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 |
|---|---|---|---|
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1rm8 | BAT | Matrix metalloproteinase-16 | 3.4.24 | 1.000 | |
| 1bzs | BSI | Neutrophil collagenase | 3.4.24.34 | 0.616 | |
| 2woa | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.613 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.612 | |
| 2wo8 | 077 | Macrophage metalloelastase | 3.4.24.65 | 0.606 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.602 | |
| 4g9l | NGH | Stromelysin-1 | 3.4.24.17 | 0.590 | |
| 1zvx | FIN | Neutrophil collagenase | 3.4.24.34 | 0.588 | |
| 1biw | S80 | Stromelysin-1 | 3.4.24.17 | 0.584 | |
| 2oy2 | ILE_ALA_GLY | Neutrophil collagenase | 3.4.24.34 | 0.583 | |
| 1g05 | BBH | Stromelysin-1 | 3.4.24.17 | 0.581 | |
| 1zs0 | EIN | Neutrophil collagenase | 3.4.24.34 | 0.578 | |
| 3tsk | QEG | Macrophage metalloelastase | 3.4.24.65 | 0.574 | |
| 1hv5 | RXP | Stromelysin-3 | 3.4.24 | 0.573 | |
| 3oho | Z79 | Stromelysin-1 | 3.4.24.17 | 0.573 | |
| 1gkc | NFH | Matrix metalloproteinase-9 | 3.4.24.35 | 0.571 | |
| 1mnc | PLH | Neutrophil collagenase | 3.4.24.34 | 0.569 | |
| 2wo8 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.567 | |
| 4gr8 | R4C | Macrophage metalloelastase | 3.4.24.65 | 0.565 | |
| 1sln | INH | Stromelysin-1 | 3.4.24.17 | 0.563 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.562 | |
| 2wo9 | 023 | Macrophage metalloelastase | 3.4.24.65 | 0.561 | |
| 1b8y | IN7 | Stromelysin-1 | 3.4.24.17 | 0.557 | |
| 2d1n | FA4 | Collagenase 3 | 3.4.24 | 0.554 | |
| 2hu6 | 37A | Macrophage metalloelastase | 3.4.24.65 | 0.551 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.546 | |
| 1d7x | SPC | Stromelysin-1 | 3.4.24.17 | 0.544 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.544 | |
| 3i7g | 732 | Collagenase 3 | 3.4.24 | 0.541 | |
| 3kec | 3KE | Collagenase 3 | 3.4.24 | 0.541 | |
| 3i7i | 518 | Collagenase 3 | 3.4.24 | 0.539 | |
| 1utt | CP8 | Macrophage metalloelastase | 3.4.24.65 | 0.535 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.534 | |
| 3zxh | E41 | Collagenase 3 | 3.4.24 | 0.533 | |
| 1ciz | DPS | Stromelysin-1 | 3.4.24.17 | 0.532 | |
| 1xur | PB5 | Collagenase 3 | 3.4.24 | 0.532 | |
| 3aig | 0ZC | Snake venom metalloproteinase adamalysin-2 | 3.4.24.46 | 0.532 | |
| 4a7b | 3W4 | Collagenase 3 | 3.4.24 | 0.530 | |
| 2ovx | 4MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.528 | |
| 4i03 | L88 | Macrophage metalloelastase | 3.4.24.65 | 0.527 | |
| 1atl | 0QI | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.526 | |
| 2i47 | KGY | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.526 | |
| 1g4k | HQQ | Stromelysin-1 | 3.4.24.17 | 0.524 | |
| 3le9 | 727 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.524 | |
| 2ovz | 5MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.522 | |
| 2xs4 | ALA_PHE_THR | Karilysin | 3.4.24 | 0.521 | |
| 2dw0 | GM6 | Zinc metalloproteinase-disintegrin-like VAP2B | 3.4.24 | 0.519 | |
| 3kmc | 403 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.514 | |
| 1dth | BAT | Snake venom metalloproteinase atrolysin-D | 3.4.24.42 | 0.511 | |
| 3kme | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.510 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.508 | |
| 2ow1 | 7MR | Matrix metalloproteinase-9 | 3.4.24.35 | 0.505 | |
| 1d5j | MM3 | Stromelysin-1 | 3.4.24.17 | 0.503 | |
| 1jk3 | BAT | Macrophage metalloelastase | 3.4.24.65 | 0.501 | |
| 3b92 | 440 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.500 | |
| 1zxc | IH6 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.499 | |
| 3l0t | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.499 | |
| 2a8h | 4NH | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.496 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.494 | |
| 1fm1 | WAY | Collagenase 3 | 3.4.24 | 0.493 | |
| 2w0d | CGS | Macrophage metalloelastase | 3.4.24.65 | 0.493 | |
| 2i47 | INN | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.489 | |
| 3ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.488 | |
| 2w13 | WR2 | Snake venom metalloproteinase BaP1 | 3.4.24 | 0.483 | |
| 1c8t | TR1 | Stromelysin-1 | 3.4.24.17 | 0.478 | |
| 4ayk | CGS | Interstitial collagenase | 3.4.24.7 | 0.478 | |
| 3ioe | A7D | Pantothenate synthetase | 6.3.2.1 | 0.475 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.473 | |
| 3ms5 | REE | Gamma-butyrobetaine dioxygenase | 1.14.11.1 | 0.472 | |
| 1qpl | 587 | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.471 | |
| 2srt | INH | Stromelysin-1 | 3.4.24.17 | 0.471 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.470 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.470 | |
| 1fls | WAY | Collagenase 3 | 3.4.24 | 0.469 | |
| 1qrr | UPG | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.469 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.468 | |
| 3zdu | 38R | Cyclin-dependent kinase-like 3 | 2.7.11.22 | 0.468 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.467 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.467 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.467 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.466 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1fm7 | DFV | Chalcone--flavonone isomerase 1 | 5.5.1.6 | 0.463 | |
| 3br3 | ET | HTH-type transcriptional regulator QacR | / | 0.463 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.463 | |
| 2jsd | NGH | Matrix metalloproteinase-20 | 3.4.24 | 0.462 | |
| 4qen | SAH | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | 2.1.1.43 | 0.462 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.461 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.461 | |
| 3lqs | PSZ | D-alanine aminotransferase | 2.6.1.21 | 0.460 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.459 | |
| 5ar4 | SB2 | Receptor-interacting serine/threonine-protein kinase 2 | 2.7.11.1 | 0.459 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.458 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.456 | |
| 1ps9 | MDE | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.456 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.456 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 3c8a | ARG_ARG_GLY_LEU_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.456 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.456 | |
| 3u04 | BB2 | Peptide deformylase | / | 0.456 | |
| 1sve | I01 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.455 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.455 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.455 | |
| 4m49 | 22Y | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.455 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.454 | |
| 2y6d | TQJ | Matrilysin | 3.4.24.23 | 0.454 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.454 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.454 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.454 | |
| 2r8o | T5X | Transketolase 1 | / | 0.452 | |
| 3pdq | KC6 | Lysine-specific demethylase 4A | 1.14.11 | 0.452 | |
| 4avl | TMP | Polymerase acidic protein | / | 0.452 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.452 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.451 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.451 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.451 | |
| 4b66 | NAP | L-ornithine N(5)-monooxygenase | / | 0.450 | |
| 3l0v | 724 | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.449 | |
| 3m6p | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.449 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.449 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.448 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.448 | |
| 4l2i | FAD | Electron transfer flavoprotein alpha/beta-subunit | / | 0.448 | |
| 4r1l | ADP | Phenylacetate-coenzyme A ligase | / | 0.448 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 2r6g | ATP | Maltose/maltodextrin import ATP-binding protein MalK | / | 0.447 | |
| 3e8x | NAP | BH1520 protein | / | 0.447 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.447 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.447 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase alpha chain | 1.13.11.3 | 0.447 | |
| 3pcg | 4HP | Protocatechuate 3,4-dioxygenase beta chain | 1.13.11.3 | 0.447 | |
| 4nwi | CTN | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.447 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.446 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.446 | |
| 4l4x | NDP | AmphI | / | 0.446 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.446 | |
| 1c3r | TSN | Acetoin utilization protein | / | 0.445 | |
| 1rx1 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 1zdf | UPG | Glycogenin-1 | 2.4.1.186 | 0.445 | |
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 3zcb | ATP | Adenosine monophosphate-protein transferase VbhT | 2.7.7.n1 | 0.445 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.445 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 4imf | SI3 | N-acetylneuraminate lyase | / | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 2z2d | HSI | Macrophage metalloelastase | 3.4.24.65 | 0.444 | |
| 3mp3 | HGG | Hydroxymethylglutaryl-CoA lyase, mitochondrial | 4.1.3.4 | 0.444 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.444 | |
| 1g2a | BB2 | Peptide deformylase | 3.5.1.88 | 0.443 | |
| 1mv8 | GDX | GDP-mannose 6-dehydrogenase | 1.1.1.132 | 0.443 | |
| 1ol6 | ATP | Aurora kinase A | 2.7.11.1 | 0.443 | |
| 1pwu | GM6 | Lethal factor | 3.4.24.83 | 0.443 | |
| 1zis | INI | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 2bfq | AR6 | [Protein ADP-ribosylglutamate] hydrolase AF_1521 | 3.2.2 | 0.443 | |
| 2r5n | TPP | Transketolase 1 | / | 0.443 | |
| 2vhw | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.443 | |
| 3c1o | NAP | Eugenol synthase | / | 0.443 | |
| 4dgo | 0JW | Casein kinase II subunit alpha | 2.7.11.1 | 0.443 | |
| 4rx6 | ATP | Nitrogen regulatory PII-like protein | / | 0.443 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 2r8p | T6F | Transketolase 1 | / | 0.442 | |
| 2xd6 | XD6 | ATP-dependent molecular chaperone HSP82 | / | 0.442 | |
| 2yvg | NAD | Ferredoxin reductase | / | 0.442 | |
| 3afh | GSU | Glutamate--tRNA ligase 2 | / | 0.442 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.442 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.442 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.441 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.441 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.441 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.441 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.441 | |
| 4txz | G2P | Cyclic GMP-AMP synthase | / | 0.441 | |
| 1daa | PLP | D-alanine aminotransferase | 2.6.1.21 | 0.440 | |
| 1ivs | VAA | Valine--tRNA ligase | 6.1.1.9 | 0.440 | |
| 1lrj | UD1 | UDP-glucose 4-epimerase | 5.1.3.2 | 0.440 | |
| 2bwp | PLG | 5-aminolevulinate synthase | 2.3.1.37 | 0.440 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.440 | |
| 2xa4 | AZ5 | Tyrosine-protein kinase JAK2 | / | 0.440 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.440 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.440 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.440 | |
| 3t2v | KKJ | Peptidoglycan recognition protein 1 | / | 0.440 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4n3c | UD1 | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.440 |