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 |
|---|---|---|---|
| 2hxd | DUP | dCTP deaminase, dUMP-forming | 3.5.4.30 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2hxd | DUP | dCTP deaminase, dUMP-forming | 3.5.4.30 | 1.000 | |
| 2qxx | TTP | dCTP deaminase | 3.5.4.13 | 0.574 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.509 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.501 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.493 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.491 | |
| 2nq8 | ZID | Enoyl-ACP reductase | / | 0.489 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.488 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.487 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.482 | |
| 1bzf | TMQ | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.478 | |
| 4y0k | NAP | AntE | / | 0.478 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.477 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.476 | |
| 1fml | RTL | Retinol dehydratase | / | 0.475 | |
| 4u7w | NDP | MxaA | / | 0.475 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.474 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.474 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.474 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.472 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.470 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.470 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1g9c | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.468 | |
| 2dwp | ACP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.468 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.468 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.466 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.466 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.466 | |
| 3owu | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.466 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.465 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.465 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.465 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.463 | |
| 2zsd | COA | Pantothenate kinase | 2.7.1.33 | 0.462 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.461 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.461 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.461 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.460 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.459 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.459 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.459 | |
| 1kl2 | FON | Serine hydroxymethyltransferase | / | 0.458 | |
| 1vzd | CB3 | Thymidylate synthase | / | 0.458 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.458 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.458 | |
| 4qer | STL | Phospholipase A2 VRV-PL-VIIIa | / | 0.458 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.458 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.457 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.457 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2oeg | UPG | UDP-glucose pyrophosphorylase | / | 0.456 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.456 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.456 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.456 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.456 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 4b67 | NAP | L-ornithine N(5)-monooxygenase | / | 0.455 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.455 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.454 | |
| 2lba | CHO | Fatty acid binding protein 6 | / | 0.454 | |
| 2wsa | 646 | Glycylpeptide N-tetradecanoyltransferase | / | 0.454 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.454 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.454 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.453 | |
| 4bfy | ZVY | Pantothenate kinase | 2.7.1.33 | 0.453 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.452 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.452 | |
| 1eio | GCH | Gastrotropin | / | 0.451 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.451 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.451 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.451 | |
| 2zsi | GA4 | Gibberellin receptor GID1A | 3 | 0.451 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.451 | |
| 4b1f | KRH | Glutamate racemase | / | 0.451 | |
| 4bz8 | J38 | Histone deacetylase | / | 0.451 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.451 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.450 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.450 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.450 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.450 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.450 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.450 | |
| 5doz | NDP | JamJ | / | 0.450 | |
| 1dr3 | HBI | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.449 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.449 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.449 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.449 | |
| 1jqd | SAH | Histamine N-methyltransferase | 2.1.1.8 | 0.448 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2e94 | 364 | Geranylgeranyl pyrophosphate synthase | / | 0.448 | |
| 3e3u | NVC | Peptide deformylase | 3.5.1.88 | 0.448 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.448 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.447 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.447 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.446 | |
| 2gzl | 2AA | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 0.446 | |
| 2nnq | T4B | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4g09 | 0VD | Histidinol dehydrogenase | / | 0.446 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.445 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.445 | |
| 3cvu | FAD | RE11660p | / | 0.445 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.445 | |
| 3eks | CY9 | Actin-5C | / | 0.445 | |
| 3had | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.445 | |
| 4bew | ACP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.445 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.445 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.444 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.444 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.443 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.443 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.443 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.443 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.443 | |
| 1s3v | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2j62 | GSZ | O-GlcNAcase NagJ | / | 0.442 | |
| 2obx | INI | 6,7-dimethyl-8-ribityllumazine synthase 2 | 2.5.1.78 | 0.442 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.442 | |
| 4e37 | NDP | Catalase | 1.11.1.6 | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.441 | |
| 1jra | FAD | FAD-linked sulfhydryl oxidase ERV2 | 1.8.3.2 | 0.441 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1s0x | C3S | Nuclear receptor ROR-alpha | / | 0.441 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.441 | |
| 2pnc | CLU | Primary amine oxidase, liver isozyme | / | 0.441 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.441 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.441 | |
| 3hf3 | FMN | Chromate reductase | / | 0.441 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.441 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.441 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.441 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.440 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.440 | |
| 3b1d | PLS | BetaC-S lyase | / | 0.440 | |
| 3c49 | KU8 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.440 | |
| 3eku | CY9 | Actin-5C | / | 0.440 | |
| 3k8q | 22A | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 4dqu | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.440 |