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 |
|---|---|---|---|
| 3hav | ATP | Aminoglycoside phosphotransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3hav | ATP | Aminoglycoside phosphotransferase | / | 1.000 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.491 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.488 | |
| 1e90 | MYC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.487 | |
| 4dca | ADP | Aminoglycoside phosphotransferase | / | 0.485 | |
| 3ls8 | AJZ | Phosphatidylinositol 3-kinase catalytic subunit type 3 | 2.7.1.137 | 0.479 | |
| 4gk2 | L66 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.479 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.478 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.477 | |
| 4fhj | 0TZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.476 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 3wnz | ADP | Alanine--anticapsin ligase | / | 0.475 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.474 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.474 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.472 | |
| 5dn1 | AMZ | Phosphoribosyl isomerase A | 5.3.1.16 | 0.472 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.471 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.471 | |
| 4u0m | GTP | Cyclic GMP-AMP synthase | / | 0.471 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.470 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.470 | |
| 2zsh | GA3 | Gibberellin receptor GID1A | 3 | 0.469 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.468 | |
| 3zvv | XAZ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.468 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.467 | |
| 3cgd | COA | Coenzyme A disulfide reductase | / | 0.467 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.467 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.467 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.466 | |
| 3ml8 | ML8 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.465 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.464 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 4fhk | 0U0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.464 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.463 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.463 | |
| 4h6p | FMN | Chromate reductase | / | 0.463 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.462 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.462 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.462 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.461 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4f1s | F1S | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.460 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.460 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.460 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3akl | ADP | Serine/threonine-protein kinase CtkA | 2.7.11.1 | 0.459 | |
| 4fjy | FJY | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3w0j | T08 | Vitamin D3 receptor | / | 0.458 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.458 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.458 | |
| 5dp2 | NAP | CurF | / | 0.458 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.457 | |
| 2a5u | QYT | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.457 | |
| 3up0 | D7S | aceDAF-12 | / | 0.456 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.456 | |
| 1dlj | UGA | UDP-glucose 6-dehydrogenase | / | 0.455 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.455 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.455 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.454 | |
| 3cgc | COA | Coenzyme A disulfide reductase | / | 0.454 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.454 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 1kc1 | NDP | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.453 | |
| 3a14 | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.453 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.453 | |
| 2b51 | UTP | RNA editing complex protein MP57 | / | 0.452 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.452 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.452 | |
| 4azm | T4B | Fatty acid-binding protein, epidermal | / | 0.452 | |
| 4ddl | 0JQ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 1a4i | NDP | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.451 | |
| 1b8v | NAD | Malate dehydrogenase | / | 0.451 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.451 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.451 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3u9e | COA | Lmo1369 protein | / | 0.450 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.449 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.449 | |
| 3a78 | 3EV | Vitamin D3 receptor | / | 0.449 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.449 | |
| 3ggc | H26 | Hypoxanthine-guanine phosphoribosyltransferase | 2.4.2.8 | 0.449 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 4hvb | 19P | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.449 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4oxi | GAP | Enterobactin synthetase component F-related protein | / | 0.449 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.448 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.448 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.448 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4fad | 0TB | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.448 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.447 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 2cgw | 3C3 | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.447 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.447 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.447 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4ffl | ADP | Uncharacterized protein | / | 0.447 | |
| 1g28 | FMN | PHY3 | / | 0.446 | |
| 1hqu | HBY | Gag-Pol polyprotein | 2.7.7.49 | 0.446 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3bbf | GDP | Nucleoside diphosphate kinase B | 2.7.4.6 | 0.446 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.446 | |
| 3rqq | BA3 | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.446 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.446 | |
| 4flh | 14K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.445 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 2hy8 | 1ST | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.445 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3vrv | YSD | Vitamin D3 receptor | / | 0.445 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4e2b | FMN | Dehydrogenase | / | 0.445 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.445 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.444 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.444 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.444 | |
| 1so2 | 666 | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.444 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2w3w | VG9 | Dihydrofolate reductase | / | 0.444 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.444 | |
| 3ml9 | ML9 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 3qgi | 33F | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 3ruv | ANP | Chaperonin | / | 0.444 | |
| 3vru | YS3 | Vitamin D3 receptor | / | 0.444 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.444 | |
| 4rqk | ATP | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.444 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.443 | |
| 1uho | VDN | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.443 | |
| 2fto | TMP | Thymidylate synthase | / | 0.443 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.443 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.443 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.443 | |
| 2znp | K55 | Peroxisome proliferator-activated receptor delta | / | 0.443 | |
| 4fjz | 4FJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.443 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.443 | |
| 4jnk | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 4rrr | A3T | Threonine--tRNA ligase | 6.1.1.3 | 0.443 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 3a8w | ATP | Protein kinase C iota type | 2.7.11.13 | 0.442 | |
| 4ezk | 0SD | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1e8z | STU | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1yli | COA | Uncharacterized acyl-CoA thioester hydrolase HI_0827 | 3.1.2 | 0.441 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.441 | |
| 3ahi | HTL | Probable phosphoketolase | / | 0.441 | |
| 3nd1 | SAH | Precorrin-6A synthase (Deacetylating) | / | 0.441 | |
| 3s2a | 2NQ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.441 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 4ezj | 0SC | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.441 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.441 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.441 | |
| 4ia1 | BIV | Vitamin D3 receptor A | / | 0.441 | |
| 4mv4 | ACP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 1nhh | ANP | DNA mismatch repair protein MutL | / | 0.440 | |
| 2bkk | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.440 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.440 | |
| 2hz4 | 4ST | Tyrosine-protein kinase ABL1 | 2.7.10.2 | 0.440 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3fgo | ACP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.440 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.440 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.440 | |
| 3zcx | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.440 |