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 |
|---|---|---|---|
| 2r3a | SAM | Histone-lysine N-methyltransferase SUV39H2 | 2.1.1.43 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2r3a | SAM | Histone-lysine N-methyltransferase SUV39H2 | 2.1.1.43 | 1.000 | |
| 3ooi | SAM | Histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specific | 2.1.1.43 | 0.493 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.486 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.481 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.475 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.474 | |
| 1lsj | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.472 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.471 | |
| 4ypa | SAM | Histone-lysine N-methyltransferase ASH1L | 2.1.1.43 | 0.471 | |
| 2ci0 | 1CM | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.469 | |
| 4cuk | NAI | D-lactate dehydrogenase | / | 0.469 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.469 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.468 | |
| 2tct | CTC | Tetracycline repressor protein class D | / | 0.467 | |
| 4ype | SAM | Histone-lysine N-methyltransferase ASH1L | 2.1.1.43 | 0.466 | |
| 2fy4 | COA | Choline O-acetyltransferase | 2.3.1.6 | 0.465 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.465 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.465 | |
| 1dz8 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.464 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.464 | |
| 4fuj | 1U9 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.464 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.463 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.463 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.463 | |
| 1obb | NAD | Alpha-glucosidase | 3.2.1.20 | 0.462 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.462 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.461 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.460 | |
| 2nr4 | FMN | Conserved protein | / | 0.459 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.458 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.458 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 2y9q | ANP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.458 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.458 | |
| 1omo | NAD | Alanine dehydrogenase | / | 0.457 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.457 | |
| 3l63 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.457 | |
| 3wid | NAP | Glucose 1-dehydrogenase | / | 0.457 | |
| 4ew2 | DXY | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.456 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1yrc | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3wrj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.455 | |
| 4kky | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.454 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.454 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.454 | |
| 5jhn | SAM | Histone-lysine N-methyltransferase EHMT2 | / | 0.454 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.453 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 4g3r | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.453 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.452 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.452 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 1rek | B8L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.451 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.451 | |
| 3vp6 | HLD | Glutamate decarboxylase 1 | 4.1.1.15 | 0.451 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4ebf | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.451 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.450 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.450 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.449 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.449 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.449 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.449 | |
| 4dti | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.449 | |
| 4jic | FMN | GTN Reductase | / | 0.449 | |
| 4tm0 | FAD | KtzI | / | 0.449 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.448 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.448 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.448 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4ew3 | DXZ | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.448 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.448 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.448 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.447 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.447 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.447 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.447 | |
| 3wrh | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 4nmc | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.446 | |
| 2cy0 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.446 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.446 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.446 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4dpu | AGS | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 5fwn | NAP | Putative dehydrogenase | / | 0.446 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.445 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.445 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.445 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.445 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.445 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.444 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.444 | |
| 1yre | COA | Uncharacterized protein | / | 0.444 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.444 | |
| 2cts | COA | Citrate synthase, mitochondrial | 2.3.3.1 | 0.444 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.444 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 2wzm | NA7 | Uncharacterized oxidoreductase MSMEG_2407/MSMEI_2346 | / | 0.444 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.444 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.444 | |
| 3qql | X03 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.444 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.444 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.444 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.444 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.443 | |
| 2zvc | SAH | Precorrin-3 C17-methyltransferase | / | 0.443 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.443 | |
| 3zv6 | 4HB | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.443 | |
| 4g6g | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.443 | |
| 4k28 | NAD | Shikimate dehydrogenase family protein | / | 0.443 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.443 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.442 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.442 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3pft | FMN | Flavin reductase | / | 0.442 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.442 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.441 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.441 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 3ag6 | PAJ | Pantothenate synthetase | / | 0.441 | |
| 3r83 | Z14 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 3rq6 | APR | ADP-dependent (S)-NAD(P)H-hydrate dehydratase | / | 0.441 | |
| 4bqu | CLR | Japanin | / | 0.441 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 5ej9 | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.441 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.440 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.440 | |
| 4e2d | FMN | Dehydrogenase | / | 0.440 | |
| 4e4q | RRH | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.440 |