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 |
|---|---|---|---|
| 2d3u | CCT | Polyprotein |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2d3u | CCT | Polyprotein | / | 1.000 | |
| 2o5d | VR1 | Genome polyprotein | 2.7.7.48 | 0.604 | |
| 2gir | NN3 | Genome polyprotein | 2.7.7.48 | 0.591 | |
| 4ju1 | 1NZ | Genome polyprotein | 2.7.7.48 | 0.552 | |
| 3cj3 | SX4 | Genome polyprotein | 2.7.7.48 | 0.551 | |
| 4ju2 | 1O0 | Genome polyprotein | 2.7.7.48 | 0.540 | |
| 4jty | 1NV | Genome polyprotein | 2.7.7.48 | 0.536 | |
| 1nhv | 154 | Genome polyprotein | 2.7.7.48 | 0.524 | |
| 4jvq | 1ML | Genome polyprotein | 2.7.7.48 | 0.522 | |
| 4jtw | 1NU | Genome polyprotein | 2.7.7.48 | 0.508 | |
| 4m11 | MXM | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.486 | |
| 4ajb | TAP | Isocitrate dehydrogenase [NADP] | 1.1.1.42 | 0.474 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 1sui | SAH | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.470 | |
| 4gyy | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.469 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.469 | |
| 4s26 | SAH | Phosphomethylpyrimidine synthase, chloroplastic | 4.1.99.17 | 0.468 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 1e80 | 0GQ | Endothiapepsin | 3.4.23.22 | 0.466 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.464 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.464 | |
| 3pww | ROC | Endothiapepsin | 3.4.23.22 | 0.463 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.463 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.461 | |
| 3fql | 79Z | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 3ijd | C2F | Methylenetetrahydrofolate reductase | / | 0.459 | |
| 3vs4 | VSF | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.459 | |
| 4l4x | NDP | AmphI | / | 0.459 | |
| 5epe | SAH | Uncharacterized protein | / | 0.459 | |
| 4ys0 | ADP | Protein translocase subunit SecA | / | 0.458 | |
| 3e2s | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.457 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1sez | OMN | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.456 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.456 | |
| 3d4s | TIM | Beta-2 adrenergic receptor | / | 0.456 | |
| 1nht | PGS | Adenylosuccinate synthetase | / | 0.455 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.455 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.455 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.455 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.454 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3ha7 | B32 | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.454 | |
| 3oia | A31 | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.453 | |
| 1z7y | AA5 | Cysteine synthase 1 | 2.5.1.47 | 0.453 | |
| 3fqk | 79Z | Genome polyprotein | 2.7.7.48 | 0.453 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.453 | |
| 4ejg | NCT | Cytochrome P450 2A13 | 1.14.14.1 | 0.453 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.453 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.452 | |
| 2wep | ADP | ATP-dependent molecular chaperone HSP82 | / | 0.452 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 5bpf | ADP | D-alanine--D-alanine ligase | / | 0.452 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.451 | |
| 2gnh | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 2ovh | AS0 | Progesterone receptor | / | 0.451 | |
| 4j6d | TES | Cytochrome P450 monooxygenase | / | 0.451 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.451 | |
| 4r1f | ADP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.451 | |
| 4wda | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.451 | |
| 4yd7 | F5N | Endothiapepsin | 3.4.23.22 | 0.451 | |
| 5bsr | COA | 4-coumarate--CoA ligase 2 | 6.2.1.12 | 0.451 | |
| 1u2o | NEC | Endoplasmin | / | 0.450 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.450 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.450 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 1eag | A70 | Candidapepsin-2 | 3.4.23.24 | 0.449 | |
| 1hqu | HBY | Gag-Pol polyprotein | 2.7.7.49 | 0.449 | |
| 1hrv | SDZ | Genome polyprotein | / | 0.449 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.449 | |
| 1khr | VIR | Streptogramin A acetyltransferase | 2.3.1 | 0.449 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.449 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.449 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.449 | |
| 4y38 | 0A9 | Endothiapepsin | 3.4.23.22 | 0.449 | |
| 1td2 | PXL | Pyridoxal kinase PdxY | / | 0.448 | |
| 1y4s | ADP | Chaperone protein HtpG | / | 0.448 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.448 | |
| 3eku | CY9 | Actin-5C | / | 0.448 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.448 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.448 | |
| 4otw | DB8 | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.448 | |
| 1sdm | ADP | Kinesin heavy chain-like protein | / | 0.447 | |
| 2a84 | ATP | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.447 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.447 | |
| 2rr1 | W8R | Genome polyprotein | / | 0.447 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.447 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.447 | |
| 3i6r | J5Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.447 | |
| 3kwn | 23Z | Cathepsin S | 3.4.22.27 | 0.447 | |
| 3vhx | GTP | ADP-ribosylation factor 6 | / | 0.447 | |
| 4eev | L1X | Hepatocyte growth factor receptor | 2.7.10.1 | 0.447 | |
| 4pd6 | URI | Nucleoside permease | / | 0.447 | |
| 4uqs | INE | Nitric oxide synthase oxygenase | 1.14.13.165 | 0.447 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.447 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.447 | |
| 4uhr | NGI | Adenosine receptor A2a | / | 0.447 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.447 | |
| 1m9t | INE | Nitric oxide synthase, inducible | 1.14.13.39 | 0.446 | |
| 1q5d | EPB | Epothilone C/D epoxidase | 1.14 | 0.446 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.446 | |
| 2ada | HPR | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 2uxw | TH3 | Very long-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.9 | 0.446 | |
| 3d84 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.446 | |
| 1a27 | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1rfg | GMP | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.445 | |
| 2hqp | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.445 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.445 | |
| 4kot | CE3 | Uncharacterized protein | / | 0.445 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 5cdg | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1il0 | CAA | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.444 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.444 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.444 | |
| 3byz | H11 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 3hbb | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.444 | |
| 3ocp | CMP | cGMP-dependent protein kinase 1 | 2.7.11.12 | 0.444 | |
| 4jvr | 1MT | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.444 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1fel | FEN | Retinol-binding protein 4 | / | 0.443 | |
| 1njf | AGS | DNA polymerase III subunit tau | 2.7.7.7 | 0.443 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2y3s | TIR | TamL | / | 0.443 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.443 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.442 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2b52 | D42 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2gev | COK | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2uz2 | BTN | Avd protein | / | 0.442 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.442 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.442 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 5hpy | GDP | Transforming protein RhoA | / | 0.442 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.441 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.441 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.441 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.441 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.441 | |
| 3ix9 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 8dfr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1osv | CHC | Bile acid receptor | / | 0.440 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.440 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.440 | |
| 2imk | GTX | AGAP009194-PA | / | 0.440 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 2v3a | FAD | Rubredoxin-NAD(+) reductase | 1.18.1.1 | 0.440 | |
| 3i68 | J4Z | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.440 | |
| 3q70 | RIT | Candidapepsin-2 | 3.4.23.24 | 0.440 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4ap3 | NAP | Steroid monooxygenase | / | 0.440 | |
| 4pzd | NAD | 3-Hydroxyacyl-CoA dehydrogenase | / | 0.440 | |
| 5ahs | COA | Acyl-CoA dehydrogenase | / | 0.440 | |
| 5byl | GCP | Bifunctional AAC/APH | 2.3.1 | 0.440 | |
| 4z35 | ON9 | Lysophosphatidic acid receptor 1 | / | 0.440 |