sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2oae | AIL | Dipeptidyl peptidase 4 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2oae | AIL | Dipeptidyl peptidase 4 | / | 1.000 | |
| 4ffw | 715 | Dipeptidyl peptidase 4 | / | 0.640 | |
| 3qbj | NXZ | Dipeptidyl peptidase 4 | / | 0.601 | |
| 3ccc | 7AC | Dipeptidyl peptidase 4 | / | 0.563 | |
| 3vjk | M51 | Dipeptidyl peptidase 4 | / | 0.559 | |
| 3opm | LUI | Dipeptidyl peptidase 4 | / | 0.553 | |
| 3f8s | PF2 | Dipeptidyl peptidase 4 | / | 0.542 | |
| 2rgu | 356 | Dipeptidyl peptidase 4 | / | 0.536 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.529 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.528 | |
| 3g0b | T22 | Dipeptidyl peptidase 4 | / | 0.527 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.527 | |
| 3vjl | W94 | Dipeptidyl peptidase 4 | / | 0.526 | |
| 3ccb | B2Y | Dipeptidyl peptidase 4 | / | 0.516 | |
| 3g0d | XIH | Dipeptidyl peptidase 4 | / | 0.504 | |
| 2aj8 | SC3 | Dipeptidyl peptidase 4 | / | 0.502 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.485 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.485 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.485 | |
| 2xug | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.484 | |
| 5d4v | YGP | Uncharacterized protein MJ0489 | / | 0.484 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.482 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.481 | |
| 2iib | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.481 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.478 | |
| 3nub | UD0 | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.476 | |
| 3pgi | F41 | Endothiapepsin | 3.4.23.22 | 0.474 | |
| 3aiv | HBO | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic | 3.2.1.182 | 0.473 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.472 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.471 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.469 | |
| 2a3b | CFF | Endochitinase B1 | 3.2.1.14 | 0.468 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.467 | |
| 4zgs | NAD | Putative D-lactate dehydrogenase | / | 0.466 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.465 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.465 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3t88 | S0N | 1,4-dihydroxy-2-naphthoyl-CoA synthase | / | 0.465 | |
| 3go4 | SAH | Uncharacterized protein | / | 0.464 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.464 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.464 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.463 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.463 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.463 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.463 | |
| 1wkg | POI | [LysW]-aminoadipate semialdehyde transaminase | / | 0.462 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.462 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.462 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.462 | |
| 3pkb | Y16 | Methionine aminopeptidase 2 | / | 0.462 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3zm6 | 2GN | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.462 | |
| 4zk6 | NTM | Quinolinate synthase A | / | 0.462 | |
| 3bus | SAH | Demethylrebeccamycin-D-glucose O-methyltransferase | / | 0.461 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.460 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.460 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.460 | |
| 3n71 | SFG | Histone-lysine N-methyltransferase Smyd1 | / | 0.460 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.460 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.460 | |
| 4kl1 | PCG | Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4 | / | 0.460 | |
| 1tco | FK5 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.459 | |
| 1tco | FK5 | Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | 3.1.3.16 | 0.459 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.459 | |
| 3pkd | Y10 | Methionine aminopeptidase 2 | / | 0.459 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.458 | |
| 1mmk | H4B | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.458 | |
| 1e81 | M91 | Endothiapepsin | 3.4.23.22 | 0.457 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.457 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.456 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.456 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.456 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.455 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.455 | |
| 2xuf | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3ko0 | TFP | Protein S100-A4 | / | 0.455 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.455 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.454 | |
| 4qt3 | RAP | Peptidylprolyl isomerase | / | 0.454 | |
| 1icq | OPD | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.453 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.453 | |
| 1w19 | T1P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.453 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.453 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.453 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.453 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.452 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.452 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.452 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.452 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.452 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.451 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.451 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2isc | 223 | Purine nucleoside phosphorylase, putative | / | 0.451 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.451 | |
| 3mp5 | HMG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.451 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.451 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.450 | |
| 2clm | F6F | Tryptophan synthase alpha chain | / | 0.450 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.450 | |
| 2psw | COA | N-alpha-acetyltransferase 50 | / | 0.450 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 1q23 | FUA | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.449 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 3pka | Y02 | Methionine aminopeptidase 2 | / | 0.449 | |
| 4b6s | 2HN | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.449 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.449 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.448 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3pke | Y10 | Methionine aminopeptidase 2 | / | 0.448 | |
| 3t7p | 7SP | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 4m0f | 1YK | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 4tvj | 09L | Poly [ADP-ribose] polymerase 2 | 2.4.2.30 | 0.448 | |
| 5c8d | 5AD | Probable transcriptional regulator | / | 0.448 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.447 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.447 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.447 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.447 | |
| 4flk | Y10 | Methionine aminopeptidase 1 | / | 0.447 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.446 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.446 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2wn6 | NDP | ADP-ribosyltransferase enzymatic component | / | 0.446 | |
| 3kp0 | Z98 | D-ornithine 4,5-aminomutase subunit beta | / | 0.446 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.446 | |
| 4krs | 1SX | Tankyrase-1 | 2.4.2.30 | 0.446 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.445 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.445 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.445 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.445 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.445 | |
| 4ldl | XQC | Beta-2 adrenergic receptor | / | 0.445 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.444 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.444 | |
| 3rib | SAH | N-lysine methyltransferase SMYD2 | / | 0.444 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.444 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.444 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1c7o | PPG | Hemolysin | / | 0.443 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.443 | |
| 3x2e | NAI | Adenosylhomocysteinase | / | 0.443 | |
| 4q4e | BB2 | Aminopeptidase N | 3.4.11.2 | 0.443 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 1pr0 | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.442 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.442 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3c8b | ARG_ARG_GLY_ILE_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.442 | |
| 3chs | 4BU | Leukotriene A-4 hydrolase | 3.3.2.6 | 0.442 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.442 | |
| 3rno | NAP | NAD(P)H-hydrate epimerase | 5.1.99.6 | 0.442 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 3up0 | D7S | aceDAF-12 | / | 0.442 | |
| 4fll | YZ6 | Methionine aminopeptidase 1 | / | 0.442 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.442 | |
| 4x7v | MIV | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.442 | |
| 5hwp | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.442 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.441 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.441 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.441 | |
| 2jf0 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3fnl | SHA | Lactoperoxidase | / | 0.441 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.441 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.440 | |
| 1q6i | FK5 | FKBP-type peptidyl-prolyl cis-trans isomerase FkpA | 5.2.1.8 | 0.440 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.440 | |
| 2p2f | COA | Acetyl-coenzyme A synthetase | / | 0.440 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.440 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.440 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3coz | 54H | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 3q8u | ADP | Nucleoside diphosphate kinase | / | 0.440 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 4qen | SAH | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | 2.1.1.43 | 0.440 | |
| 4zwp | M44 | Xaa-Pro dipeptidase | 3.4.13.9 | 0.440 |