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 |
|---|---|---|---|
| 1txr | BES | Bacterial leucyl aminopeptidase | 3.4.11.10 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1txr | BES | Bacterial leucyl aminopeptidase | 3.4.11.10 | 1.000 | |
| 1xry | BES | Bacterial leucyl aminopeptidase | 3.4.11.10 | 0.735 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.503 | |
| 1r5h | AO2 | Methionine aminopeptidase 2 | / | 0.494 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.490 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.490 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.483 | |
| 1w6j | R71 | Lanosterol synthase | 5.4.99.7 | 0.483 | |
| 3jpu | TY4 | Transcriptional activator protein LasR | / | 0.483 | |
| 2vcz | VC3 | Hematopoietic prostaglandin D synthase | / | 0.481 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.480 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.478 | |
| 2gfx | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.478 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.477 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.477 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.476 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.475 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.473 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.471 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.471 | |
| 4xrb | NDP | Possible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc | / | 0.471 | |
| 3dds | 26B | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.469 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 1r5g | AO1 | Methionine aminopeptidase 2 | / | 0.466 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.466 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.466 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.465 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.465 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.465 | |
| 4dk7 | 0KS | Oxysterols receptor LXR-beta | / | 0.465 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.465 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.464 | |
| 1zxm | ANP | DNA topoisomerase 2-alpha | 5.99.1.3 | 0.464 | |
| 2bxo | OPB | Serum albumin | / | 0.464 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.464 | |
| 1kqw | RTL | Cellular retinol-binding protein type II | / | 0.463 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 3apw | DP0 | Alpha-1-acid glycoprotein 2 | / | 0.463 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.463 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.462 | |
| 1rx7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.461 | |
| 1uxk | NAD | Malate dehydrogenase | / | 0.461 | |
| 2fbw | CBE | Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial | 1.3.5.1 | 0.461 | |
| 2fbw | CBE | Succinate dehydrogenase cytochrome b, large subunit | / | 0.461 | |
| 3e8x | NAP | BH1520 protein | / | 0.461 | |
| 3eig | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 3koy | Z97 | D-ornithine 4,5-aminomutase subunit beta | / | 0.461 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.460 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.460 | |
| 1nmk | SFM | Peptidyl-prolyl cis-trans isomerase A | 5.2.1.8 | 0.460 | |
| 4h9t | HL4 | Phosphotriesterase | / | 0.460 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.459 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.459 | |
| 2q3e | NAI | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.459 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.459 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.459 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.458 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.458 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.458 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.458 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.457 | |
| 2j5x | GSP | ADP-ribosylation factor 6 | / | 0.457 | |
| 3hnz | PMN | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.457 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.457 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.456 | |
| 3cot | STR | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4a86 | H35 | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 4lzw | THM | Uridine phosphorylase | / | 0.456 | |
| 1qyw | 5SD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.455 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.455 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.455 | |
| 3ix8 | TX3 | Transcriptional activator protein LasR | / | 0.455 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.455 | |
| 4an4 | DUD | Putative glycosyl transferase | / | 0.455 | |
| 4kot | CE3 | Uncharacterized protein | / | 0.455 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.454 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.454 | |
| 2pb6 | SAH | Diphthine synthase | / | 0.454 | |
| 3bgx | TMP | Thymidylate synthase | / | 0.454 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4kov | KOV | Uncharacterized protein | / | 0.454 | |
| 1k5d | GNP | GTP-binding nuclear protein Ran | / | 0.453 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2b0q | ADP | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.453 | |
| 3pgh | FLP | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.453 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 2d1o | FA4 | Stromelysin-1 | 3.4.24.17 | 0.452 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.452 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.452 | |
| 2j9g | ANP | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 2p99 | YE6 | Methionine aminopeptidase | / | 0.452 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 2emr | SAH | Diphthine synthase | / | 0.451 | |
| 2zs8 | ADP | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 3ix4 | TX1 | Transcriptional activator protein LasR | / | 0.451 | |
| 4ej1 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.451 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.450 | |
| 3c1o | NAP | Eugenol synthase | / | 0.450 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 3g0g | RUM | Dipeptidyl peptidase 4 | / | 0.450 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 3p9t | TCL | Repressor | / | 0.450 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.450 | |
| 4c6u | TLG | 3-oxoacyl-ACP synthase | / | 0.450 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.450 | |
| 3vw7 | VPX | Proteinase-activated receptor 1 | / | 0.450 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.449 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.449 | |
| 4c72 | TLG | 3-oxoacyl-ACP synthase | / | 0.449 | |
| 2gqp | PA7 | Endoplasmin | / | 0.448 | |
| 2ixk | TDO | dTDP-4-dehydrorhamnose 3,5-epimerase | 5.1.3.13 | 0.448 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 3w3l | RX8 | Toll-like receptor 8 | / | 0.448 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.448 | |
| 1txt | CAA | HMG-CoA synthase | / | 0.447 | |
| 2emu | SAH | Diphthine synthase | / | 0.447 | |
| 2iya | ZIO | Oleandomycin glycosyltransferase | / | 0.447 | |
| 2vb8 | TLM | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.447 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 1ngs | TPP | Transketolase 1 | 2.2.1.1 | 0.446 | |
| 1pq6 | 965 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 1xrp | PRO_LEU_GLY_GLY | Proline iminopeptidase | 3.4.11.5 | 0.446 | |
| 1z2n | ADP | Inositol-tetrakisphosphate 1-kinase | 2.7.1.134 | 0.446 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.446 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.446 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.446 | |
| 4jlm | 1NN | Deoxycytidine kinase | 2.7.1.74 | 0.446 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.445 | |
| 2cmf | F11 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 2dxd | ANP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.445 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.445 | |
| 2x06 | NAD | L-sulfolactate dehydrogenase | / | 0.445 | |
| 2zev | B71 | Geranylgeranyl pyrophosphate synthase | / | 0.445 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.445 | |
| 3dv0 | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.445 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3g0d | XIH | Dipeptidyl peptidase 4 | / | 0.445 | |
| 3jun | AKD | Phenazine biosynthesis protein A/B | / | 0.445 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 4na4 | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.445 | |
| 5dw6 | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.445 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1nhk | CMP | Nucleoside diphosphate kinase | 2.7.4.6 | 0.444 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.444 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 4axa | RKD | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.444 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.443 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.443 | |
| 2vd0 | D27 | Hematopoietic prostaglandin D synthase | / | 0.443 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.443 | |
| 3oia | A31 | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.443 | |
| 3uzz | TES | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 4ffr | ATP | Uncharacterized protein | / | 0.443 | |
| 1ahi | CHO | 7-alpha-hydroxysteroid dehydrogenase | 1.1.1.159 | 0.442 | |
| 1n4p | CYS_VAL_ILE_LEU_GER | Geranylgeranyl transferase type-1 subunit beta | 2.5.1.59 | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.442 | |
| 1yw7 | A41 | Methionine aminopeptidase 2 | / | 0.442 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.442 | |
| 2r5n | TPP | Transketolase 1 | / | 0.442 | |
| 2vat | COA | Acetyl-CoA--deacetylcephalosporin C acetyltransferase | 2.3.1.175 | 0.442 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.442 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.442 | |
| 4a32 | 2CD | Glycylpeptide N-tetradecanoyltransferase | / | 0.442 | |
| 4dxl | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 4x7u | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.442 | |
| 4yao | FAD | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 2d81 | RB3 | Poly(3-hydroxybutyrate) depolymerase | / | 0.441 | |
| 2ejk | SAH | Diphthine synthase | / | 0.441 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.441 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.441 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.441 | |
| 3gf4 | UPG | UDP-galactopyranose mutase | 5.4.99.9 | 0.441 | |
| 3pn4 | BB2 | Peptide deformylase 1B, chloroplastic/mitochondrial | 3.5.1.88 | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4e2w | JHZ | Methyltransferase | / | 0.441 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.440 | |
| 2ew5 | Y12 | Peptide deformylase | / | 0.440 | |
| 2wwj | Y28 | Lysine-specific demethylase 4A | / | 0.440 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.440 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3eku | CY9 | Actin-5C | / | 0.440 | |
| 3m2u | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 4e2d | FMN | Dehydrogenase | / | 0.440 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.440 |