0.443 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3zuy | TCH | Transporter | / | 0.442 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.442 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.442 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.441 | |
| 4a1z | ADP | Kinesin-like protein KIF11 | / | 0.441 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.441 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.440 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.440 | |
| 2y4g | TIR | TamL | / | 0.440 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.440 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 4dqh | 017 | Gag-Pol polyprotein | / | 0.440 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.440 | |
| 4n5n | NAP | Acetoacetyl-CoA reductase | 1.1.1.36 | 0.440 |