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 |
|---|---|---|---|
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 1.000 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.601 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.588 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.560 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.554 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.553 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.552 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.552 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.552 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.549 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.547 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.545 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.545 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.543 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.543 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.541 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.539 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.537 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.537 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.532 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.528 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.527 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.526 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.525 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.523 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.523 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.521 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.519 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.519 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.518 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.518 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.517 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.516 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.512 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.512 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.511 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.510 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.508 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.507 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.507 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.506 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.506 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.504 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.504 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.500 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.498 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.496 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.494 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.493 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.492 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.489 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.487 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.486 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.481 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.477 | |
| 2vo7 | M05 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.473 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.473 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.473 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.472 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.472 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.471 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.470 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.468 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.467 | |
| 4afg | QMR | Achbp | / | 0.467 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.467 | |
| 1ozh | HE3 | Acetolactate synthase, catabolic | 2.2.1.6 | 0.466 | |
| 2uzu | L20 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.464 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.463 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.463 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.463 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.463 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.460 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 5dp2 | NAP | CurF | / | 0.459 | |
| 1o76 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.458 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.458 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.456 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.456 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.454 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.454 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.454 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.453 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.453 | |
| 2b8j | ADN | Class B acid phosphatase | 3.1.3.2 | 0.452 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.452 | |
| 4anu | EM7 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.452 | |
| 2jnp | NGH | Stromelysin-1 | 3.4.24.17 | 0.450 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.450 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.450 | |
| 1fml | RTL | Retinol dehydratase | / | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 1dz4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.448 | |
| 2b4t | AES | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.448 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.448 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.448 | |
| 3isj | A8D | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 1dhj | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1dyi | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.447 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.447 | |
| 1m0b | 0ZQ | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.446 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.446 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 4jc5 | 1K5 | Stimulator of interferon genes protein | / | 0.446 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.445 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.445 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.445 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.445 | |
| 1ykf | NAP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.444 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.444 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.444 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 3zsr | O3N | Integrase | / | 0.444 | |
| 4cez | O3N | Integrase | / | 0.444 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.444 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3cwj | 321 | Genome polyprotein | 2.7.7.48 | 0.443 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.443 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.442 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 0.442 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.442 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.442 | |
| 2p3b | 3TL | V-1 protease | / | 0.442 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.442 | |
| 3eks | CY9 | Actin-5C | / | 0.442 | |
| 4nvk | 2NY | Peroxidase | / | 0.442 | |
| 5cyo | GDP | Septin-9 | / | 0.442 | |
| 1t88 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.441 | |
| 1g93 | UPG | N-acetyllactosaminide alpha-1,3-galactosyltransferase | / | 0.440 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.440 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3c8b | ARG_ARG_GLY_ILE_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.440 | |
| 4ek1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 |