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 |
|---|---|---|---|
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 1.000 | |
| 4lsa | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.692 | |
| 3rgz | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 | 0.547 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.491 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.489 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.484 | |
| 1pz1 | NAP | General stress protein 69 | / | 0.483 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.480 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.479 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.478 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.478 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.477 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.477 | |
| 2ejz | SAH | Diphthine synthase | / | 0.476 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.476 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.476 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.473 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.471 | |
| 1vkg | CRI | Histone deacetylase 8 | 3.5.1.98 | 0.470 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.470 | |
| 1pj6 | FOL | Dimethylglycine oxidase | 1.5.3.10 | 0.469 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.469 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.469 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.468 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.467 | |
| 3b82 | NAD | Exotoxin A | 2.4.2.36 | 0.466 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.465 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.465 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.464 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.464 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.464 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.463 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.463 | |
| 4eph | 0RK | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.463 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.462 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.462 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.462 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.462 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.462 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.462 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1s7g | NAD | NAD-dependent protein deacylase 2 | / | 0.461 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.461 | |
| 2qe2 | 452 | Polyprotein | / | 0.461 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.461 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.461 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 4e2z | JHZ | Methyltransferase | / | 0.460 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.460 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1sqi | 869 | 4-hydroxyphenylpyruvate dioxygenase | / | 0.459 | |
| 1fwy | UD1 | Bifunctional protein GlmU | / | 0.458 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.458 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.458 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.457 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 1lc3 | NAD | Biliverdin reductase A | 1.3.1.24 | 0.456 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.456 | |
| 4lm4 | JPZ | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.456 | |
| 2g7y | MO9 | Cathepsin S | 3.4.22.27 | 0.455 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.455 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.455 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.455 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.455 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.454 | |
| 3uph | 0C1 | Genome polyprotein | 2.7.7.48 | 0.454 | |
| 4phl | PIL | Phosphodiesterase | / | 0.454 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.454 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.453 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.453 | |
| 2r0p | K2C | Putative FAD-monooxygenase | / | 0.453 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.453 | |
| 4iae | 1DX | Alr2278 protein | / | 0.453 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.453 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.453 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.452 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.452 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.452 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 2zs9 | ADP | Pantothenate kinase | 2.7.1.33 | 0.452 | |
| 4e2x | TYD | Methyltransferase | / | 0.452 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 1qrs | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.451 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.451 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.451 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.451 | |
| 4jq3 | NAP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2pnj | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.450 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.450 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.449 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2e8u | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.449 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 3g4g | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.449 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2r86 | ATP | 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase | / | 0.448 | |
| 4ajd | F04 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4llk | MEW | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4xoq | F42 | Coenzyme F420:L-glutamate ligase | / | 0.448 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.447 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.447 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.447 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 3ox2 | 79X | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.447 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.447 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.447 | |
| 4jey | PLP | Acetylornithine/succinyldiaminopimelate aminotransferase | 2.6.1.11 | 0.447 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.447 | |
| 1zdw | FLV | Prenyltransferase | / | 0.446 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.446 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 4amj | CVD | Beta-1 adrenergic receptor | / | 0.446 | |
| 4bvn | P32 | Beta-1 adrenergic receptor | / | 0.446 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.446 | |
| 4j7g | TRH | PCZA361.3 | / | 0.446 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.445 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.445 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.445 | |
| 3sl6 | JN8 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.445 | |
| 4boe | CLR | Japanin | / | 0.445 | |
| 4e2y | JHZ | Methyltransferase | / | 0.445 | |
| 1p91 | SAM | 23S rRNA (guanine(745)-N(1))-methyltransferase | / | 0.444 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.444 | |
| 3bj8 | COA | Diamine acetyltransferase 1 | / | 0.444 | |
| 3bsy | ACO | UDP-N-acetylbacillosamine N-acetyltransferase | 2.3.1.203 | 0.444 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.444 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.444 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.444 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.444 | |
| 4k4e | K4E | Tankyrase-1 | 2.4.2.30 | 0.444 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.444 | |
| 5ah5 | LSS | Leucine--tRNA ligase | / | 0.444 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.444 | |
| 1e1f | PSG | 4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic | 3.2.1.182 | 0.443 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 1xor | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.443 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.443 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.443 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4a86 | 2AN | Major pollen allergen Bet v 1-A | / | 0.443 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.442 | |
| 1ro6 | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2fq6 | P3F | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.442 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.442 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.442 | |
| 3zbz | OVE | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 4g1f | 0WG | Dipeptidyl peptidase 4 | / | 0.442 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.442 | |
| 5cho | FAD | Flavin reductase | / | 0.442 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3cav | CI2 | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.441 | |
| 3up0 | D7S | aceDAF-12 | / | 0.441 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.441 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.440 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.440 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.440 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.440 | |
| 4e32 | DWN | Methyltransferase | / | 0.440 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.440 |