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 |
|---|---|---|---|
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4xt8 | TMQ | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 1.000 | |
| 2a59 | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.498 | |
| 2xje | U5P | Cytosolic purine 5'-nucleotidase | 3.1.3.5 | 0.479 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.478 | |
| 1ry0 | PG2 | Aldo-keto reductase family 1 member C3 | / | 0.477 | |
| 3ihg | VAK | Aklavinone 12-hydroxylase RdmE | / | 0.477 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.474 | |
| 2a57 | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.473 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 4dz5 | NAP | Aldo-keto reductase family 1 member C3 | / | 0.472 | |
| 1rxj | BNI | Streptavidin | / | 0.469 | |
| 1yry | MSG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.469 | |
| 1e66 | HUX | Acetylcholinesterase | 3.1.1.7 | 0.468 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.467 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1pwy | AC2 | Purine nucleoside phosphorylase | 2.4.2.1 | 0.466 | |
| 3dzj | NMN | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.466 | |
| 1kyx | CRM | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.465 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.465 | |
| 3jq6 | DX1 | Pteridine reductase, putative | / | 0.465 | |
| 1odj | GMP | Purine nucleoside phosphorylase | / | 0.464 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.463 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.463 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.462 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.462 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.461 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.460 | |
| 1s1r | NAP | Aldo-keto reductase family 1 member C3 | / | 0.460 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.460 | |
| 3pm1 | ET | HTH-type transcriptional regulator QacR | / | 0.460 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.460 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.460 | |
| 1kyy | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.459 | |
| 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 | 0.459 | |
| 3jq7 | DX2 | Pteridine reductase, putative | / | 0.459 | |
| 4k37 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.459 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 4zzj | CNA | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.458 | |
| 1ut6 | A8N | Acetylcholinesterase | 3.1.1.7 | 0.457 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.457 | |
| 5cxv | 0HK | Muscarinic acetylcholine receptor M1 | / | 0.457 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 3hl4 | CDC | Choline-phosphate cytidylyltransferase A | / | 0.455 | |
| 4h6p | FMN | Chromate reductase | / | 0.455 | |
| 1vbi | NAD | Malate/L-lactate dehydrogenase family protein | / | 0.454 | |
| 4yfy | 0FX | VioF | / | 0.454 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3ai0 | PNW | Beta-glucosidase | / | 0.453 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.453 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 4y9u | NAP | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 4yao | 2AM | NADPH--cytochrome P450 reductase | / | 0.453 | |
| 1c7o | PPG | Hemolysin | / | 0.452 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.452 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.452 | |
| 3prf | FP3 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.452 | |
| 4b6u | M7G | Eukaryotic translation initiation factor 4E type 3 | / | 0.452 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.452 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1zgc | A2E | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.451 | |
| 2o6h | INI | 6,7-dimethyl-8-ribityllumazine synthase 1 | 2.5.1.78 | 0.451 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.451 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.451 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.450 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.450 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.450 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.450 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.449 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 2po3 | T4K | 4-dehydrase | / | 0.449 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.449 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4iwn | GEK | Carboxy-S-adenosyl-L-methionine synthase | / | 0.449 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.449 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.448 | |
| 1k9s | FM1 | Purine nucleoside phosphorylase DeoD-type | / | 0.448 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.448 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.448 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.447 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3gn7 | 3GN | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.447 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.447 | |
| 4br3 | U85 | Choline kinase alpha | 2.7.1.32 | 0.447 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.447 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.446 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.446 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 2c9b | PUG | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.446 | |
| 3uzx | AOX | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2vz0 | D64 | Pteridine reductase | / | 0.445 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.445 | |
| 3nyt | ULP | UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase | 2.6.1.98 | 0.445 | |
| 3ry2 | BTN | Streptavidin | / | 0.445 | |
| 4xmx | BES | Aminopeptidase N | 3.4.11.2 | 0.445 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.444 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 1w19 | T4P | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.444 | |
| 2aou | CQA | Histamine N-methyltransferase | 2.1.1.8 | 0.444 | |
| 2rtn | IMI | Streptavidin | / | 0.444 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.444 | |
| 3inr | GDU | UDP-galactopyranose mutase | 5.4.99.9 | 0.444 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.443 | |
| 4b2g | V1N | Uncharacterized protein | / | 0.443 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.443 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.443 | |
| 4lcw | 1VY | Major histocompatibility complex class I-related gene protein | / | 0.443 | |
| 4yal | 2AM | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 4zr5 | RDF | Neprilysin | / | 0.443 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.442 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.442 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.442 | |
| 2c1z | KMP | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.442 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.442 | |
| 3arv | SAU | Chitinase A | / | 0.442 | |
| 3bld | PRF | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.442 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.442 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3v2u | ATP | Protein GAL3 | / | 0.442 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.442 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.441 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.441 | |
| 2x86 | ADP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 3bur | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.441 | |
| 5d7o | AR6 | NAD-dependent protein deacetylase sirtuin-2 | 3.5.1 | 0.441 | |
| 1re0 | AFB | ADP-ribosylation factor 1 | / | 0.440 | |
| 1re0 | AFB | ARF guanine-nucleotide exchange factor 1 | / | 0.440 | |
| 2idv | M7G | Eukaryotic translation initiation factor 4E-1 | / | 0.440 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.440 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.440 | |
| 3mtw | M3R | Xaa-Pro dipeptidase, putative | / | 0.440 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4dne | DTB | Streptavidin | / | 0.440 | |
| 4rvf | TYD | D-mycarose 3-C-methyltransferase | / | 0.440 |