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 |
|---|---|---|---|
| 1ve7 | 4NP | Acylamino-acid-releasing enzyme | 3.4.19.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1ve7 | 4NP | Acylamino-acid-releasing enzyme | 3.4.19.1 | 1.000 | |
| 2psj | CEI | Renilla-luciferin 2-monooxygenase | 1.13.12.5 | 0.503 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.490 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.482 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.482 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.476 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.475 | |
| 4nv1 | 0FX | Formyl transferase | / | 0.473 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.472 | |
| 3n3z | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.472 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.469 | |
| 5dp2 | NAP | CurF | / | 0.468 | |
| 4jpg | 1OX | Pyruvate kinase PKM | 2.7.1.40 | 0.467 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.466 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.466 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.466 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.466 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 4nv1 | TYD | Formyl transferase | / | 0.464 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.463 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.462 | |
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.462 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.460 | |
| 3tky | N7I | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.459 | |
| 4l8v | NAP | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.459 | |
| 4lsa | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.459 | |
| 5cho | FAD | Flavin reductase | / | 0.459 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.457 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 4h7c | 10H | Aldo-keto reductase family 1 member C3 | / | 0.456 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.455 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.455 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.455 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.454 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.453 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.452 | |
| 1zkn | IBM | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.452 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.452 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.452 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.452 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 3rgz | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.451 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.451 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.450 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.450 | |
| 2pnu | ENM | Androgen receptor | / | 0.450 | |
| 2xvw | 9NR | Serum albumin | / | 0.450 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.450 | |
| 4wev | SUZ | Aldo-keto reductase family 1 member B10 | 1.1.1 | 0.450 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1xi2 | CB1 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.449 | |
| 3euf | BAU | Uridine phosphorylase 1 | / | 0.449 | |
| 3jt4 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.449 | |
| 3sni | 546 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.449 | |
| 4n1g | CEI | Obelin | / | 0.449 | |
| 4yfy | 0FX | VioF | / | 0.449 | |
| 1gaq | FAD | Ferredoxin | / | 0.448 | |
| 3o57 | ZG2 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.448 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.448 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1g60 | SAM | Modification methylase MboII | 2.1.1.72 | 0.447 | |
| 1r00 | SAH | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.447 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 3c1o | NAP | Eugenol synthase | / | 0.447 | |
| 3sfy | 3FY | Uncharacterized protein | / | 0.447 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.446 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.446 | |
| 2aaw | GTX | Glutathione S-transferase | 2.5.1.18 | 0.446 | |
| 3jt6 | H4B | Nitric oxide synthase, brain | 1.14.13.39 | 0.446 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.446 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.446 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4dbs | 0HV | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.446 | |
| 4hut | ATP | Cob(I)yrinic acid a,c-diamide adenosyltransferase | 2.5.1.17 | 0.446 | |
| 4kn0 | MTX | Folate receptor beta | / | 0.446 | |
| 4kn1 | 04J | Folate receptor beta | / | 0.446 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.445 | |
| 1tl7 | ONM | Adenylate cyclase type 2 | / | 0.445 | |
| 1tl7 | ONM | Adenylate cyclase type 5 | / | 0.445 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.445 | |
| 2jgs | BTN | Avidin | / | 0.445 | |
| 2ovv | PFH | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.445 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.445 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.445 | |
| 1ni1 | 2C5 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 1rvv | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.444 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.444 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.444 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.444 | |
| 4y17 | LAE | Transcriptional regulator of ftsQAZ gene cluster | / | 0.444 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2b04 | CHO | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.443 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 4nqg | CZH | Mitrocomin | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 2b01 | TUD | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.442 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.442 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.442 | |
| 1euy | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.441 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.441 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.441 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.441 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.441 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.441 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.441 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 3qpo | PFR | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3uwe | VJJ | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.441 | |
| 4fa3 | 0SL | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.441 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.440 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.440 | |
| 2wpw | ACO | Orf14 | / | 0.440 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3wb5 | 0B4 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.440 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.440 |