sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1mq0 | BRD | Cytidine deaminase | 3.5.4.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mq0 | BRD | Cytidine deaminase | 3.5.4.5 | 1.000 | |
| 2yac | 937 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.526 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.517 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.510 | |
| 4nbb | 9CA | Terminal oxygenase component of carbazole | / | 0.500 | |
| 2ejz | SAH | Diphthine synthase | / | 0.497 | |
| 4a4o | 664 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.496 | |
| 2emu | SAH | Diphthine synthase | / | 0.493 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.488 | |
| 2owf | SAH | Diphthine synthase | / | 0.485 | |
| 2eh5 | SAH | Diphthine synthase | / | 0.482 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.482 | |
| 2ojg | 19A | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.481 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.480 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.479 | |
| 2emr | SAH | Diphthine synthase | / | 0.479 | |
| 2e08 | SAH | Diphthine synthase | / | 0.478 | |
| 2egb | SAH | Diphthine synthase | / | 0.478 | |
| 2owu | SAH | Diphthine synthase | / | 0.474 | |
| 1vce | SAH | Diphthine synthase | / | 0.471 | |
| 2hux | SAH | Diphthine synthase | / | 0.471 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.469 | |
| 3ox3 | 4X4 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.469 | |
| 2oli | IOP | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.468 | |
| 2dv4 | SAH | Diphthine synthase | / | 0.466 | |
| 3m6p | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.466 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.466 | |
| 1lbb | KAI | Glutamate receptor 2 | / | 0.465 | |
| 2dsg | SAH | Diphthine synthase | / | 0.465 | |
| 2ejk | SAH | Diphthine synthase | / | 0.465 | |
| 2v0u | FMN | NPH1-1 | / | 0.465 | |
| 3blo | QEI | Queuine tRNA-ribosyltransferase | 2.4.2.29 | 0.465 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.465 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.464 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.464 | |
| 2dek | SAH | Diphthine synthase | / | 0.463 | |
| 2ek7 | SAH | Diphthine synthase | / | 0.463 | |
| 2pcm | SAH | Diphthine synthase | / | 0.463 | |
| 2wnb | C5P | CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1 | 2.4.99.4 | 0.463 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.463 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.462 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.462 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.462 | |
| 2pch | SAH | Diphthine synthase | / | 0.462 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 2z6r | SAH | Diphthine synthase | / | 0.461 | |
| 1gw2 | FER | Peroxidase C1A | 1.11.1.7 | 0.460 | |
| 1u2r | SO1 | Elongation factor 2 | / | 0.460 | |
| 3o73 | O73 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.460 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.460 | |
| 1q12 | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.459 | |
| 2huv | SAH | Diphthine synthase | / | 0.459 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 3uay | ADN | Purine nucleoside phosphorylase DeoD-type | / | 0.459 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.459 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.459 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4j52 | 1J3 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.459 | |
| 2ek4 | SAH | Diphthine synthase | / | 0.458 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.458 | |
| 2rku | R78 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.458 | |
| 5dp2 | NAP | CurF | / | 0.458 | |
| 2ehl | SAH | Diphthine synthase | / | 0.457 | |
| 2el0 | SAH | Diphthine synthase | / | 0.457 | |
| 3biz | 61E | Wee1-like protein kinase | 2.7.10.2 | 0.457 | |
| 3egv | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.457 | |
| 1rpw | DID | HTH-type transcriptional regulator QacR | / | 0.456 | |
| 2f6r | ACO | Bifunctional coenzyme A synthase | / | 0.456 | |
| 2v1a | FMN | NPH1-1 | / | 0.456 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.455 | |
| 1kms | LIH | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1kqu | BR4 | Phospholipase A2, membrane associated | / | 0.455 | |
| 2e4n | SAH | Diphthine synthase | / | 0.455 | |
| 2e8q | SAH | Diphthine synthase | / | 0.455 | |
| 2eld | SAH | Diphthine synthase | / | 0.455 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.455 | |
| 1g28 | FMN | PHY3 | / | 0.454 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.454 | |
| 2oth | NIM | Basic phospholipase A2 VRV-PL-VIIIa | 3.1.1.4 | 0.454 | |
| 2pca | SAH | Diphthine synthase | / | 0.454 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.454 | |
| 4a4l | 939 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.454 | |
| 4bmp | FMN | Protein NrdI | / | 0.454 | |
| 4u14 | 0HK | Muscarinic acetylcholine receptor M3 | / | 0.454 | |
| 2eeq | SAH | Diphthine synthase | / | 0.453 | |
| 3wqu | ATP | Cell division protein FtsA | / | 0.453 | |
| 2pcg | SAH | Diphthine synthase | / | 0.452 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.452 | |
| 3u2l | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.452 | |
| 2e8h | SAH | Diphthine synthase | / | 0.451 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2owg | SAH | Diphthine synthase | / | 0.451 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.451 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 4b6l | 9ZP | Serine/threonine-protein kinase PLK3 | 2.7.11.21 | 0.451 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.450 | |
| 2eni | SAH | Diphthine synthase | / | 0.450 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.450 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.450 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.450 | |
| 4gr9 | 372 | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.450 | |
| 2e07 | SAH | Diphthine synthase | / | 0.449 | |
| 2egl | SAH | Diphthine synthase | / | 0.449 | |
| 2p6l | SAH | Diphthine synthase | / | 0.449 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.449 | |
| 4qem | HC4 | Phospholipase A2 VRV-PL-VIIIa | / | 0.449 | |
| 5efw | FMN | NPH1-1 | / | 0.449 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.448 | |
| 1v5e | FAD | Pyruvate oxidase | / | 0.448 | |
| 2h44 | 7CA | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.448 | |
| 3i7v | B4P | AP4A hydrolase | / | 0.448 | |
| 3p0f | BAU | Uridine phosphorylase 2 | 2.4.2.3 | 0.448 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.448 | |
| 4egn | TWO | Cytochrome P450 | / | 0.448 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.448 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.447 | |
| 1uwh | BAX | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.447 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.447 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.447 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2dxv | SAH | Diphthine synthase | / | 0.447 | |
| 2dxw | SAH | Diphthine synthase | / | 0.447 | |
| 2en5 | SAH | Diphthine synthase | / | 0.447 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.447 | |
| 2huq | SAH | Diphthine synthase | / | 0.447 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.447 | |
| 2xk3 | XK3 | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.447 | |
| 3iex | GMP | Purine nucleoside phosphorylase | / | 0.447 | |
| 4i6f | 1C7 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.447 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.446 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.446 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.446 | |
| 1wng | SAH | Diphthine synthase | / | 0.446 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.446 | |
| 1yw8 | A75 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2ele | SAH | Diphthine synthase | / | 0.446 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.446 | |
| 2v19 | FMN | Dodecin | / | 0.446 | |
| 3ce0 | P34 | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.446 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.446 | |
| 4bwa | N0B | Pyrrolysine--tRNA ligase | / | 0.446 | |
| 4bzn | UGX | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 1gt5 | BZQ | Odorant-binding protein | / | 0.445 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 1s3w | TQT | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.445 | |
| 2pci | SAH | Diphthine synthase | / | 0.445 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3cjt | SAH | Ribosomal protein L11 methyltransferase | 2.1.1 | 0.445 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.445 | |
| 3pqb | VGP | Putative oxidoreductase | / | 0.445 | |
| 3u57 | DH8 | Raucaffricine-O-beta-D-glucosidase | 3.2.1.125 | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4qys | PLR | Tryptophan synthase beta chain 2 | 4.2.1.20 | 0.445 | |
| 5aaj | HSC | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.445 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.444 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.444 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.444 | |
| 2e16 | SAH | Diphthine synthase | / | 0.444 | |
| 2owv | SAH | Diphthine synthase | / | 0.444 | |
| 2qqf | A1R | NAD-dependent protein deacetylase HST2 | 3.5.1 | 0.444 | |
| 2v18 | FMN | Dodecin | / | 0.444 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4tnz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.444 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.443 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.443 | |
| 2eju | SAH | tRNA (guanine(26)-N(2))-dimethyltransferase | / | 0.443 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.443 | |
| 3a3y | OBN | Sodium/potassium-transporting ATPase subunit alpha | / | 0.443 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4i6h | 1C8 | Serine/threonine-protein kinase PLK2 | 2.7.11.21 | 0.443 | |
| 4nbh | 9CA | Terminal oxygenase component of carbazole | / | 0.443 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.442 | |
| 1pua | COA | HAT A1 | / | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 1yc2 | NAD | NAD-dependent protein deacylase 2 | / | 0.442 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 2egs | SAH | Diphthine synthase | / | 0.442 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.442 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.442 | |
| 3be2 | RAJ | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.442 | |
| 3cqu | CQU | RAC-alpha serine/threonine-protein kinase | 2.7.11.1 | 0.442 | |
| 3phj | DHK | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.442 | |
| 3tif | ADP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.442 | |
| 4dpd | DHF | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.442 | |
| 4ise | 1FW | Glucokinase | 2.7.1.2 | 0.442 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.442 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1njj | ORX | Ornithine decarboxylase | / | 0.441 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.441 | |
| 1tl7 | ONM | Adenylate cyclase type 2 | / | 0.441 | |
| 1tl7 | ONM | Adenylate cyclase type 5 | / | 0.441 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.441 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.441 | |
| 1yci | NDF | Hypoxia-inducible factor 1-alpha inhibitor | 1.14.11.30 | 0.441 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.441 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.441 | |
| 2xnp | WCX | Serine/threonine-protein kinase Nek2 | 2.7.11.1 | 0.441 | |
| 4a2a | ATP | Cell division protein FtsA | / | 0.441 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.441 | |
| 4boe | CLR | Japanin | / | 0.441 | |
| 4mm7 | 29J | Na(+):neurotransmitter symporter (Snf family) | / | 0.441 | |
| 4qfz | TTP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.441 | |
| 4qtn | NNR | Nicotinamide riboside transporter PnuC | / | 0.441 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1tou | B1V | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 2e95 | B75 | Geranylgeranyl pyrophosphate synthase | / | 0.440 | |
| 2hut | SAH | Diphthine synthase | / | 0.440 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.440 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.440 | |
| 3fvq | ATP | Fe(3+) ions import ATP-binding protein FbpC | / | 0.440 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.440 | |
| 3mjr | AC2 | Deoxycytidine kinase | 2.7.1.74 | 0.440 |