sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 1.000 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.627 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.624 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.595 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.583 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.580 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.578 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.577 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.571 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.568 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.567 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.566 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.563 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.562 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.561 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.560 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.559 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.557 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.556 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.552 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.551 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.550 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.549 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.547 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.546 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.546 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.544 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.543 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.539 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.538 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.535 | |
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 0.534 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.533 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.532 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.529 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.528 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.528 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.526 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.526 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.523 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.522 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.521 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.520 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.520 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.517 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.512 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.511 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.510 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.508 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.497 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.497 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.496 | |
| 3mp5 | HMG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.488 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.485 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.479 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.476 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.476 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.473 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.473 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.470 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.470 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.470 | |
| 2ejz | SAH | Diphthine synthase | / | 0.469 | |
| 5hwr | COA | Hydroxymethylglutaryl-CoA synthase | / | 0.469 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.467 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.467 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.467 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.466 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.464 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.464 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.463 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.463 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.463 | |
| 4wdf | A2P | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.463 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.462 | |
| 2nua | COA | Succinate--CoA ligase [ADP-forming] subunit alpha | 6.2.1.5 | 0.462 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.461 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.461 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.461 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.460 | |
| 3ieu | GDP | GTPase Era | / | 0.460 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.459 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.459 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.459 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.459 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.458 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.458 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.458 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.457 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.457 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.456 | |
| 2dsg | SAH | Diphthine synthase | / | 0.456 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.456 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.455 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.455 | |
| 4a2z | VIQ | Glycylpeptide N-tetradecanoyltransferase | / | 0.455 | |
| 3eku | CY9 | Actin-5C | / | 0.454 | |
| 4cax | 646 | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.454 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.453 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.453 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.453 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.453 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.452 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.452 | |
| 2yvg | NAD | Ferredoxin reductase | / | 0.452 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.452 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 1teh | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.451 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.451 | |
| 4h8n | NDP | NADPH-dependent conjugated polyketone reductase C2 | / | 0.451 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.450 | |
| 2eeq | SAH | Diphthine synthase | / | 0.450 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.450 | |
| 5hbr | COA | Acyl-CoA synthetase (NDP forming) | / | 0.450 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.449 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.449 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.449 | |
| 4twn | B96 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.449 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.449 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 2c9b | PUG | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.447 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.447 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.447 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.447 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 4mk7 | 28O | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.446 | |
| 4kp8 | E1G | Carbonic anhydrase 12 | 4.2.1.1 | 0.446 | |
| 5hwq | CAA | Hydroxymethylglutaryl-CoA synthase | / | 0.446 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.445 | |
| 1txz | APR | Probable ADP-ribose 1''-phosphate phosphatase YML087W | 3.1.3.84 | 0.445 | |
| 2wya | HMG | Hydroxymethylglutaryl-CoA synthase, mitochondrial | 2.3.3.10 | 0.445 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.445 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.445 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.445 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.445 | |
| 3tso | GNP | Ras-related protein Rab-25 | / | 0.445 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.445 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4tm1 | FDA | KtzI | / | 0.445 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.444 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.444 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.444 | |
| 3ibd | CPZ | Cytochrome P450 2B6 | 1.14.13 | 0.444 | |
| 3q33 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.444 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4l4x | NDP | AmphI | / | 0.444 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.444 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2b4q | NAP | Rhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase | 1.1.1.100 | 0.443 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.443 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3mp3 | HGG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.443 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4e2y | JHZ | Methyltransferase | / | 0.443 | |
| 1bmd | NAD | Malate dehydrogenase | / | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 2yph | QQY | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.442 | |
| 3ozc | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.442 | |
| 4a84 | DXC | Major pollen allergen Bet v 1-A | / | 0.442 | |
| 4c0b | ATP | mRNA cleavage and polyadenylation factor CLP1 | / | 0.442 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.442 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4j3m | AJ8 | Tankyrase-2 | 2.4.2.30 | 0.442 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.442 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.441 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.441 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 2y3s | TIR | TamL | / | 0.441 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.441 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.441 | |
| 4rx6 | ATP | Nitrogen regulatory PII-like protein | / | 0.441 | |
| 1ahi | CHO | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.440 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.440 | |
| 1u0w | STL | Chalcone synthase 2 | 2.3.1.74 | 0.440 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.440 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 2emu | SAH | Diphthine synthase | / | 0.440 | |
| 3eks | CY9 | Actin-5C | / | 0.440 |