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 |
|---|---|---|---|
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4gr3 | R45 | Macrophage metalloelastase | 3.4.24.65 | 1.000 | |
| 3ljg | EEF | Macrophage metalloelastase | 3.4.24.65 | 0.753 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.663 | |
| 4guy | KLJ | Macrophage metalloelastase | 3.4.24.65 | 0.651 | |
| 4gql | R47 | Macrophage metalloelastase | 3.4.24.65 | 0.637 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.637 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.614 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.610 | |
| 3lil | EEA | Macrophage metalloelastase | 3.4.24.65 | 0.604 | |
| 2woa | 576 | Macrophage metalloelastase | 3.4.24.65 | 0.603 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.600 | |
| 2wo9 | 068 | Macrophage metalloelastase | 3.4.24.65 | 0.594 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.593 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.593 | |
| 3lik | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.593 | |
| 1hy7 | MBS | Stromelysin-1 | 3.4.24.17 | 0.591 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.591 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.590 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.587 | |
| 3ts4 | EEG | Macrophage metalloelastase | 3.4.24.65 | 0.582 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.578 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.578 | |
| 3o2x | 3O2 | Collagenase 3 | 3.4.24 | 0.575 | |
| 3kry | 3KR | Collagenase 3 | 3.4.24 | 0.574 | |
| 2ow0 | 6MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.570 | |
| 4h76 | 10B | Macrophage metalloelastase | 3.4.24.65 | 0.567 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.566 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.566 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.565 | |
| 1ztq | 033 | Collagenase 3 | 3.4.24 | 0.565 | |
| 3kej | 3EJ | Collagenase 3 | 3.4.24 | 0.563 | |
| 4a7b | 3W5 | Collagenase 3 | 3.4.24 | 0.559 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.559 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.557 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.556 | |
| 1caq | DPS | Stromelysin-1 | 3.4.24.17 | 0.550 | |
| 4gr0 | R4B | Macrophage metalloelastase | 3.4.24.65 | 0.547 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.546 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.544 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.536 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.536 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.534 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.530 | |
| 3kek | 3EK | Collagenase 3 | 3.4.24 | 0.529 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.526 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.523 | |
| 1you | PFD | Collagenase 3 | 3.4.24 | 0.521 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.520 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.519 | |
| 2oxw | ILE_ALA_GLY | Macrophage metalloelastase | 3.4.24.65 | 0.518 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.516 | |
| 1bqo | N25 | Stromelysin-1 | 3.4.24.17 | 0.515 | |
| 2ow2 | 8MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.512 | |
| 1g49 | 111 | Stromelysin-1 | 3.4.24.17 | 0.507 | |
| 1xuc | PB3 | Collagenase 3 | 3.4.24 | 0.506 | |
| 3e8r | 615 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.494 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.491 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.487 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.484 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.484 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.483 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.478 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.476 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.475 | |
| 2rjp | 886 | A disintegrin and metalloproteinase with thrombospondin motifs 4 | 3.4.24.82 | 0.473 | |
| 4dx9 | SER_ALA_VAL_THR | Integrin beta-1 | / | 0.473 | |
| 4dx9 | SER_ALA_VAL_THR | Integrin beta-1-binding protein 1 | / | 0.473 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.472 | |
| 1hov | I52 | 72 kDa type IV collagenase | 3.4.24.24 | 0.471 | |
| 1soz | VAL_TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.470 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.469 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.468 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.465 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.464 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.463 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.463 | |
| 3tog | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.462 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.461 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.461 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.460 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4eb5 | PLP | Cysteine desulfurase IscS 2 | / | 0.459 | |
| 4fue | 7UP | Urokinase-type plasminogen activator | 3.4.21.73 | 0.459 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.457 | |
| 3cz7 | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.457 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.457 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.456 | |
| 2q5g | 1FA | Peroxisome proliferator-activated receptor delta | / | 0.456 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.455 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.455 | |
| 5dp2 | NAP | CurF | / | 0.455 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.454 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.454 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.454 | |
| 3jw2 | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.454 | |
| 4e2y | JHZ | Methyltransferase | / | 0.454 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.454 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.453 | |
| 3ekp | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3q8h | AO9 | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.453 | |
| 1d8m | BBH | Stromelysin-1 | 3.4.24.17 | 0.452 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.452 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.452 | |
| 2gfd | RDA | Endoplasmin | / | 0.452 | |
| 2xhr | C0P | Heat shock protein HSP 90-alpha | / | 0.452 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3mvq | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.452 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.452 | |
| 1bdq | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.451 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.451 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.451 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.451 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.450 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 1y0s | 331 | Peroxisome proliferator-activated receptor delta | / | 0.450 | |
| 2h3w | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 3lzs | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.450 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.450 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.450 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.449 | |
| 2ejj | SAH | Diphthine synthase | / | 0.449 | |
| 2fxe | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.449 | |
| 2vzz | SCA | Putative succinyl-CoA transferase Rv0802c | 2.8.3 | 0.449 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.449 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4blr | UTP | NTPase P4 | / | 0.449 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1cbq | RE9 | Cellular retinoic acid-binding protein 2 | / | 0.448 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.448 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.448 | |
| 3tfy | COA | N-alpha-acetyltransferase 50 | 2.3.1 | 0.448 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.448 | |
| 1iy8 | NAD | Levodione reductase | / | 0.447 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.447 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 4eak | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.447 | |
| 5kjc | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.446 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.446 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.446 | |
| 4i8z | G08 | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 1dhr | NAD | Dihydropteridine reductase | 1.5.1.34 | 0.445 | |
| 1qy5 | NEC | Endoplasmin | / | 0.445 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.445 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.445 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.445 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.445 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.444 | |
| 1sdw | IYT | Peptidyl-glycine alpha-amidating monooxygenase | 1.14.17.3 | 0.444 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.444 | |
| 2hps | CTZ | Ca2+-triggered coelenterazine-binding protein 1 | / | 0.444 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.444 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.444 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.444 | |
| 3s3r | 0IW | Cathepsin B-like peptidase (C01 family) | / | 0.444 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.443 | |
| 1hbv | GAN | Gag-Pol polyprotein | / | 0.443 | |
| 2zfn | ACO | Histone acetyltransferase RTT109 | 2.3.1.48 | 0.443 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.443 | |
| 3hek | BD0 | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.443 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.443 | |
| 4tm1 | FDA | KtzI | / | 0.443 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 5b1y | NDP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.442 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.442 | |
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 0.442 | |
| 1t7i | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2nry | STU | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.442 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.442 | |
| 2p3b | 3TL | V-1 PROTEASE protein | / | 0.442 | |
| 2p3b | 3TL | V-1 protease | / | 0.442 | |
| 3csc | ACO | Citrate synthase, mitochondrial | 2.3.3.1 | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.442 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.442 | |
| 4bcr | WY1 | Peroxisome proliferator-activated receptor alpha | / | 0.442 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.442 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.442 | |
| 1di8 | DTQ | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.441 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.441 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.441 | |
| 2i4x | KGQ | Protease | / | 0.441 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3zpu | M8B | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.441 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.441 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.440 | |
| 1jip | KTN | 6-deoxyerythronolide B hydroxylase | / | 0.440 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.440 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.440 | |
| 2hch | N5A | Endoplasmin | / | 0.440 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2q5k | AB1 | Protease | / | 0.440 | |
| 2y8q | ADP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.440 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.440 | |
| 2z6r | SAH | Diphthine synthase | / | 0.440 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.440 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3vf7 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4tlx | FDA | KtzI | / | 0.440 |