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 |
|---|---|---|---|
| 1z0u | NAP | NAD kinase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1z0u | NAP | NAD kinase | / | 1.000 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.481 | |
| 2a1m | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 4l4d | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.469 | |
| 1phe | PIY | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.468 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.467 | |
| 3pnd | FAD | FAD:protein FMN transferase | / | 0.467 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.466 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 4eu5 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.464 | |
| 4l4x | NDP | AmphI | / | 0.464 | |
| 3sp6 | IL2 | Peroxisome proliferator-activated receptor alpha | / | 0.463 | |
| 1svm | ATP | Large T antigen | 3.6.4 | 0.462 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.462 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3vaq | ADN | Putative adenosine kinase | / | 0.462 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1pvg | ANP | DNA topoisomerase 2 | 5.99.1.3 | 0.461 | |
| 2ibz | UQ6 | Cytochrome b | / | 0.461 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.460 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.459 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.459 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.458 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.457 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.456 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.456 | |
| 2okl | BB2 | Peptide deformylase 2 | / | 0.456 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.456 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.455 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4l8u | 9AZ | Serum albumin | / | 0.455 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.454 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.454 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 3nxx | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4i9b | NAD | Putative betaine aldehyde dehyrogenase | / | 0.453 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 3jvv | ACP | Twitching mobility protein | / | 0.452 | |
| 4dt9 | GMP | APH(2'')-Id | / | 0.452 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.452 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.451 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.451 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 1okz | UCN | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.450 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.450 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.450 | |
| 4dtb | GMP | APH(2'')-Id | / | 0.450 | |
| 4fkv | 61K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.450 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.450 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.450 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.449 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2uyi | ADP | Kinesin-like protein KIF11 | / | 0.449 | |
| 2zxu | DST | tRNA dimethylallyltransferase | 2.5.1.75 | 0.449 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.449 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 3pcr | GTP | ADP-ribosylation factor 6 | / | 0.449 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4an9 | 2P7 | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.449 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.449 | |
| 1lol | XMP | Orotidine 5'-phosphate decarboxylase | 4.1.1.23 | 0.448 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 1x15 | NAD | NAD(P) transhydrogenase subunit alpha | 1.6.1.2 | 0.448 | |
| 1z0s | ATP | NAD kinase | / | 0.448 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.448 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.448 | |
| 4i6a | HMG | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.88 | 0.448 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.447 | |
| 1gvt | 2ZS | Endothiapepsin | 3.4.23.22 | 0.447 | |
| 1ksz | PGS | Adenylosuccinate synthetase | / | 0.447 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.447 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 1dds | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1rdw | LAR | Actin, alpha skeletal muscle | / | 0.446 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.446 | |
| 1dyh | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1qlh | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.445 | |
| 1u4d | DBQ | Activated CDC42 kinase 1 | / | 0.445 | |
| 5aga | ANP | DNA polymerase theta | / | 0.445 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.444 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.444 | |
| 1lny | IMO | Adenylosuccinate synthetase isozyme 1 | / | 0.444 | |
| 1y7l | ASN_LEU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.444 | |
| 1z1f | STL | Resveratrol synthase | / | 0.444 | |
| 3kcc | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.444 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.444 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.444 | |
| 3ryp | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.444 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.444 | |
| 4qmz | B49 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.444 | |
| 1c3e | NHR | Phosphoribosylglycinamide formyltransferase | / | 0.443 | |
| 1cg1 | IMO | Adenylosuccinate synthetase | / | 0.443 | |
| 1dq8 | COA | 3-hydroxy-3-methylglutaryl-coenzyme A reductase | 1.1.1.34 | 0.443 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1t87 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.443 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.443 | |
| 2ww4 | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | 2.7.1.148 | 0.443 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3ojx | NAP | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3ow3 | SMY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 5epe | SAH | Uncharacterized protein | / | 0.443 | |
| 1hon | GNH | Adenylosuccinate synthetase | / | 0.442 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.442 | |
| 4jaj | XU1 | Aurora kinase A | 2.7.11.1 | 0.442 | |
| 4lj7 | MNT | Chaperone protein ClpB | / | 0.442 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.442 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.441 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.441 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2jds | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3iaf | TPP | Benzaldehyde lyase | / | 0.441 | |
| 4bdi | HAU | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.441 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.440 | |
| 1njs | KEU | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.440 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.440 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 2hxl | 422 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 2nli | FMN | Lactate oxidase | / | 0.440 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.440 | |
| 3ey9 | TDP | Pyruvate dehydrogenase [ubiquinone] | 1.2.5.1 | 0.440 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.440 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.440 |