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 |
|---|---|---|---|
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3std | MQ0 | Scytalone dehydratase | 4.2.1.94 | 1.000 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.747 | |
| 7std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.619 | |
| 6std | MS2 | Scytalone dehydratase | 4.2.1.94 | 0.618 | |
| 2std | CRP | Scytalone dehydratase | 4.2.1.94 | 0.533 | |
| 4std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.533 | |
| 1std | BFS | Scytalone dehydratase | 4.2.1.94 | 0.529 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.493 | |
| 4iae | 1DX | Alr2278 protein | / | 0.493 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.488 | |
| 1fml | RTL | Retinol dehydratase | / | 0.486 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.485 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.485 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.478 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.476 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.474 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.473 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.473 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.469 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.468 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.467 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.467 | |
| 3sn7 | 540 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 4boe | CLR | Japanin | / | 0.466 | |
| 4dvi | 2IW | Tankyrase-1 | 2.4.2.30 | 0.466 | |
| 4phl | PIL | Phosphodiesterase | / | 0.466 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.465 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.465 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 4iah | 1DX | Alr2278 protein | / | 0.464 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.462 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.461 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.461 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.461 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.460 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.458 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.457 | |
| 2pnu | ENM | Androgen receptor | / | 0.457 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4tjy | 3GN | Tankyrase-2 | 2.4.2.30 | 0.457 | |
| 4zqc | F6F | Tryptophan synthase alpha chain | / | 0.457 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.456 | |
| 2q7o | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.456 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.456 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.455 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.455 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.453 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.453 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.452 | |
| 3c1o | NAP | Eugenol synthase | / | 0.452 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.452 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.450 | |
| 1r58 | AO5 | Methionine aminopeptidase 2 | / | 0.450 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.450 | |
| 4kln | AGS | Transitional endoplasmic reticulum ATPase | 3.6.4.6 | 0.450 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.449 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4jxz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.449 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.448 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.448 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.448 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 4n1g | CEI | Obelin | / | 0.448 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.447 | |
| 2xvv | 9DN | Serum albumin | / | 0.447 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.446 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.446 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.446 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.445 | |
| 3rgz | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.445 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.444 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.444 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.444 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 4j7g | TRH | PCZA361.3 | / | 0.444 | |
| 4l5b | 1UX | Deoxycytidine kinase | 2.7.1.74 | 0.444 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 2rl5 | 2RL | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.443 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.443 | |
| 4n4t | 2GV | Tankyrase-1 | 2.4.2.30 | 0.443 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1qvu | PRL | HTH-type transcriptional regulator QacR | / | 0.442 | |
| 1ro9 | 8BR | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 1uhh | CZP | Aequorin-2 | / | 0.442 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.442 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 4jxx | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 2bfm | TOP | Pteridine reductase 1 | 1.5.1.33 | 0.441 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.441 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.441 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 3b9l | AZZ | Serum albumin | / | 0.440 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.440 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.440 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.440 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4rtb | SAM | Putative thiazole biosynthesis protein ThiH | / | 0.440 |