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 |
|---|---|---|---|
| 4ffw | 715 | Dipeptidyl peptidase 4 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ffw | 715 | Dipeptidyl peptidase 4 | / | 1.000 | |
| 2oae | AIL | Dipeptidyl peptidase 4 | / | 0.633 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.630 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.613 | |
| 3vjk | M51 | Dipeptidyl peptidase 4 | / | 0.589 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.585 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.573 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.570 | |
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 0.567 | |
| 3vjl | W94 | Dipeptidyl peptidase 4 | / | 0.562 | |
| 2rgu | 356 | Dipeptidyl peptidase 4 | / | 0.546 | |
| 3ccb | B2Y | Dipeptidyl peptidase 4 | / | 0.528 | |
| 3g0d | XIH | Dipeptidyl peptidase 4 | / | 0.527 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.517 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.508 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.486 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.482 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.481 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.480 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.479 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.476 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.475 | |
| 4lut | DCS | Alanine racemase | / | 0.474 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.473 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.472 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.471 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.470 | |
| 3e6e | DCS | Alanine racemase | / | 0.468 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.467 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.467 | |
| 3fsj | D7K | Benzoylformate decarboxylase | 4.1.1.7 | 0.467 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.466 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.465 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.465 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.463 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4gv8 | DUP | DUTPase | / | 0.461 | |
| 2xuq | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.460 | |
| 3nd6 | ATP | Phosphopantetheine adenylyltransferase | / | 0.460 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.459 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.459 | |
| 1nb6 | UTP | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.458 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.457 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.457 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.457 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.457 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.456 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.455 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.455 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3c1o | NAP | Eugenol synthase | / | 0.455 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.455 | |
| 5dro | ZH2 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.455 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.454 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.454 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 5c8d | 5AD | Probable transcriptional regulator | / | 0.454 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.453 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.453 | |
| 2dxi | ATP | Glutamate--tRNA ligase | 6.1.1.17 | 0.452 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.452 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.452 | |
| 3jyp | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.452 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.451 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.450 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.450 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.450 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.449 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.449 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.448 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.448 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.448 | |
| 3zxi | TYA | Tyrosine--tRNA ligase, mitochondrial | 6.1.1.1 | 0.448 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4lnb | ED5 | CaaX farnesyltransferase beta subunit Ram1 | / | 0.448 | |
| 2wca | NP6 | O-GlcNAcase BT_4395 | / | 0.447 | |
| 2wd8 | VGF | Pteridine reductase | / | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3dzi | RGT | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.447 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4gi5 | FAD | Putative NAD(P)H dehydrogenase (Quinone) | / | 0.447 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2vut | NAD | Nitrogen metabolite repression protein nmrA | / | 0.446 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.446 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3say | OFT | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.446 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4nv1 | TYD | Formyl transferase | / | 0.446 | |
| 1pr6 | XYA | Purine nucleoside phosphorylase DeoD-type | / | 0.445 | |
| 2gmu | PDG | Putative pyridoxamine 5-phosphate-dependent dehydrase | / | 0.445 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.445 | |
| 4d6q | PD2 | Lysine-specific demethylase 4D | 1.14.11 | 0.445 | |
| 4da7 | AC2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.445 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.445 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.445 | |
| 3p3c | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.444 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.444 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 1po7 | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.443 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2ges | COK | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.443 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.442 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.442 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.442 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.442 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.442 | |
| 2gc8 | 885 | Polyprotein | / | 0.442 | |
| 2qe2 | 452 | Polyprotein | / | 0.442 | |
| 2xuk | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 3opx | U5P | Suppressor of disruption of TFIIS | / | 0.442 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.442 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.442 | |
| 4nv1 | 4TG | Formyl transferase | / | 0.442 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.441 | |
| 1jik | 545 | Tyrosine--tRNA ligase | / | 0.441 | |
| 1qbq | HFP | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.441 | |
| 1qbq | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.441 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.441 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.440 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.440 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.440 | |
| 3d28 | B34 | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.440 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.440 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.440 |