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 |
|---|---|---|---|
| 1xjj | DGT | Vitamin B12-dependent ribonucleotide reductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1xjj | DGT | Vitamin B12-dependent ribonucleotide reductase | / | 1.000 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.486 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.482 | |
| 1udb | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.477 | |
| 2zdt | 46C | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.477 | |
| 5e8w | STU | TGF-beta receptor type-1 | 2.7.11.30 | 0.477 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.475 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.473 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.470 | |
| 4xx0 | COA | Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial | 6.2.1.4 | 0.470 | |
| 1xjn | DTP | Vitamin B12-dependent ribonucleotide reductase | / | 0.469 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.469 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.469 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.467 | |
| 1adf | TAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.466 | |
| 5bsf | NAD | Pyrroline-5-carboxylate reductase | / | 0.466 | |
| 1a9y | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.465 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.465 | |
| 3vth | APC | Carbamoyltransferase | / | 0.465 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.465 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.464 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.463 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.463 | |
| 4riy | ADP | Epidermal growth factor receptor | 2.7.10.1 | 0.463 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.462 | |
| 2dq7 | STU | Tyrosine-protein kinase Fyn | 2.7.10.2 | 0.462 | |
| 2wd9 | IBP | Acyl-coenzyme A synthetase ACSM2A, mitochondrial | 6.2.1.2 | 0.462 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.461 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 3hl7 | I47 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 1xjk | DGT | Vitamin B12-dependent ribonucleotide reductase | / | 0.458 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.457 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.457 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.456 | |
| 1ho5 | ADN | Protein UshA | 3.1.3.5 | 0.455 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.455 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.455 | |
| 4a30 | QMI | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.454 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.454 | |
| 4hnf | 16W | Casein kinase I isoform delta | 2.7.11.1 | 0.454 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.453 | |
| 1udc | UFM | UDP-glucose 4-epimerase | 5.1.3.2 | 0.452 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.452 | |
| 3ump | ATP | ATP-dependent 6-phosphofructokinase isozyme 2 | 2.7.1.11 | 0.452 | |
| 4eji | 0QA | Cytochrome P450 2A13 | 1.14.14.1 | 0.452 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.451 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.451 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4fr4 | STU | Serine/threonine-protein kinase 32A | 2.7.11.1 | 0.451 | |
| 4kl9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.451 | |
| 1eh4 | IC1 | Casein kinase I homolog 1 | 2.7.11.1 | 0.450 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.450 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.450 | |
| 2w0j | ZAT | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.450 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.450 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 5im3 | DTP | Ribonucleoside-diphosphate reductase | / | 0.450 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 1jpa | ANP | Ephrin type-B receptor 2 | 2.7.10.1 | 0.449 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.448 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.448 | |
| 3ics | COA | Coenzyme A disulfide reductase | / | 0.448 | |
| 4g16 | 0VM | Casein kinase I isoform gamma-3 | 2.7.11.1 | 0.448 | |
| 4riy | ANP | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.448 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.448 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.447 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.447 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.447 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.447 | |
| 3vev | 0H4 | Glucokinase | 2.7.1.2 | 0.447 | |
| 4otw | DB8 | Receptor tyrosine-protein kinase erbB-3 | 2.7.10.1 | 0.447 | |
| 4qmz | B49 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.447 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1pmn | 984 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.446 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 3ik6 | HCZ | Glutamate receptor 2 | / | 0.446 | |
| 4l9i | 8PR | Rhodopsin kinase | / | 0.446 | |
| 1gih | 1PU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.445 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.445 | |
| 1u59 | STU | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.445 | |
| 2cig | 1DG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.445 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.445 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.445 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4a4v | YFD | Peroxisome proliferator-activated receptor gamma | / | 0.445 | |
| 5ecc | NAP | Dehydrofolate reductase type I | / | 0.445 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1vjy | 460 | TGF-beta receptor type-1 | 2.7.11.30 | 0.444 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2ow9 | SP6 | Collagenase 3 | 3.4.24 | 0.444 | |
| 2x9d | ITC | Tetracycline repressor protein class D | / | 0.444 | |
| 2zbz | VDX | Vitamin D3 dihydroxylase | / | 0.444 | |
| 4a6r | TA8 | Probable aminotransferase | / | 0.444 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4e4m | 0NH | Tyrosine-protein kinase JAK2 | / | 0.444 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.444 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.443 | |
| 1oiy | N41 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.443 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.443 | |
| 3d4p | NAD | L-lactate dehydrogenase 1 | 1.1.1.27 | 0.443 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.443 | |
| 4gj3 | 0XP | Non-receptor tyrosine-protein kinase TYK2 | 2.7.10.2 | 0.443 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 1x2h | LPA | Lipoate-protein ligase A | 6.3.1.20 | 0.442 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.442 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.442 | |
| 4kqr | VPP | Peptidoglycan D,D-transpeptidase FtsI | / | 0.442 | |
| 4ks8 | B49 | Serine/threonine-protein kinase PAK 6 | 2.7.11.1 | 0.442 | |
| 4nb6 | 444 | Nuclear receptor ROR-gamma | / | 0.442 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.442 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.442 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 2hwr | DRD | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.441 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.441 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.441 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.441 | |
| 3vth | AP2 | Carbamoyltransferase | / | 0.441 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.441 | |
| 4bf2 | STU | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 1eio | GCH | Gastrotropin | / | 0.440 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2j8z | NAP | Quinone oxidoreductase PIG3 | 1 | 0.440 | |
| 2vtt | LZD | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.440 | |
| 2xik | J60 | Serine/threonine-protein kinase 25 | 2.7.11.1 | 0.440 | |
| 2yiq | YIQ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.440 | |
| 3bc3 | OPT | Cathepsin L1 | 3.4.22.15 | 0.440 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 | |
| 3zly | YSO | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.440 | |
| 4ft5 | H2K | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.440 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.440 | |
| 4gub | 0Y4 | Casein kinase II subunit alpha | 2.7.11.1 | 0.440 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.440 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.440 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.440 |