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 |
|---|---|---|---|
| 3fmm | XI2 | Mitogen-activated protein kinase 14 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3fmm | XI2 | Mitogen-activated protein kinase 14 | / | 1.000 | |
| 3fko | FKO | Mitogen-activated protein kinase 14 | / | 0.713 | |
| 3fkn | FKN | Mitogen-activated protein kinase 14 | / | 0.667 | |
| 3itz | P66 | Mitogen-activated protein kinase 14 | / | 0.625 | |
| 1zzl | TZY | Mitogen-activated protein kinase 14 | / | 0.605 | |
| 3hub | 469 | Mitogen-activated protein kinase 14 | / | 0.601 | |
| 3zsh | 469 | Mitogen-activated protein kinase 14 | / | 0.584 | |
| 2gfs | PQB | Mitogen-activated protein kinase 14 | / | 0.572 | |
| 3fls | FLS | Mitogen-activated protein kinase 14 | / | 0.557 | |
| 2zb1 | GK4 | Mitogen-activated protein kinase 14 | / | 0.547 | |
| 3fmj | FMJ | Mitogen-activated protein kinase 14 | / | 0.542 | |
| 3bx5 | 304 | Mitogen-activated protein kinase 14 | / | 0.540 | |
| 3rin | I2O | Mitogen-activated protein kinase 14 | / | 0.536 | |
| 3hl7 | I47 | Mitogen-activated protein kinase 14 | / | 0.534 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.530 | |
| 3fly | FLY | Mitogen-activated protein kinase 14 | / | 0.528 | |
| 3fml | FML | Mitogen-activated protein kinase 14 | / | 0.528 | |
| 3gc9 | B45 | Mitogen-activated protein kinase 11 | 2.7.11.24 | 0.527 | |
| 3nww | 3NW | Mitogen-activated protein kinase 14 | / | 0.524 | |
| 3fl4 | FL4 | Mitogen-activated protein kinase 14 | / | 0.523 | |
| 2yix | YIX | Mitogen-activated protein kinase 14 | / | 0.522 | |
| 4lop | SB4 | Mitogen-activated protein kinase 14 | / | 0.522 | |
| 3fkl | FKL | Mitogen-activated protein kinase 14 | / | 0.519 | |
| 3e92 | G6A | Mitogen-activated protein kinase 14 | / | 0.517 | |
| 3fmh | 533 | Mitogen-activated protein kinase 14 | / | 0.517 | |
| 3fmk | FMK | Mitogen-activated protein kinase 14 | / | 0.517 | |
| 3hp5 | 52P | Mitogen-activated protein kinase 14 | / | 0.517 | |
| 3c5u | P41 | Mitogen-activated protein kinase 14 | / | 0.516 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.512 | |
| 1ywr | LI9 | Mitogen-activated protein kinase 14 | / | 0.511 | |
| 3flw | FLW | Mitogen-activated protein kinase 14 | / | 0.510 | |
| 3flz | FLZ | Mitogen-activated protein kinase 14 | / | 0.510 | |
| 4h38 | 0YX | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.506 | |
| 3s4q | NK0 | Mitogen-activated protein kinase 14 | / | 0.505 | |
| 3roc | 29A | Mitogen-activated protein kinase 14 | / | 0.497 | |
| 3fmn | 530 | Mitogen-activated protein kinase 14 | / | 0.495 | |
| 3o8t | BMU | Mitogen-activated protein kinase 14 | / | 0.495 | |
| 3bv2 | P38 | Mitogen-activated protein kinase 14 | / | 0.494 | |
| 3fi4 | FI4 | Mitogen-activated protein kinase 14 | / | 0.494 | |
| 3uib | SB2 | Putative mitogen-activated protein kinase | / | 0.493 | |
| 1zyj | BI5 | Mitogen-activated protein kinase 14 | / | 0.491 | |
| 1ouk | 084 | Mitogen-activated protein kinase 14 | / | 0.490 | |
| 1yqj | 6NP | Mitogen-activated protein kinase 14 | / | 0.488 | |
| 1ouy | 094 | Mitogen-activated protein kinase 14 | / | 0.487 | |
| 3dt1 | P40 | Mitogen-activated protein kinase 14 | / | 0.487 | |
| 3fln | 3FN | Mitogen-activated protein kinase 14 | / | 0.487 | |
| 3mpa | SB2 | Mitogen-activated protein kinase 14 | / | 0.487 | |
| 3d7z | GK5 | Mitogen-activated protein kinase 14 | / | 0.482 | |
| 3lfc | Z86 | Mitogen-activated protein kinase 14 | / | 0.481 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.480 | |
| 3gfe | P37 | Mitogen-activated protein kinase 14 | / | 0.479 | |
| 1bl6 | SB6 | Mitogen-activated protein kinase 14 | / | 0.478 | |
| 1wbw | LI4 | Mitogen-activated protein kinase 14 | / | 0.478 | |
| 3pg3 | DG7 | Mitogen-activated protein kinase 14 | / | 0.477 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.476 | |
| 3l8s | BFF | Mitogen-activated protein kinase 14 | / | 0.476 | |
| 3ha8 | 5JZ | Mitogen-activated protein kinase 14 | / | 0.475 | |
| 3iph | G11 | Mitogen-activated protein kinase 14 | / | 0.473 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.472 | |
| 3sgx | 0FW | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.471 | |
| 3mvl | 38P | Mitogen-activated protein kinase 14 | / | 0.470 | |
| 4g34 | 924 | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.470 | |
| 4loq | SB4 | Mitogen-activated protein kinase 14 | / | 0.470 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 3uvq | FS8 | Mitogen-activated protein kinase 14 | / | 0.469 | |
| 3hll | I45 | Mitogen-activated protein kinase 14 | / | 0.468 | |
| 3hng | 8ST | Vascular endothelial growth factor receptor 1 | 2.7.10.1 | 0.468 | |
| 2aqh | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.467 | |
| 2exc | JNK | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.467 | |
| 2zb0 | GK3 | Mitogen-activated protein kinase 14 | / | 0.467 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.467 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.466 | |
| 4az0 | S61 | Lysosomal protective protein | 3.4.16.5 | 0.466 | |
| 1m7q | DQO | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4l8u | 9AZ | Serum albumin | / | 0.465 | |
| 4loo | SB4 | Mitogen-activated protein kinase 14 | / | 0.465 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.465 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.465 | |
| 3iw8 | HIZ | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 4eh5 | 0OM | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 4eh6 | 0ON | Mitogen-activated protein kinase 14 | / | 0.464 | |
| 3kf7 | L9G | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 3tti | KBI | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.463 | |
| 4aa5 | NQB | Mitogen-activated protein kinase 14 | / | 0.463 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.462 | |
| 2chz | 093 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 3fc1 | 52P | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 4kip | 1R9 | Mitogen-activated protein kinase 14 | / | 0.462 | |
| 2ewa | SB2 | Mitogen-activated protein kinase 14 | / | 0.461 | |
| 3ey4 | 352 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 2rg6 | 287 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3bv3 | P39 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 3zsg | T75 | Mitogen-activated protein kinase 14 | / | 0.460 | |
| 4ap0 | ADP | Kinesin-like protein KIF11 | / | 0.460 | |
| 4jvb | 1M0 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.460 | |
| 1qvn | FRI | Interleukin-2 | / | 0.459 | |
| 1w83 | L11 | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.459 | |
| 2bal | PQA | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 2qd9 | LGF | Mitogen-activated protein kinase 14 | / | 0.459 | |
| 4cd2 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 1f17 | NAI | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.457 | |
| 3l8x | N4D | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 4eh7 | 0OO | Mitogen-activated protein kinase 14 | / | 0.457 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4kcf | AKM | FAD-dependent oxidoreductase | / | 0.456 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.455 | |
| 3tea | 4CO | 4-hydroxybenzoyl-CoA thioesterase | 3.1.2.23 | 0.455 | |
| 4kuh | CAA | 3-hydroxybutyryl-CoA dehydrogenase | / | 0.455 | |
| 3s2p | PMU | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.454 | |
| 4g31 | 0WH | Eukaryotic translation initiation factor 2-alpha kinase 3 | 2.7.11.1 | 0.454 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.454 | |
| 3oqu | A8S | Abscisic acid receptor PYL9 | / | 0.453 | |
| 4nxv | GDP | Mitochondrial dynamics protein MID51 | / | 0.453 | |
| 1sui | FRE | Caffeoyl-CoA O-methyltransferase | 2.1.1.104 | 0.452 | |
| 3b8r | 887 | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.452 | |
| 3vrw | YS5 | Vitamin D3 receptor | / | 0.452 | |
| 4jv8 | 1M1 | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.452 | |
| 1osv | CHC | Bile acid receptor | / | 0.451 | |
| 3p6m | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4dxh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 5kjc | PFB | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1f12 | 3HC | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.450 | |
| 1ybg | TAV | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.450 | |
| 2aib | ERG | Beta-elicitin cinnamomin | / | 0.450 | |
| 2o0u | C0M | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.450 | |
| 2qo9 | ANP | Ephrin type-A receptor 3 | 2.7.10.1 | 0.450 | |
| 3w1w | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 4k9n | TZD | Benzoylformate decarboxylase | 4.1.1.7 | 0.450 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.449 | |
| 2hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.449 | |
| 3f5p | 741 | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.449 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.449 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.449 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.449 | |
| 4ma6 | 28E | Ara h 8 allergen | / | 0.449 | |
| 4pds | ANP | Serine/threonine-protein kinase RAD53 | 2.7.12.1 | 0.449 | |
| 4yp5 | NAP | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.449 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.448 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.448 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.448 | |
| 5c7h | NDP | Putative oxidoreductase | / | 0.448 | |
| 1kzj | CB3 | Thymidylate synthase | / | 0.447 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4anq | VGH | ALK tyrosine kinase receptor | 2.7.10.1 | 0.447 | |
| 4b5p | ACO | Alpha-tubulin N-acetyltransferase 1 | / | 0.447 | |
| 4eil | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.447 | |
| 4gt3 | ATP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.447 | |
| 4hys | 1BJ | Mitogen-activated protein kinase 8 | 2.7.11.24 | 0.447 | |
| 4nks | 2M2 | Fibroblast growth factor receptor 1 | / | 0.447 | |
| 1jut | LYD | Thymidylate synthase | / | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 2jfz | 003 | Glutamate racemase | / | 0.446 | |
| 3cv9 | VDX | Vitamin D3 dihydroxylase | / | 0.446 | |
| 3vs4 | VSF | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.446 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.446 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.445 | |
| 1fbm | RTL | Cartilage oligomeric matrix protein | / | 0.445 | |
| 1uuo | BRF | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.445 | |
| 1yw2 | PGJ | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.445 | |
| 3d5w | ADP | Serine/threonine-protein kinase PLK | / | 0.445 | |
| 3gcq | 1BU | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 3u8w | 09J | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4ku5 | DCC | 3-oxoacyl-[ACP] synthase III | / | 0.445 | |
| 1dis | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.444 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.444 | |
| 3wec | AUI | Cytochrome P450 | / | 0.444 | |
| 3zsi | 52P | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4gyz | D5M | Tyrosyl-DNA phosphodiesterase 2 | 3.1.4 | 0.444 | |
| 4o7u | THF | Thymidylate synthase | / | 0.444 | |
| 4pd6 | URI | Nucleoside permease | / | 0.444 | |
| 1lso | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.443 | |
| 1pme | SB2 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.443 | |
| 1zdw | FLV | Prenyltransferase | / | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2oh0 | 2PY | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.443 | |
| 3p6o | ETG | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.443 | |
| 3vid | 4TT | Vascular endothelial growth factor receptor 2 | 2.7.10.1 | 0.443 | |
| 4aa4 | QC0 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 4btj | ATP | Tau-tubulin kinase 1 | 2.7.11.1 | 0.443 | |
| 4l23 | X6K | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform | / | 0.443 | |
| 2bxo | OPB | Serum albumin | / | 0.442 | |
| 2ilt | NN1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2yfx | VGH | ALK tyrosine kinase receptor | 2.7.10.1 | 0.442 | |
| 3cwk | REA | Cellular retinoic acid-binding protein 2 | / | 0.442 | |
| 4kiq | 1RA | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 1esv | LAR | Actin, alpha skeletal muscle | / | 0.441 | |
| 1gqy | ACP | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.441 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.441 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.441 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.441 | |
| 2ydo | ADN | Adenosine receptor A2a | / | 0.441 | |
| 3p6n | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.441 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.441 | |
| 3w78 | CBD | FMN-dependent NADH-azoreductase | / | 0.441 | |
| 4bi1 | ZO6 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.441 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.441 | |
| 4ez8 | DHF | Thymidylate synthase | 2.1.1.45 | 0.441 | |
| 5jad | FB2 | Platelet-activating factor acetylhydrolase | 3.1.1.47 | 0.441 | |
| 1lhv | NOG | Sex hormone-binding globulin | / | 0.440 | |
| 1ppj | ANY | Cytochrome b | / | 0.440 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2f7e | 2EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.440 | |
| 3bfb | 9OD | Pheromone-binding protein ASP1 | / | 0.440 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3iw5 | DF3 | Mitogen-activated protein kinase 14 | / | 0.440 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4ans | VGH | ALK tyrosine kinase receptor | 2.7.10.1 | 0.440 | |
| 4g1y | 0VO | Vitamin D3 receptor A | / | 0.440 | |
| 4nkv | AER | Steroid 17-alpha-hydroxylase/17,20 lyase | / | 0.440 | |
| 4oae | CLM | Uncharacterized protein | / | 0.440 |