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 |
|---|---|---|---|
| 2uup | LK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2uup | LK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 1.000 | |
| 1uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.724 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.659 | |
| 2jfh | LK1 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.651 | |
| 2y67 | N21 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.631 | |
| 2vte | IK4 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.613 | |
| 2y66 | N04 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.610 | |
| 2uuo | LK3 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.603 | |
| 2jfg | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.577 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.519 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.500 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.498 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.497 | |
| 3uag | UMA | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.493 | |
| 2xpc | 051 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.490 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.486 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.482 | |
| 1xuz | MMN | Capsule biosynthesis protein | / | 0.480 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.478 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.477 | |
| 1qcj | APT | Antiviral protein I | 3.2.2.22 | 0.476 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.475 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.475 | |
| 1l8a | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.474 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.474 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.474 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.473 | |
| 2r2n | KYN | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.472 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.471 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.471 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.471 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.470 | |
| 2wqp | WQP | Polysialic acid capsule biosynthesis protein SiaC | / | 0.469 | |
| 1akc | PPE | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.468 | |
| 4to3 | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.468 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.467 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.467 | |
| 2wzy | SQX | Soluble acetylcholine receptor | / | 0.467 | |
| 3e6y | CW1 | 14-3-3-like protein C | / | 0.467 | |
| 4y9u | NAP | NADPH--cytochrome P450 reductase | / | 0.466 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.465 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.464 | |
| 1lwi | NAP | 3-alpha-hydroxysteroid dehydrogenase | 1.1.1.50 | 0.464 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.464 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.463 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.463 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.463 | |
| 5ccy | TMP | Polymerase acidic protein | / | 0.463 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 1lke | DOG | Bilin-binding protein | / | 0.462 | |
| 1toi | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.462 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.462 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.462 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.461 | |
| 1qrt | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.461 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.461 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.461 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.461 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.461 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.460 | |
| 2xnv | VU3 | Soluble acetylcholine receptor | / | 0.459 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.459 | |
| 3hdq | GDU | UDP-galactopyranose mutase | / | 0.459 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.459 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.459 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.458 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3rbq | GLY_ALA_GLY_ALA_DAO | Protein unc-119 homolog A | / | 0.458 | |
| 4zwe | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.458 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.457 | |
| 3abx | RCB | Glucanase | / | 0.457 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.457 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.456 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.456 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.456 | |
| 1fml | RTL | Retinol dehydratase | / | 0.455 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.455 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.455 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.455 | |
| 3iog | SDF | Metallo-beta-lactamase type 2 | / | 0.455 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.455 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.454 | |
| 3fr4 | F8A | Fatty acid-binding protein, adipocyte | / | 0.454 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.454 | |
| 2xyt | TC9 | Soluble acetylcholine receptor | / | 0.453 | |
| 3cmf | PDN | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 4dbc | 3QP | Aspartate aminotransferase | 2.6.1.1 | 0.453 | |
| 4gd4 | 0WS | Lysine-specific demethylase 4A | 1.14.11 | 0.453 | |
| 5ao1 | DG3 | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.453 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.452 | |
| 1pag | FMP | Antiviral protein I | 3.2.2.22 | 0.452 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.452 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.452 | |
| 2rtd | BTN | Streptavidin | / | 0.452 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2ylr | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.452 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.452 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.452 | |
| 1xq0 | 4TR | Carbonic anhydrase 2 | 4.2.1.1 | 0.451 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.451 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.451 | |
| 3eku | CY9 | Actin-5C | / | 0.451 | |
| 3lkh | LT6 | Genome polyprotein | 2.7.7.48 | 0.451 | |
| 4kc4 | WS3 | Histo-blood group ABO system transferase | / | 0.451 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.451 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3zvm | ADP | Bifunctional polynucleotide phosphatase/kinase | 2.7.1.78 | 0.450 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.450 | |
| 4ito | MPX | Carbonic anhydrase 2 | 4.2.1.1 | 0.450 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.450 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.450 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.449 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.449 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.449 | |
| 2g5w | 8PG | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.449 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.449 | |
| 3d9z | D9Z | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 3oim | VZ5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.449 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.449 | |
| 1ex7 | 5GP | Guanylate kinase | 2.7.4.8 | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.448 | |
| 3faz | NOS | Purine nucleoside phosphorylase | / | 0.448 | |
| 3mj4 | URM | UDP-galactopyranose mutase | / | 0.448 | |
| 3ry2 | BTN | Streptavidin | / | 0.448 | |
| 4b68 | NAP | L-ornithine N(5)-monooxygenase | / | 0.448 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.448 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.448 | |
| 4u07 | ATP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.448 | |
| 4u0s | ADP | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.448 | |
| 4u0z | APC | Adenosine monophosphate-protein transferase FICD | 2.7.7.n1 | 0.448 | |
| 1t7o | 152 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.447 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.447 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.447 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.447 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3zhu | TD8 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.447 | |
| 4gdd | NAI | UDP-galactopyranose mutase | / | 0.447 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.447 | |
| 1fxo | TMP | Glucose-1-phosphate thymidylyltransferase | / | 0.446 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.446 | |
| 1okm | SAB | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.446 | |
| 1ttm | 667 | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 1tys | DHF | Thymidylate synthase | / | 0.446 | |
| 1wkl | ATP | Nucleoside diphosphate kinase | / | 0.446 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.446 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2iu8 | UD1 | UDP-3-O-acylglucosamine N-acyltransferase | 2.3.1 | 0.446 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.446 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.446 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.446 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.446 | |
| 1n5v | NOM | ActVA 6 protein | / | 0.445 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 2bn4 | NAP | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.445 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.445 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.445 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3oyq | OYQ | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4bf1 | 9FK | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 4kap | 1QV | Carbonic anhydrase 2 | 4.2.1.1 | 0.445 | |
| 1akb | PPD | Aspartate aminotransferase, mitochondrial | 2.6.1.1 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.444 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.444 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 4a33 | PS8 | Glycylpeptide N-tetradecanoyltransferase | / | 0.444 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.444 | |
| 1bn1 | AL5 | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 1bnm | AL8 | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 1eji | THF | Serine hydroxymethyltransferase, cytosolic | / | 0.443 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.443 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 2c4i | BTN | Avidin | / | 0.443 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.443 | |
| 3dbu | D8W | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 3dc3 | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.443 | |
| 3dhb | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.443 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 4dne | DTB | Streptavidin | / | 0.443 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.442 | |
| 2r5n | TPP | Transketolase 1 | / | 0.442 | |
| 3bl7 | DD1 | m7GpppX diphosphatase | 3.6.1.59 | 0.442 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.442 | |
| 4xwt | U5P | Ribonuclease J | / | 0.442 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 2izf | BTN | Streptavidin | / | 0.441 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.441 | |
| 3g0y | P9A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.441 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.441 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.441 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.440 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.440 | |
| 2pow | I7C | Carbonic anhydrase 2 | 4.2.1.1 | 0.440 | |
| 2x91 | LPR | Angiotensin-converting enzyme | 3.4.15.1 | 0.440 | |
| 3evb | SAH | Genome polyprotein | 2.1.1.56 | 0.440 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3v2u | ATP | Protein GAL3 | / | 0.440 | |
| 3zhv | TDW | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 |