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 |
|---|---|---|---|
| 3rj0 | BLD | Protein BRASSINOSTEROID INSENSITIVE 1 | 2.7.10.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site 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 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.495 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.495 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.492 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.491 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.490 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.490 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.489 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.485 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.484 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.482 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 1y60 | H4M | 5,6,7,8-tetrahydromethanopterin hydro-lyase | 4.2.1.147 | 0.480 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.480 | |
| 3g1r | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.480 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.479 | |
| 1xon | PIL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.479 | |
| 2yne | YNE | Glycylpeptide N-tetradecanoyltransferase | / | 0.479 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.478 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.474 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.472 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.472 | |
| 5bt4 | 2LO | Bromodomain-containing protein 4 | / | 0.472 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.471 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.471 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.470 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.470 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.470 | |
| 2e9a | B28 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | 2.5.1.31 | 0.469 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.469 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.469 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.468 | |
| 3hky | IX6 | Genome polyprotein | 2.7.7.48 | 0.468 | |
| 3zia | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.468 | |
| 4e2z | JHZ | Methyltransferase | / | 0.467 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.466 | |
| 3b82 | NAD | Exotoxin A | 2.4.2.36 | 0.466 | |
| 4n4v | 2GY | Tankyrase-1 | 2.4.2.30 | 0.466 | |
| 1sqi | 869 | 4-hydroxyphenylpyruvate dioxygenase | / | 0.465 | |
| 2zu9 | GDP | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.465 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.465 | |
| 4usq | FAD | Pyridine nucleotide-disulfide oxidoreductase | / | 0.464 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.464 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.463 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.462 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.462 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.462 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.462 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 3dyq | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 3g86 | T18 | Genome polyprotein | 2.7.7.48 | 0.461 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.460 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.460 | |
| 4amj | CVD | Beta-1 adrenergic receptor | / | 0.460 | |
| 4iae | 1DX | Alr2278 protein | / | 0.460 | |
| 4o9c | COA | Acetyl-CoA acetyltransferase | 2.3.1.9 | 0.460 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3gyn | B42 | Genome polyprotein | 2.7.7.48 | 0.458 | |
| 3uzw | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.458 | |
| 4phl | PIL | Phosphodiesterase | / | 0.458 | |
| 2ycz | I32 | Beta-1 adrenergic receptor | / | 0.458 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.457 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.457 | |
| 3v0o | 4GW | Histo-blood group ABO system transferase | / | 0.457 | |
| 4bvn | P32 | Beta-1 adrenergic receptor | / | 0.457 | |
| 4e2y | JHZ | Methyltransferase | / | 0.457 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.457 | |
| 1p8d | CO1 | Oxysterols receptor LXR-beta | / | 0.456 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.456 | |
| 2f98 | NGV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.456 | |
| 3buv | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.456 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.456 | |
| 4e2x | TYD | Methyltransferase | / | 0.456 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.456 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.455 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 3hmv | HBT | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.455 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.455 | |
| 4mka | 2AY | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.454 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 4wo5 | 324 | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.454 | |
| 5d5a | CAU | Beta-2 adrenergic receptor | / | 0.454 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1pj6 | FOL | Dimethylglycine oxidase | 1.5.3.10 | 0.453 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.453 | |
| 4fcb | 0T7 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.453 | |
| 5a8e | XTK | Beta-1 adrenergic receptor | / | 0.453 | |
| 3bj8 | COA | Diamine acetyltransferase 1 | / | 0.452 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4mkb | 28V | Genome polyprotein | 2.7.7.48 | 0.452 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.452 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.451 | |
| 1pj7 | FFO | Dimethylglycine oxidase | 1.5.3.10 | 0.451 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.451 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.451 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3g4i | D71 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.451 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.451 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.450 | |
| 5dbf | NDP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 2cbq | TH2 | Neocarzinostatin | / | 0.449 | |
| 2f38 | 15M | Aldo-keto reductase family 1 member C3 | / | 0.449 | |
| 2giq | NN2 | Genome polyprotein | 2.7.7.48 | 0.449 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.449 | |
| 5std | UNN | Scytalone dehydratase | 4.2.1.94 | 0.449 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.448 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.448 | |
| 3a1l | 2CC | Cytochrome P450 | / | 0.448 | |
| 4bbx | LKF | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.448 | |
| 4iaq | 2GM | 5-hydroxytryptamine receptor 1B | / | 0.448 | |
| 1fdw | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4boe | CLR | Japanin | / | 0.447 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.447 | |
| 4j7g | TRH | PCZA361.3 | / | 0.447 | |
| 1nqv | LMZ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2abj | CBC | Branched-chain-amino-acid aminotransferase, cytosolic | 2.6.1.42 | 0.446 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.446 | |
| 3g58 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.446 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.446 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.446 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.445 | |
| 1zq5 | E04 | Aldo-keto reductase family 1 member C3 | / | 0.445 | |
| 2y0j | AXC | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.445 | |
| 3wav | DWV | Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 | 3.1.4.39 | 0.445 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.445 | |
| 4mk9 | 28R | Genome polyprotein | 2.7.7.48 | 0.445 | |
| 4p9d | TMP | Deoxycytidylate deaminase | / | 0.445 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.445 | |
| 1dig | L37 | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.444 | |
| 1vrq | FON | Subunit alpha of sarocosine oxidase | / | 0.444 | |
| 2bjs | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3gsi | THG | Dimethylglycine oxidase | 1.5.3.10 | 0.444 | |
| 3hxe | BD8 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.444 | |
| 3q9o | NAD | Cholix toxin | 2.4.2.36 | 0.444 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.444 | |
| 4jt8 | 1NR | NAD-dependent protein deacetylase sirtuin-3, mitochondrial | 3.5.1 | 0.444 | |
| 1ejb | INJ | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.443 | |
| 1soj | IBM | cGMP-inhibited 3',5'-cyclic phosphodiesterase B | 3.1.4.17 | 0.443 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 2ym2 | NAP | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.443 | |
| 3b9o | FMN | Alkane monoxygenase | / | 0.443 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.443 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.443 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.443 | |
| 4e32 | DWN | Methyltransferase | / | 0.443 | |
| 4hhy | 15R | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1krr | ACO | Galactoside O-acetyltransferase | 2.3.1.18 | 0.442 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.442 | |
| 1q6n | P90 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.442 | |
| 1tl7 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1tl7 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 3g4k | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 4c2z | 646 | Glycylpeptide N-tetradecanoyltransferase 1 | / | 0.442 | |
| 4fcd | 0T6 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.442 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.442 | |
| 4wlj | IK2 | Kynurenine--oxoglutarate transaminase 1 | 2.6.1.7 | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 1dgf | NDP | Catalase | 1.11.1.6 | 0.441 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 3bgx | MEF | Thymidylate synthase | / | 0.441 | |
| 3up0 | D7S | aceDAF-12 | / | 0.441 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.441 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.441 | |
| 3qak | UKA | Adenosine receptor A2a | / | 0.441 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 2fq6 | P3F | Cystathionine beta-lyase MetC | 4.4.1.8 | 0.440 | |
| 2ouy | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3caq | NDP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.440 | |
| 3u4r | 08F | Genome polyprotein | 2.7.7.48 | 0.440 | |
| 3wd9 | QPC | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.440 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.440 | |
| 4b13 | X25 | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4drh | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.440 | |
| 4drh | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.440 | |
| 4edf | UPG | UDP-glucose 6-dehydrogenase | 1.1.1.22 | 0.440 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.440 |