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 |
|---|---|---|---|
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4jwf | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 1.000 | |
| 4jwh | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.512 | |
| 4eu9 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.500 | |
| 3u9e | COA | Lmo1369 protein | / | 0.492 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.491 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.486 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.484 | |
| 4rcv | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.482 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.481 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.481 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.480 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.479 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.478 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.474 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.473 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.472 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.471 | |
| 3bbh | SFG | Ribosomal RNA small subunit methyltransferase Nep1 | 2.1.1 | 0.471 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.470 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.470 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 4eu8 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.470 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.468 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.467 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.467 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.466 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.466 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.466 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.464 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.464 | |
| 3w2j | QRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.464 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.463 | |
| 4xbo | SAH | tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ | 2.1.1.200 | 0.463 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.462 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.461 | |
| 4d0l | 093 | Phosphatidylinositol 4-kinase beta | 2.7.1.67 | 0.461 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.460 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.460 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 4yek | THM | Thymidine phosphorylase | / | 0.459 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 4eua | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.458 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.457 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.457 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.457 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.456 | |
| 4umx | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.456 | |
| 1fwk | ADP | Homoserine kinase | 2.7.1.39 | 0.455 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 3p0h | FSE | Putative tyrosyl-tRNA synthetase | / | 0.455 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.455 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.455 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.454 | |
| 3w1x | XRO | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.454 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.454 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.453 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.453 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.452 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.452 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.452 | |
| 4i02 | CMP | cAMP-activated global transcriptional regulator CRP | / | 0.452 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.451 | |
| 2y3r | TIR | TamL | / | 0.451 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 3w3o | ROE | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.451 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.451 | |
| 4jwj | SAH | tRNA (guanine(9)-N1)-methyltransferase | / | 0.451 | |
| 5d3q | GDP | Dynamin-1 | 3.6.5.5 | 0.451 | |
| 1drf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.450 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.450 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.450 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.450 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.450 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.450 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.449 | |
| 2xck | MH4 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.449 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.449 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.449 | |
| 3vqh | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.449 | |
| 4dfr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.449 | |
| 1e7q | NAP | GDP-L-fucose synthase | / | 0.448 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.448 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.448 | |
| 2a1o | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.448 | |
| 2bxm | IMN | Serum albumin | / | 0.448 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 4l4x | NDP | AmphI | / | 0.448 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.448 | |
| 4xr9 | NAD | CalS8 | / | 0.448 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.447 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.447 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.447 | |
| 3a20 | FMN | FMN-binding protein | / | 0.447 | |
| 3k6l | 2BB | Peptide deformylase | 3.5.1.88 | 0.447 | |
| 3w2u | ROU | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.447 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.447 | |
| 1rz0 | FAD | Phenol 2-hydroxylase component B | / | 0.446 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.446 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.446 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.446 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.446 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.446 | |
| 3kjm | 245 | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.446 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4e2d | FMN | Dehydrogenase | / | 0.446 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.445 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3rh7 | FMN | Uncharacterized protein | / | 0.445 | |
| 4bii | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.445 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 1zji | 2PG | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.444 | |
| 3ruk | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.444 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.444 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.444 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 1owp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.443 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.443 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.443 | |
| 4eu4 | COA | Succinyl-CoA:acetate CoA-transferase | / | 0.443 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.443 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.443 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.442 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 1ydr | IQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2c1b | CQP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 2q85 | 973 | UDP-N-acetylenolpyruvoylglucosamine reductase | 1.3.1.98 | 0.442 | |
| 2q9c | GNP | Signal recognition particle receptor FtsY | / | 0.442 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.442 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.442 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1hon | GNH | Adenylosuccinate synthetase | / | 0.441 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1q8w | M77 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.441 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.441 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3h8b | NSY | Cathepsin L1 | 3.4.22.15 | 0.441 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.441 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.441 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.441 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.441 | |
| 5d4u | SAM | Uncharacterized protein MJ0489 | / | 0.441 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.441 | |
| 1dg8 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1npd | NAD | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 1p0f | NAP | NADP-dependent alcohol dehydrogenase | 1.1.1.2 | 0.440 | |
| 1q8u | H52 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 1rb3 | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1tw4 | CHD | Fatty acid-binding protein, liver | / | 0.440 | |
| 1xh8 | R55 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 1xha | R68 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.440 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 2uzw | SS4 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.440 | |
| 3uku | C69 | Actin-related protein 3 | / | 0.440 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.440 | |
| 4mcc | 21X | tRNA (guanine-N(1)-)-methyltransferase | 2.1.1.228 | 0.440 |