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 |
|---|---|---|---|
| 2mm3 | GCH | Gastrotropin |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2mm3 | GCH | Gastrotropin | / | 1.000 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.512 | |
| 3kdj | A8S | Abscisic acid receptor PYL1 | / | 0.484 | |
| 3kb0 | A8S | Abscisic acid receptor PYL2 | / | 0.480 | |
| 3h03 | UBP | Glutamate receptor 2 | / | 0.478 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.477 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.474 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.473 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.472 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.472 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.469 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.469 | |
| 4a51 | DQ8 | Kinesin-like protein KIF11 | / | 0.468 | |
| 4fgc | PQ0 | NADPH-dependent 7-cyano-7-deazaguanine reductase | 1.7.1.13 | 0.467 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.467 | |
| 4oic | A8S | Bet v I allergen-like | / | 0.467 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.465 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.463 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.463 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.463 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.461 | |
| 1q6n | P90 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.460 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.460 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.459 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.459 | |
| 4zqm | XMP | Inosine-5'-monophosphate dehydrogenase | / | 0.458 | |
| 3rmw | UPG | Glycogenin-1 | 2.4.1.186 | 0.457 | |
| 2acw | UPG | Glycosyltransferase | / | 0.456 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.456 | |
| 1eqb | FFO | Serine hydroxymethyltransferase | 2.1.2.1 | 0.455 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.455 | |
| 5dhg | DGV | Nociceptin receptor | / | 0.455 | |
| 3nmv | PYV | Abscisic acid receptor PYL2 | / | 0.454 | |
| 4xba | 5GP | Aprataxin-like protein | 3 | 0.454 | |
| 4yqf | GDP | Septin-9 | / | 0.454 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.454 | |
| 1i75 | NOJ | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.452 | |
| 2ble | 5GP | GMP reductase 1 | / | 0.452 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.452 | |
| 3njo | P2M | Abscisic acid receptor PYR1 | / | 0.452 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.452 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.451 | |
| 2clf | F6F | Tryptophan synthase alpha chain | / | 0.451 | |
| 2j7c | IDE | Beta-glucosidase A | 3.2.1.21 | 0.451 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.451 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.451 | |
| 2bwg | 5GP | GMP reductase 1 | / | 0.450 | |
| 2qzr | S79 | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.450 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 3k90 | A8S | Abscisic acid receptor PYR1 | / | 0.450 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.450 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.449 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.449 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.449 | |
| 4cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.449 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.449 | |
| 4ww9 | ADP | EKC/KEOPS complex subunit BUD32 | 3.6 | 0.449 | |
| 2op1 | 8PC | Enoyl-ACP reductase | / | 0.448 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.448 | |
| 5g53 | NEC | Adenosine receptor A2a | / | 0.448 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.447 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.447 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.447 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3ceh | AVE | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.447 | |
| 3qfc | NAP | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.447 | |
| 4dsc | A8S | Abscisic acid receptor PYL3 | / | 0.447 | |
| 4gi4 | 0EX | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.447 | |
| 2j0s | ANP | Eukaryotic initiation factor 4A-III | 3.6.4.13 | 0.446 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.445 | |
| 3gxo | MQA | Mitomycin biosynthesis 6-O-methyltransferase | / | 0.445 | |
| 4c71 | 7RD | 3-oxoacyl-ACP synthase | / | 0.445 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 4l17 | DNQ | Glutamate receptor 2 | / | 0.445 | |
| 1ori | SAH | Protein arginine N-methyltransferase 1 | / | 0.444 | |
| 2xjg | XJG | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.444 | |
| 4xcz | T3Q | Qdtf | / | 0.444 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.443 | |
| 1k4g | AIQ | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.443 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.443 | |
| 1rt2 | TNK | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 3i0r | RT3 | Gag-Pol polyprotein | 2.7.7.49 | 0.443 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.443 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.443 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.443 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 2vce | U2F | UDP-glycosyltransferase 72B1 | / | 0.442 | |
| 3kb3 | A8S | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4mub | OAQ | Sulfotransferase oxamniquine resistance protein | / | 0.442 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 2oc4 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.441 | |
| 3ebf | 332 | Nitric oxide synthase, inducible | 1.14.13.39 | 0.441 | |
| 3gb4 | D3M | DdmC | / | 0.441 | |
| 3gwu | SRE | Na(+):neurotransmitter symporter (Snf family) | / | 0.441 | |
| 3i1y | 33N | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.441 | |
| 3lq2 | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 4bur | NAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.441 | |
| 4ea3 | 0NN | Nociceptin receptor | / | 0.441 | |
| 1cs4 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cs4 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1q19 | SSC | Carbapenam-3-carboxylate synthase | 6.3.3.6 | 0.440 | |
| 2az3 | CDP | Nucleoside diphosphate kinase | / | 0.440 | |
| 2cdu | FAD | NADH oxidase | / | 0.440 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3r04 | UNQ | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.440 |