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 |
|---|---|---|---|
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3v1s | 0LH | Strictosidine synthase | 4.3.3.2 | 1.000 | |
| 4iyg | 1HU | Strictosidine synthase | 4.3.3.2 | 0.616 | |
| 4jlj | 1NM | Deoxycytidine kinase | 2.7.1.74 | 0.503 | |
| 2fpc | SCG | Strictosidine synthase | 4.3.3.2 | 0.499 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.498 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.497 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.493 | |
| 3nj0 | PYV | Abscisic acid receptor PYL2 | / | 0.492 | |
| 4jlk | 1NO | Deoxycytidine kinase | 2.7.1.74 | 0.492 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.489 | |
| 3ns2 | PYV | Abscisic acid receptor PYL2 | / | 0.478 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.477 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.475 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.473 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.473 | |
| 4jda | A9S | Abscisic acid receptor PYL3 | / | 0.473 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.472 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.471 | |
| 4l4a | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.471 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.467 | |
| 3l6j | Z90 | Alr2278 protein | / | 0.467 | |
| 4j8t | DOG | Uncharacterized PhzA/B-like protein PA3332 | / | 0.467 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 3g49 | 3G4 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.466 | |
| 3ixp | 834 | Ecdysone receptor | / | 0.466 | |
| 1fml | RTL | Retinol dehydratase | / | 0.465 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.465 | |
| 4l4c | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.465 | |
| 3t5i | SER_SER_CMT_FAR | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.464 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 2uxp | CLM | HTH-type transcriptional regulator TtgR | / | 0.463 | |
| 4hnc | 0UT | Mandelate racemase | / | 0.463 | |
| 1e7v | LY2 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.462 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.462 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.461 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.461 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.460 | |
| 3p9t | TCL | Repressor | / | 0.460 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.459 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.459 | |
| 4gnc | ASO | Regucalcin | 3.1.1.17 | 0.459 | |
| 5c1m | CLR | Mu-type opioid receptor | / | 0.459 | |
| 1c7o | PPG | Hemolysin | / | 0.458 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.458 | |
| 1fmj | RTL | Retinol dehydratase | / | 0.457 | |
| 2c6h | PXI | Cytochrome P450 monooxygenase PikC | / | 0.457 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.457 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.457 | |
| 3ov4 | EQU | Steroid Delta-isomerase | 5.3.3.1 | 0.457 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 1a4i | NDP | C-1-tetrahydrofolate synthase, cytoplasmic | 1.5.1.5 | 0.456 | |
| 2acw | UPG | Glycosyltransferase | / | 0.456 | |
| 2cd8 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.456 | |
| 2uxi | G50 | HTH-type transcriptional regulator TtgR | / | 0.456 | |
| 2v4l | ABJ | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.456 | |
| 3cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 3t3q | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.456 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.455 | |
| 2b37 | 8PS | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 2wqp | WQP | Polysialic acid capsule biosynthesis protein SiaC | / | 0.455 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.455 | |
| 4l4b | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 4la7 | A1O | Abscisic acid receptor PYL2 | / | 0.455 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.454 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.454 | |
| 3eon | 341 | Glutaryl-CoA dehydrogenase | / | 0.454 | |
| 3f5p | 741 | Insulin-like growth factor 1 receptor | 2.7.10.1 | 0.454 | |
| 3oji | PYV | Abscisic acid receptor PYL3 | / | 0.454 | |
| 3rbq | GLY_ALA_GLY_ALA_DAO | Protein unc-119 homolog A | / | 0.454 | |
| 4bb6 | HD1 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4g2l | 0WL | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.454 | |
| 4lga | A2O | Abscisic acid receptor PYL2 | / | 0.454 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.453 | |
| 3dha | C6L | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.453 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.453 | |
| 3zk5 | Z18 | Cytochrome P450 monooxygenase PikC | / | 0.453 | |
| 4lrr | CF9 | Thymidylate synthase | / | 0.453 | |
| 1iwi | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.452 | |
| 1kfc | IPL | Tryptophan synthase alpha chain | / | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.452 | |
| 1zga | HMK | Isoflavone 4'-O-methyltransferase | / | 0.452 | |
| 2oax | SNL | Mineralocorticoid receptor | / | 0.452 | |
| 2our | CMP | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.452 | |
| 3jzi | JZL | Biotin carboxylase | 6.3.4.14 | 0.452 | |
| 4pd6 | URI | Nucleoside permease | / | 0.452 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.452 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.451 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.451 | |
| 2pau | D5M | 5'-deoxynucleotidase YfbR | / | 0.451 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 3d75 | NBB | Pheromone-binding protein ASP1 | / | 0.451 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.451 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4jhz | 1KV | Beta-glucuronidase | 3.2.1.31 | 0.451 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.450 | |
| 2m56 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3bxx | QUE | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.450 | |
| 3c14 | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 3c14 | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.450 | |
| 4qa2 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.450 | |
| 1d2s | DHT | Sex hormone-binding globulin | / | 0.449 | |
| 1eio | GCH | Gastrotropin | / | 0.449 | |
| 1enp | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.449 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.449 | |
| 1tez | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.449 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3vtd | TKD | Vitamin D3 receptor | / | 0.449 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.449 | |
| 2w6z | L21 | Biotin carboxylase | 6.3.4.14 | 0.448 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.448 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.448 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.448 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.448 | |
| 3zvu | A8S | Abscisic acid receptor PYR1 | / | 0.448 | |
| 4isg | 1FY | Glucokinase | 2.7.1.2 | 0.448 | |
| 4jqh | 1MF | Alr2278 protein | / | 0.448 | |
| 4lg5 | A1O | Abscisic acid receptor PYL2 | / | 0.448 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.448 | |
| 1geb | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1t86 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 3nx2 | FER | Ferulic acid decarboxylase | / | 0.447 | |
| 3vt8 | YI3 | Vitamin D3 receptor | / | 0.447 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 4czt | CPS | CBL-interacting serine/threonine-protein kinase 23 | 2.7.11.1 | 0.447 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.447 | |
| 1boz | PRD | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 1kij | NOV | DNA gyrase subunit B | / | 0.446 | |
| 1xp9 | AIJ | Estrogen receptor | / | 0.446 | |
| 2npn | SAM | Putative cobalamin synthesis related protein | / | 0.446 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.446 | |
| 3kdi | A8S | Abscisic acid receptor PYL2 | / | 0.446 | |
| 4e5p | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.446 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1u59 | STU | Tyrosine-protein kinase ZAP-70 | 2.7.10.2 | 0.445 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 1wpg | ADP | Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 | 3.6.3.8 | 0.445 | |
| 2b36 | 5PP | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2bkt | RPF | Renin | 3.4.23.15 | 0.445 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.445 | |
| 2uxu | NAR | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 2xsz | ATP | RuvB-like 2 | 3.6.4.12 | 0.445 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.445 | |
| 3nmn | PYV | Abscisic acid receptor PYL1 | / | 0.445 | |
| 3qlz | QLZ | Uncharacterized protein | / | 0.445 | |
| 4c3y | ANB | 3-ketosteroid dehydrogenase | / | 0.445 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4iae | 1DX | Alr2278 protein | / | 0.445 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.445 | |
| 1w22 | NHB | Histone deacetylase 8 | 3.5.1.98 | 0.444 | |
| 1zkl | IBM | High affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A | 3.1.4.53 | 0.444 | |
| 2v59 | LZK | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.444 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.444 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3vt9 | YI4 | Vitamin D3 receptor | / | 0.444 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4b5b | BBE | Glucose-1-phosphate thymidylyltransferase | / | 0.444 | |
| 4bqu | CLR | Japanin | / | 0.444 | |
| 4c9p | CAM | Cytochrome P450 | / | 0.444 | |
| 1ej2 | NAD | Nicotinamide-nucleotide adenylyltransferase | 2.7.7.1 | 0.443 | |
| 1lb9 | DNQ | Glutamate receptor 2 | / | 0.443 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.443 | |
| 2vzm | NRB | Cytochrome P450 monooxygenase PikC | / | 0.443 | |
| 2z97 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3akn | 11D | Fatty acid-binding protein, intestinal | / | 0.443 | |
| 3dyl | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.443 | |
| 3fwf | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 3ibq | ATP | Pyridoxal kinase | / | 0.443 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.443 | |
| 3um5 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.443 | |
| 4xym | COA | Acyl-CoA synthetase (NDP forming) | / | 0.443 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.442 | |
| 1f4e | TPR | Thymidylate synthase | / | 0.442 | |
| 1k7f | IAV | Tryptophan synthase alpha chain | / | 0.442 | |
| 1t85 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2qbo | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 2vn0 | TDZ | Cytochrome P450 2C8 | / | 0.442 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 2xf3 | J01 | Uncharacterized protein | / | 0.442 | |
| 3gkj | HC3 | Niemann-Pick C1 protein | / | 0.442 | |
| 3hf6 | LX0 | Tryptophan 5-hydroxylase 1 | 1.14.16.4 | 0.442 | |
| 3jun | AJD | Phenazine biosynthesis protein A/B | / | 0.442 | |
| 3lxi | CAM | Cytochrome P450 | / | 0.442 | |
| 3ogw | IMN | Lactoperoxidase | 1.11.1.7 | 0.442 | |
| 3ua5 | 06X | Cytochrome P450 2B6 | 1.14.13 | 0.442 | |
| 3w5p | 4OA | Vitamin D3 receptor | / | 0.442 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 4g1z | 0VP | Vitamin D3 receptor A | / | 0.442 | |
| 4ihl | 1F5 | 14-3-3 protein zeta/delta | / | 0.442 | |
| 1cqp | 803 | Integrin alpha-L | / | 0.441 | |
| 1dv2 | ATP | Biotin carboxylase | 6.3.4.14 | 0.441 | |
| 1owl | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.441 | |
| 1ppj | ANY | Cytochrome b | / | 0.441 | |
| 1qkn | RAL | Estrogen receptor beta | / | 0.441 | |
| 1wdk | ACO | 3-ketoacyl-CoA thiolase | / | 0.441 | |
| 2hl0 | A3S | Threonine--tRNA ligase | 6.1.1.3 | 0.441 | |
| 2j62 | GSZ | O-GlcNAcase NagJ | / | 0.441 | |
| 2qo5 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.441 | |
| 3p3e | 3P3 | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.441 | |
| 3q2j | CKI | Aminoglycoside 3'-phosphotransferase | 2.7.1.95 | 0.441 | |
| 3w9r | A8S | Abscisic acid receptor PYL9 | / | 0.441 | |
| 4bid | IE8 | Mitogen-activated protein kinase kinase kinase 5 | 2.7.11.25 | 0.441 | |
| 4bqh | 9VU | UDP-N-acetylglucosamine pyrophosphorylase, putative | / | 0.441 | |
| 4iv4 | 1GS | Estrogen receptor | / | 0.441 | |
| 4qa0 | SHH | Histone deacetylase 8 | 3.5.1.98 | 0.441 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.441 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.441 | |
| 4z34 | ON7 | Lysophosphatidic acid receptor 1 | / | 0.441 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1h36 | R88 | Squalene--hopene cyclase | 4.2.1.129 | 0.440 | |
| 1l2i | ETC | Estrogen receptor | / | 0.440 | |
| 1m9k | 7NI | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.440 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1osv | CHC | Bile acid receptor | / | 0.440 | |
| 2ea4 | F79 | Methionine aminopeptidase 2 | / | 0.440 | |
| 3da2 | 4MD | Carbonic anhydrase 13 | 4.2.1.1 | 0.440 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 3juq | AJD | Phenazine biosynthesis protein A/B | / | 0.440 | |
| 3koo | 24D | Bifunctional epoxide hydrolase 2 | 3.3.2.10 | 0.440 | |
| 3nmh | PYV | Abscisic acid receptor PYL2 | / | 0.440 | |
| 3qpv | ADP | 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 | 2.7.1.105 | 0.440 | |
| 3zku | HCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.440 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.440 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 |