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 |
|---|---|---|---|
| 3oii | SAH | Ribosomal RNA small subunit methyltransferase NEP1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3oii | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 1.000 | |
| 3oij | SAH | Ribosomal RNA small subunit methyltransferase NEP1 | / | 0.598 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.502 | |
| 3o7b | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | / | 0.498 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.484 | |
| 3dnd | LL2 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.484 | |
| 4xcz | FON | Qdtf | / | 0.483 | |
| 3bbd | SAH | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.482 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.480 | |
| 2ien | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.480 | |
| 1svg | I04 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.478 | |
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.478 | |
| 5cyo | GDP | Septin-9 | / | 0.477 | |
| 1sve | I01 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.474 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.474 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.469 | |
| 1ydr | IQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.468 | |
| 2uzw | SS4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.467 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.467 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.465 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1xl5 | 190 | Gag-Pol polyprotein | 3.4.23.16 | 0.464 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.464 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.463 | |
| 3s7d | LEU_SER_LYS_LYS_MLZ | N-lysine methyltransferase SMYD2 | / | 0.463 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.462 | |
| 3nk7 | SAM | 23S rRNA (adenosine(1067)-2'-O)-methyltransferase | / | 0.462 | |
| 3s7b | NH5 | N-lysine methyltransferase SMYD2 | / | 0.462 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.461 | |
| 3vqh | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.461 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.460 | |
| 2uw0 | GVK | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.460 | |
| 3pwm | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.460 | |
| 1bx6 | BA1 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.459 | |
| 1owm | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.458 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.458 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.457 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 2ha8 | SAH | Probable methyltransferase TARBP1 | / | 0.456 | |
| 3bwj | ARX | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.456 | |
| 1py5 | PY1 | TGF-beta receptor type-1 | 2.7.11.30 | 0.455 | |
| 2uzl | C94 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.455 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.455 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.454 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.454 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.454 | |
| 2uw7 | GVP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.454 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.453 | |
| 4q1x | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 1rej | B1L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 2owf | SAH | Diphthine synthase | / | 0.452 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.452 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.451 | |
| 3w1t | WRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.451 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.450 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.450 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.450 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.450 | |
| 4eue | NAI | Trans-2-enoyl-CoA reductase [NADH] | / | 0.450 | |
| 4j1t | NAD | NAD/NADP transhydrogenase alpha subunit 1 | / | 0.450 | |
| 1bxq | PP8 | Penicillopepsin-1 | 3.4.23.20 | 0.449 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2f2u | M77 | Rho-associated protein kinase 2 | 2.7.11.1 | 0.449 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.449 | |
| 2p3b | 3TL | V-1 protease | / | 0.449 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.449 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.449 | |
| 3ex8 | AIF | Riboflavin biosynthesis protein RibD | 1.1.1.193 | 0.449 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.449 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.448 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.448 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.448 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 3qx2 | X63 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3qzf | X66 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.448 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.448 | |
| 4kin | 1M8 | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 4yj2 | GTP | Tubulin alpha-1B chain | / | 0.448 | |
| 1hon | GNH | Adenylosuccinate synthetase | / | 0.447 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.447 | |
| 1q8t | Y27 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2izr | BRK | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.447 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.447 | |
| 4lj8 | ADP | Chaperone protein ClpB | / | 0.447 | |
| 4yqf | GDP | Septin-9 | / | 0.447 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 1xh6 | R94 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 2c6t | DT5 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.446 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.446 | |
| 4ib4 | ERM | 5-hydroxytryptamine receptor 2B | / | 0.446 | |
| 4l2o | NAD | Aldehyde dehydrogenase, dimeric NADP-preferring | / | 0.446 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.445 | |
| 1eio | GCH | Gastrotropin | / | 0.445 | |
| 3ing | NDP | Homoserine dehydrogenase related protein | / | 0.445 | |
| 3oog | YTP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.445 | |
| 4a9e | 3PF | Bromodomain-containing protein 2 | / | 0.445 | |
| 4dfg | 0JV | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.445 | |
| 1kp2 | ATP | Argininosuccinate synthase | 6.3.4.5 | 0.444 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.444 | |
| 2b4y | APR | NAD-dependent protein deacylase sirtuin-5, mitochondrial | / | 0.444 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.444 | |
| 2x8i | X8I | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.444 | |
| 3o9a | K14 | Pol polyprotein | / | 0.444 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.444 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.444 | |
| 1q8w | M77 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 1u33 | LM2 | Pancreatic alpha-amylase | / | 0.443 | |
| 1zrz | BI1 | Protein kinase C iota type | 2.7.11.13 | 0.443 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2e8h | SAH | Diphthine synthase | / | 0.443 | |
| 2r8p | T6F | Transketolase 1 | / | 0.443 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.443 | |
| 3em3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 3ts1 | TYA | Tyrosine--tRNA ligase | 6.1.1.1 | 0.443 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3w0n | ANP | Hygromycin-B 4-O-kinase | 2.7.1.163 | 0.443 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.443 | |
| 1d7a | AIR | N5-carboxyaminoimidazole ribonucleotide mutase | / | 0.442 | |
| 1la2 | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.442 | |
| 1n77 | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.442 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.442 | |
| 1u30 | GOX | Pancreatic alpha-amylase | / | 0.442 | |
| 3a2o | KNJ | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.442 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3n10 | CMP | Adenylate cyclase 2 | / | 0.442 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 3zhy | FM6 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.442 | |
| 4fv6 | E57 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.442 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4ihl | 1F5 | 14-3-3 protein zeta/delta | / | 0.442 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.441 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2p6i | SAH | Diphthine synthase | / | 0.441 | |
| 2pcm | SAH | Diphthine synthase | / | 0.441 | |
| 2z54 | AB1 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4a9h | TVP | Bromodomain-containing protein 2 | / | 0.441 | |
| 4ftr | 5HK | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4iwo | 1H4 | Serine/threonine-protein kinase TBK1 | 2.7.11.1 | 0.441 | |
| 4mk0 | 29X | Beta-adrenergic receptor kinase 1 | 2.7.11.15 | 0.441 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.441 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.441 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.440 | |
| 1l4m | NCN | Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase | 2.4.2.21 | 0.440 | |
| 1n2j | PAF | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.440 | |
| 2ejj | SAH | Diphthine synthase | / | 0.440 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 2uzt | SS3 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2uzv | SS5 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2vo6 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3lit | E15 | Protease | / | 0.440 | |
| 3zo4 | QWI | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 4bur | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.440 | |
| 4i13 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 5egh | PC | Ectonucleotide pyrophosphatase/phosphodiesterase family member 6 | / | 0.440 |