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 |
|---|---|---|---|
| 4jjk | FOL | Formate--tetrahydrofolate ligase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4jjk | FOL | Formate--tetrahydrofolate ligase | / | 1.000 | |
| 4iom | FOL | Formate--tetrahydrofolate ligase | / | 0.674 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.489 | |
| 3gnv | XNZ | Genome polyprotein | 2.7.7.48 | 0.487 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.486 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.486 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.478 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.478 | |
| 3p8h | P8H | Lethal(3)malignant brain tumor-like protein 1 | / | 0.476 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.476 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.473 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.472 | |
| 3ske | 054 | Genome polyprotein | 2.7.7.48 | 0.471 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.469 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.468 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.465 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.464 | |
| 3cso | XNI | Genome polyprotein | 2.7.7.48 | 0.464 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.463 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.463 | |
| 3v2u | ATP | Protein GAL3 | / | 0.462 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.462 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.462 | |
| 1a4i | NDP | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.460 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 5cc9 | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.460 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.459 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 3h2l | YAK | Genome polyprotein | 2.7.7.48 | 0.459 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.458 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.458 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 3ntr | NAD | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.458 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.457 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.456 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.455 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.455 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.454 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.454 | |
| 1kw6 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.453 | |
| 1kw9 | BPY | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.453 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 3c4h | DRL | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.453 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.452 | |
| 1h69 | ARH | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.452 | |
| 2x1e | X1E | Acyl-coenzyme A:6-aminopenicillanic-acid-acyltransferase 40 kDa form | 2.3.1.164 | 0.452 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 3tky | N7I | (Iso)eugenol O-methyltransferase | 2.1.1.146 | 0.452 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.451 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.451 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.451 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.451 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.451 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.450 | |
| 2aj4 | ANP | Galactokinase | 2.7.1.6 | 0.450 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.450 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.450 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.450 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.450 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.449 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.449 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.448 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.448 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.448 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.448 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.448 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.447 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1nzy | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.447 | |
| 1uhh | CZP | Aequorin-2 | / | 0.447 | |
| 2dsh | SAH | Diphthine synthase | / | 0.447 | |
| 2idk | C2F | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.447 | |
| 3njo | PYV | Abscisic acid receptor PYR1 | / | 0.447 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.447 | |
| 1m4i | COA | Aminoglycoside 2'-N-acetyltransferase | 2.3.1 | 0.446 | |
| 1o6q | R17 | Squalene--hopene cyclase | 4.2.1.129 | 0.446 | |
| 1ych | FMN | Nitric oxide reductase | 1 | 0.446 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2xkf | BX1 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.446 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.446 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.446 | |
| 3l9m | L9M | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 1uys | H1L | Acetyl-CoA carboxylase | / | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1y2d | 4DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 2zsb | ADP | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 3l3m | A92 | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.445 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.445 | |
| 4yfy | 1YJ | VioF | / | 0.445 | |
| 1k4h | APQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.444 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1vp5 | NAP | Oxidoreductase, aldo/keto reductase family | / | 0.444 | |
| 2qe2 | 452 | Polyprotein | / | 0.444 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.443 | |
| 4c49 | HCY | Corticosteroid-binding globulin | / | 0.443 | |
| 4j7h | TRH | PCZA361.3 | / | 0.443 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1vce | SAH | Diphthine synthase | / | 0.442 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.442 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.442 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.442 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.442 | |
| 1a26 | CNA | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.441 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.441 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.441 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.441 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.440 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 1p4a | PCP | Pur operon repressor | / | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3d5m | 4MS | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3g5i | DNB | Pyrimidine-specific ribonucleoside hydrolase RihA | / | 0.440 | |
| 3h0w | N8M | S-adenosylmethionine decarboxylase proenzyme | 4.1.1.50 | 0.440 |