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 |
|---|---|---|---|
| 1isg | AGS | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1isg | AGS | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 | 1.000 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.501 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.497 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.495 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.483 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.478 | |
| 4lcw | 1VY | Major histocompatibility complex class I-related gene protein | / | 0.476 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.475 | |
| 1efy | BZC | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.473 | |
| 2ejz | SAH | Diphthine synthase | / | 0.472 | |
| 4b65 | NDP | L-ornithine N(5)-monooxygenase | / | 0.471 | |
| 1isj | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2 | 3.2.2.6 | 0.470 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.469 | |
| 2y1w | 849 | Histone-arginine methyltransferase CARM1 | / | 0.468 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.466 | |
| 3zj7 | C1K | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.466 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.463 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.462 | |
| 2tpl | HPP | Tyrosine phenol-lyase | 4.1.99.2 | 0.461 | |
| 1lnm | DTX | Bilin-binding protein | / | 0.460 | |
| 3aiq | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic | 3.2.1.182 | 0.459 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.458 | |
| 1x2b | STX | Proline iminopeptidase | 3.4.11.5 | 0.457 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.457 | |
| 3dz4 | C8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.457 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 1vot | HUP | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.454 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.454 | |
| 1pxg | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.453 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.453 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.453 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1xf0 | ASD | Aldo-keto reductase family 1 member C3 | / | 0.451 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.451 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.451 | |
| 1eko | I84 | Aldose reductase | 1.1.1.21 | 0.450 | |
| 1pax | DHQ | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.449 | |
| 4hhy | 15R | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.449 | |
| 4j7h | TRH | PCZA361.3 | / | 0.449 | |
| 2j7d | GI1 | Beta-glucosidase A | 3.2.1.21 | 0.448 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.447 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.447 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.447 | |
| 5dsy | UHB | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.447 | |
| 1q83 | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.446 | |
| 3bur | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 3e6e | DCS | Alanine racemase | / | 0.446 | |
| 3mau | PLR | Putative sphingosine-1-phosphate lyase | / | 0.446 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4jyz | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.446 | |
| 1ld7 | U66 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.445 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.445 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.445 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.445 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.445 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.445 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.445 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 2iej | S48 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.444 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.444 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.444 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 4jxx | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.444 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.443 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 3ce0 | P34 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.443 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.443 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.443 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.443 | |
| 3qgi | 33F | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.442 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.442 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 4dbw | 511 | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4je5 | PLP | Aromatic/aminoadipate aminotransferase 1 | 2.6.1.39 | 0.442 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.441 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.441 | |
| 2pdj | 393 | Aldose reductase | 1.1.1.21 | 0.441 | |
| 2xeg | CI9 | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.441 | |
| 2xuj | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.441 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.441 | |
| 4gm4 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.441 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.441 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.440 | |
| 2xlp | NAP | Putative flavin-containing monooxygenase | / | 0.440 | |
| 3l3l | L3L | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.440 | |
| 3u5y | SCG | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.440 | |
| 3zj6 | VM2 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.440 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.440 |