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 |
|---|---|---|---|
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3l0d | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 1.000 | |
| 3gnq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.597 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.590 | |
| 1nbo | NAD | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.588 | |
| 1dc6 | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.580 | |
| 1jn0 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.580 | |
| 3v1y | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.579 | |
| 4boy | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.579 | |
| 1rm4 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.574 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.573 | |
| 1vc2 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.570 | |
| 1a7k | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.569 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.568 | |
| 1hdg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.563 | |
| 1j0x | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.561 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.556 | |
| 2b4r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.556 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.552 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.551 | |
| 1rm5 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.549 | |
| 1u8f | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.547 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.547 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.545 | |
| 5c7o | NAD | Glyceraldehyde-3-phosphate dehydrogenase, testis-specific | 1.2.1.12 | 0.542 | |
| 1ihx | SND | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.541 | |
| 2pkr | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.538 | |
| 4dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.537 | |
| 2ep7 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.536 | |
| 4o63 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.535 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.534 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.533 | |
| 4lsm | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.533 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.532 | |
| 1znq | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.531 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.528 | |
| 1rm3 | NDP | Glyceraldehyde-3-phosphate dehydrogenase A, chloroplastic | 1.2.1.13 | 0.522 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.522 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.519 | |
| 1nqa | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.516 | |
| 3k2b | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.516 | |
| 2d2i | NAP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.511 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.509 | |
| 2vyn | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.504 | |
| 1gad | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.503 | |
| 3cmc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.496 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.490 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.486 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.485 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.481 | |
| 4g9k | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.481 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.480 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.473 | |
| 1gae | NAD | Glyceraldehyde-3-phosphate dehydrogenase A | / | 0.472 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.471 | |
| 2giv | ACO | Histone acetyltransferase KAT8 | / | 0.468 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.468 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.463 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.463 | |
| 1dhi | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.462 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.461 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.460 | |
| 1ihy | APR | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.460 | |
| 3bgc | LJH | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.458 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.458 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.457 | |
| 2x0r | NAD | Malate dehydrogenase | / | 0.457 | |
| 3gob | HXX | DdmC | / | 0.457 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.456 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.456 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.456 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.456 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.453 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.453 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.453 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.452 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.452 | |
| 1dir | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.451 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.451 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.451 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2ooy | ATP | 5'-AMP-activated protein kinase subunit gamma | / | 0.450 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 4cta | ATP | CinA-like protein | / | 0.450 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.450 | |
| 4dja | FAD | (6-4) photolyase | / | 0.449 | |
| 4ite | TEY | Vitamin D3 receptor | / | 0.449 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.449 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.448 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.448 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.448 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.448 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.448 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.448 | |
| 1fml | RTL | Retinol dehydratase | / | 0.447 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.447 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.447 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.446 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.446 | |
| 4rww | 2BA | Lmo2692 protein | / | 0.446 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.445 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.445 | |
| 4eut | BX7 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.445 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1jio | DEB | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.444 | |
| 2q59 | 240 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.444 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.444 | |
| 5a3b | APR | SIR2 family protein | / | 0.444 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 4iwq | 1FV | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.443 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.443 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.442 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.442 | |
| 2jlb | UDM | Uncharacterized protein | / | 0.442 | |
| 3orf | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.442 | |
| 3s8c | CDP | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.442 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.442 | |
| 4nxw | ADP | Mitochondrial dynamics protein MID51 | / | 0.442 | |
| 1fm6 | BRL | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.441 | |
| 2ceo | T44 | Thyroxine-binding globulin | / | 0.441 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.441 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.441 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.441 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 0.440 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.440 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 4u7w | NDP | MxaA | / | 0.440 |