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 |
|---|---|---|---|
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ibt | NEA | Modification methylase TaqI | 2.1.1.72 | 1.000 | |
| 1g38 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.594 | |
| 2np7 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.578 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.566 | |
| 3qv2 | SAH | 5-cytosine DNA methyltransferase | / | 0.498 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.489 | |
| 2g1p | SAH | DNA adenine methylase | 2.1.1.72 | 0.487 | |
| 4fr0 | SAM | Arsenic methyltransferase | / | 0.485 | |
| 2azz | TCH | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.484 | |
| 1osv | CHC | Bile acid receptor | / | 0.477 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.477 | |
| 2zwv | SAH | Probable ribosomal RNA small subunit methyltransferase | / | 0.476 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.476 | |
| 3tm5 | SFG | Uncharacterized protein | / | 0.476 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.475 | |
| 4jv6 | 18F | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.475 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.473 | |
| 3g7j | GTX | Glutathione transferase GST1-4 | / | 0.472 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.470 | |
| 2ca0 | PXI | Cytochrome P450 monooxygenase PikC | / | 0.468 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.467 | |
| 3kjr | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.467 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.465 | |
| 1s3z | COA | Aminoglycoside N(6')-acetyltransferase type 1 | / | 0.465 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.465 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.463 | |
| 3vt4 | 5YI | Vitamin D3 receptor | / | 0.463 | |
| 3vt5 | YI2 | Vitamin D3 receptor | / | 0.463 | |
| 4eqg | A5A | Histidine triad nucleotide-binding protein 1 | 3 | 0.463 | |
| 1o1v | TCH | Gastrotropin | / | 0.462 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.461 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.461 | |
| 2yki | YKI | Heat shock protein HSP 90-alpha | / | 0.461 | |
| 3l0l | HC3 | Nuclear receptor ROR-gamma | / | 0.461 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.461 | |
| 3pt6 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.461 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.460 | |
| 4qms | 1N1 | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.459 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.458 | |
| 4ly9 | 1YY | Glucokinase regulatory protein | / | 0.458 | |
| 4rtl | SFG | DNA adenine methylase | 2.1.1.72 | 0.458 | |
| 1nbi | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.457 | |
| 1y5r | C0R | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 2c0o | L2G | Tyrosine-protein kinase HCK | 2.7.10.2 | 0.457 | |
| 4nie | NBH | Nuclear receptor ROR-gamma | / | 0.457 | |
| 4uy6 | SAH | Histidine N-alpha-methyltransferase | / | 0.457 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.456 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 3dmh | SAM | Probable ribosomal RNA small subunit methyltransferase | / | 0.456 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.456 | |
| 2xiq | 5AD | Methylmalonyl-CoA mutase, mitochondrial | / | 0.455 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.455 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3hdm | MMG | Serine/threonine-protein kinase Sgk1 | 2.7.11.1 | 0.455 | |
| 3vt3 | VDX | Vitamin D3 receptor | / | 0.455 | |
| 1nw6 | SFG | Modification methylase RsrI | 2.1.1.72 | 0.454 | |
| 2ch6 | ADP | N-acetyl-D-glucosamine kinase | 2.7.1.59 | 0.454 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.454 | |
| 3sjz | GNP | Translation initiation factor 2 subunit gamma | / | 0.454 | |
| 2ore | SAH | DNA adenine methylase | 2.1.1.72 | 0.453 | |
| 4geb | 0LD | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.453 | |
| 4rto | SFG | DNA adenine methylase | 2.1.1.72 | 0.453 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.452 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.452 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.452 | |
| 4da4 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.452 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.452 | |
| 1guf | NDP | Enoyl-[acyl-carrier-protein] reductase 1, mitochondrial | 1.3.1.10 | 0.451 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 2aqu | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 3kq7 | KQ7 | Mitogen-activated protein kinase 14 | / | 0.451 | |
| 3w0c | 6DS | Vitamin D3 receptor | / | 0.451 | |
| 4tuv | CPZ | Cytochrome P450 119 | 1.14 | 0.451 | |
| 2a7r | 5GP | GMP reductase 2 | / | 0.450 | |
| 2zlc | VDX | Vitamin D3 receptor | / | 0.450 | |
| 3te4 | ACO | Dopamine N-acetyltransferase | / | 0.450 | |
| 3zcn | ATP | Adenosine monophosphate-protein transferase SoFic | 2.7.7.n1 | 0.450 | |
| 1m13 | HYF | Nuclear receptor subfamily 1 group I member 2 | / | 0.449 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.449 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.449 | |
| 2fsv | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.449 | |
| 2ham | C33 | Vitamin D3 receptor | / | 0.449 | |
| 3dey | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 3klm | DHT | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.449 | |
| 4gbe | SAH | DNA adenine methylase | 2.1.1.72 | 0.449 | |
| 4h0n | SAH | Dnmt2 | / | 0.449 | |
| 4y95 | 746 | Tyrosine-protein kinase | / | 0.449 | |
| 1d3h | A26 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.448 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.448 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.448 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3qv1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic | 1.2.1.13 | 0.448 | |
| 4wxx | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.448 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.448 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.448 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.448 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 2fto | CB3 | Thymidylate synthase | / | 0.447 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.447 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.447 | |
| 3ds6 | A17 | Mitogen-activated protein kinase 14 | / | 0.447 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3pb3 | SAH | 16S rRNA (adenine(1408)-N(1))-methyltransferase | 2.1.1.180 | 0.447 | |
| 3qd4 | 3Q6 | 3-phosphoinositide-dependent protein kinase 1 | 2.7.11.1 | 0.447 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.447 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 3s1s | SAH | Restriction endonuclease BpuSI | / | 0.447 | |
| 4isk | 1JY | Thymidylate synthase | / | 0.447 | |
| 4l8u | 9AZ | Serum albumin | / | 0.447 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1kia | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.446 | |
| 1o5r | FR9 | Adenosine deaminase | 3.5.4.4 | 0.446 | |
| 2rkf | AB1 | Pol protein | / | 0.446 | |
| 2vna | NAP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3ioc | A5D | Pantothenate synthetase | 6.3.2.1 | 0.446 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.446 | |
| 4ryv | ZEA | Protein LlR18A | / | 0.446 | |
| 1sh9 | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1skm | SAH | Modification methylase HhaI | 2.1.1.37 | 0.445 | |
| 2h3w | COA | Carnitine O-acetyltransferase | 2.3.1.7 | 0.445 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.445 | |
| 2zl9 | VDA | Vitamin D3 receptor | / | 0.445 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3pm9 | FAD | Putative oxidoreductase | / | 0.445 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.445 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.445 | |
| 3w2s | W2R | Epidermal growth factor receptor | 2.7.10.1 | 0.445 | |
| 4dja | FAD | (6-4) photolyase | / | 0.445 | |
| 4er6 | AW2 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.445 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.445 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.445 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.444 | |
| 1p0h | COA | Mycothiol acetyltransferase | 2.3.1.189 | 0.444 | |
| 1ppj | ANY | Cytochrome b | / | 0.444 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.444 | |
| 1q20 | PLO | Sulfotransferase family cytosolic 2B member 1 | 2.8.2.2 | 0.444 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 2har | OCC | Vitamin D3 receptor | / | 0.444 | |
| 2hmy | SAM | Modification methylase HhaI | 2.1.1.37 | 0.444 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.444 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 2tps | TPS | Thiamine-phosphate synthase | / | 0.444 | |
| 3ekw | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3w5q | 3KL | Vitamin D3 receptor | / | 0.444 | |
| 4aa0 | AA0 | Mitogen-activated protein kinase 14 | / | 0.444 | |
| 4e2b | FMN | Dehydrogenase | / | 0.444 | |
| 4eiy | ZMA | Adenosine receptor A2a | / | 0.444 | |
| 4gb9 | 0WR | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.444 | |
| 4ri1 | ACO | UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase | 2.3.1.202 | 0.444 | |
| 4y93 | 746 | Tyrosine-protein kinase | / | 0.444 | |
| 10mh | SAH | Modification methylase HhaI | 2.1.1.37 | 0.443 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1geu | NAD | Glutathione reductase | 1.8.1.7 | 0.443 | |
| 1k6c | MK1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.443 | |
| 1rfv | ADP | Pyridoxal kinase | 2.7.1.35 | 0.443 | |
| 2q66 | ATP | Poly(A) polymerase | 2.7.7.19 | 0.443 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.443 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.443 | |
| 3lby | SAH | Uncharacterized protein | / | 0.443 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.443 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.443 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.443 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.443 | |
| 4k88 | HFG | Bifunctional glutamate/proline--tRNA ligase | 6.1.1.15 | 0.443 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.442 | |
| 2b0m | 201 | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.442 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.442 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.442 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.442 | |
| 2uuv | FAD | Alkyldihydroxyacetonephosphate synthase | 2.5.1.26 | 0.442 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3oxk | 5GP | Histidine triad nucleotide-binding protein | 3 | 0.442 | |
| 3oxx | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 3tda | PN0 | Cytochrome P450 2D6 | / | 0.442 | |
| 4awo | 99B | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4id7 | 1G0 | Activated CDC42 kinase 1 | / | 0.442 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.441 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.441 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2qd4 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 2ykc | YKC | Heat shock protein HSP 90-alpha | / | 0.441 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.441 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.441 | |
| 3vtb | TKA | Vitamin D3 receptor | / | 0.441 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.441 | |
| 4b4w | 9L9 | Bifunctional protein FolD | / | 0.441 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.441 | |
| 5cvf | ATP | Casein kinase II subunit alpha | 2.7.11.1 | 0.441 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.440 | |
| 1f4f | TP3 | Thymidylate synthase | / | 0.440 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.440 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.440 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.440 | |
| 1qan | SAH | rRNA adenine N-6-methyltransferase | 2.1.1.184 | 0.440 | |
| 1tqp | ATP | RIO-type serine/threonine-protein kinase Rio2 | 2.7.11.1 | 0.440 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.440 | |
| 2gci | MRR | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.440 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.440 | |
| 2x3n | FAD | Probable FAD-dependent monooxygenase | / | 0.440 | |
| 2ykj | YKJ | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.440 | |
| 3kxw | 1ZZ | Saframycin Mx1 synthetase B | / | 0.440 | |
| 3qk0 | QK0 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.440 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.440 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3tm4 | SAM | Uncharacterized protein | / | 0.440 | |
| 3vrt | YS2 | Vitamin D3 receptor | / | 0.440 | |
| 3zlx | 5EZ | Dual specificity mitogen-activated protein kinase kinase 1 | 2.7.12.2 | 0.440 | |
| 4jvf | 17X | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | / | 0.440 | |
| 4ruo | BIV | Vitamin D3 receptor A | / | 0.440 |