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 |
|---|---|---|---|
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 1.000 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.658 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.654 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.654 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.648 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.647 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.646 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.631 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.625 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.622 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.622 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.620 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.617 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.615 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.612 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.611 | |
| 4k9d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.609 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.607 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.601 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.601 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.601 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.599 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.598 | |
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.594 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.593 | |
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.590 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.590 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.588 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.588 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.588 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.584 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.580 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.578 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.578 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.578 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.571 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.569 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.568 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.568 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.559 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.559 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.555 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.554 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.551 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.548 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.540 | |
| 1gae | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.493 | |
| 1nq5 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.472 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.472 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.461 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.460 | |
| 1j21 | ATP | Argininosuccinate synthase | / | 0.458 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.457 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.456 | |
| 4ydu | ADP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.456 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.455 | |
| 3wbb | NAP | Meso-diaminopimelate D-dehydrogenase | / | 0.455 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 3uoy | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.454 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.454 | |
| 1kh2 | ATP | Argininosuccinate synthase | / | 0.453 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.453 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.453 | |
| 2bri | ANP | Uridylate kinase | 2.7.4.22 | 0.452 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.452 | |
| 3cbs | R12 | Cellular retinoic acid-binding protein 2 | / | 0.452 | |
| 3vs3 | VSE | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.451 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.450 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.450 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.449 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 1a5b | IGP | Tryptophan synthase alpha chain | / | 0.447 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.447 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.446 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.446 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.446 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.445 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 3u9e | COA | Lmo1369 protein | / | 0.445 | |
| 4o2b | LOC | Tubulin beta-2B chain | / | 0.445 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.445 | |
| 3h86 | AP5 | Adenylate kinase | / | 0.444 | |
| 3wyc | NAP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.444 | |
| 4b4o | NDP | Epimerase family protein SDR39U1 | / | 0.444 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 1orr | NAD | CDP-paratose 2-epimerase | / | 0.443 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 4jlc | SU6 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.443 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.443 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.442 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.442 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.442 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.442 | |
| 1pl8 | NAD | Sorbitol dehydrogenase | 1.1.1.14 | 0.441 | |
| 3ggf | GVD | Serine/threonine-protein kinase 26 | / | 0.441 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.441 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.440 | |
| 1rj6 | AZM | Carbonic anhydrase 14 | 4.2.1.1 | 0.440 | |
| 3ge1 | ADP | Glycerol kinase | / | 0.440 | |
| 3i6i | NDP | Putative leucoanthocyanidin reductase 1 | / | 0.440 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.440 | |
| 4o0r | X4Z | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.440 | |
| 5akk | 1P8 | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.440 |