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 |
|---|---|---|---|
| 1t6z | RBF | Riboflavin biosynthesis protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1t6z | RBF | Riboflavin biosynthesis protein | / | 1.000 | |
| 1t6y | FMN | Riboflavin biosynthesis protein | / | 0.486 | |
| 1nb9 | RBF | Riboflavin kinase | 2.7.1.26 | 0.483 | |
| 3uhm | RFN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.482 | |
| 2gd2 | CAA | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.481 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.473 | |
| 4fv9 | E71 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.472 | |
| 4hhz | 15S | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.472 | |
| 5k2b | ZMA | Adenosine receptor A2a | / | 0.469 | |
| 1w2x | RCP | Acetyl-CoA carboxylase | / | 0.467 | |
| 1idb | 0DO | Gag-Pol polyprotein | / | 0.466 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.466 | |
| 3tvu | B37 | Acetyl-CoA carboxylase | / | 0.466 | |
| 3tz3 | B36 | Acetyl-CoA carboxylase | / | 0.465 | |
| 3t1t | GDP | Probable gliding protein mglA | / | 0.462 | |
| 4hjo | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.462 | |
| 1p4m | FMN | Riboflavin kinase | 2.7.1.26 | 0.461 | |
| 1r6g | 442 | Thyroid hormone receptor beta | / | 0.461 | |
| 4anv | 751 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.461 | |
| 4id7 | 1G0 | Activated CDC42 kinase 1 | / | 0.461 | |
| 4lxh | C1E | Alpha/beta hydrolase fold | / | 0.461 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.459 | |
| 3aid | ARQ | Gag-Pol polyprotein | 3.4.23.16 | 0.459 | |
| 5k2a | ZMA | Adenosine receptor A2a | / | 0.459 | |
| 3mws | 017 | Pol protein | / | 0.458 | |
| 3sgt | P09 | Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) | / | 0.458 | |
| 3t11 | 3T1 | Gag-Pol polyprotein | 3.4.23.16 | 0.458 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.458 | |
| 4xxv | NAD | 3-isopropylmalate dehydrogenase | / | 0.458 | |
| 4ylh | YE1 | (3,5-dihydroxyphenyl)acetyl-CoA 1,2-dioxygenase | / | 0.458 | |
| 1mb9 | ATP | Carboxyethyl-arginine beta-lactam-synthase | 6.3.3.4 | 0.457 | |
| 2vw5 | BC6 | ATP-dependent molecular chaperone HSP82 | / | 0.457 | |
| 4hjf | C2E | GGDEF family protein | / | 0.457 | |
| 2bx8 | AZQ | Serum albumin | / | 0.456 | |
| 2npa | MMB | Peroxisome proliferator-activated receptor alpha | / | 0.456 | |
| 3w33 | W19 | Epidermal growth factor receptor | 2.7.10.1 | 0.456 | |
| 1m17 | AQ4 | Epidermal growth factor receptor | 2.7.10.1 | 0.455 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2upj | U02 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3w1f | 1O5 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.455 | |
| 1osv | CHC | Bile acid receptor | / | 0.454 | |
| 2v9j | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.454 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.454 | |
| 5iu4 | ZMA | Adenosine receptor A2a | / | 0.454 | |
| 1c6z | ROC | Protease | / | 0.453 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.453 | |
| 3nwx | KVS | Gag-Pol polyprotein | 3.4.23.16 | 0.453 | |
| 3p79 | P79 | Mitogen-activated protein kinase 14 | / | 0.453 | |
| 4fki | 09K | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.453 | |
| 2fle | AI | Protease | / | 0.452 | |
| 2gci | MRR | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.452 | |
| 3gcn | TYR_GLN_PHE | Serine endoprotease DegS | 3.4.21.107 | 0.452 | |
| 4dgg | I76 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.452 | |
| 5jtb | ZMA | Adenosine receptor A2a | / | 0.452 | |
| 1i7i | AZ2 | Peroxisome proliferator-activated receptor gamma | / | 0.451 | |
| 2pym | 1UN | Gag-Pol polyprotein | 3.4.23.16 | 0.451 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.451 | |
| 3img | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 3kb1 | ADP | Iron-sulfur cluster carrier protein | / | 0.451 | |
| 3qzg | X67 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.451 | |
| 4eqc | XR1 | Serine/threonine-protein kinase PAK 1 | 2.7.11.1 | 0.451 | |
| 4l42 | 5FI | Ribosomal protein S6 kinase beta-1 | 2.7.11.1 | 0.451 | |
| 5k2d | ZMA | Adenosine receptor A2a | / | 0.451 | |
| 3f46 | I2C | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.450 | |
| 4gk4 | L90 | Ephrin type-A receptor 3 | 2.7.10.1 | 0.450 | |
| 5uvi | ZMA | Adenosine receptor A2a | / | 0.450 | |
| 1hii | C20 | Gag-Pol polyprotein | / | 0.449 | |
| 1k74 | 544 | Peroxisome proliferator-activated receptor gamma | / | 0.449 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.449 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.449 | |
| 3jyn | NDP | Quinone oxidoreductase | / | 0.449 | |
| 3ndx | RIT | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3nx4 | NAP | Putative oxidoreductase | / | 0.449 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.449 | |
| 3qrm | NK7 | Gag-Pol polyprotein | 3.4.23.16 | 0.449 | |
| 3wv9 | FEG | Hmd co-occurring protein HcgE | / | 0.449 | |
| 4bn1 | ADP | Aurora kinase A | 2.7.11.1 | 0.449 | |
| 4hvh | 19R | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.449 | |
| 4y8w | STR | Steroid 21-hydroxylase | / | 0.449 | |
| 1m2j | APR | NAD-dependent protein deacylase 1 | / | 0.448 | |
| 1ot7 | CHC | Bile acid receptor | / | 0.448 | |
| 2f4b | EHA | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 2pvl | P55 | Casein kinase II subunit alpha | 2.7.11.1 | 0.448 | |
| 2wti | WTI | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.448 | |
| 3w0y | DS4 | Vitamin D3 receptor | / | 0.448 | |
| 4a9m | P9M | Bromodomain-containing protein 2 | / | 0.448 | |
| 4afj | SJJ | Glycogen synthase kinase-3 beta | 2.7.11.26 | 0.448 | |
| 4jib | 1L6 | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.448 | |
| 4xiw | AZM | Carbonic anhydrase, alpha type | / | 0.448 | |
| 1a94 | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.447 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.447 | |
| 3kga | LX9 | MAP kinase-activated protein kinase 2 | 2.7.11.1 | 0.447 | |
| 4bi1 | ZO6 | Dual specificity protein kinase TTK | 2.7.12.1 | 0.447 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.447 | |
| 4i2q | 1BT | Gag-Pol polyprotein | 2.7.7.49 | 0.447 | |
| 5k2c | ZMA | Adenosine receptor A2a | / | 0.447 | |
| 2brh | DFW | Serine/threonine-protein kinase Chk1 | 2.7.11.1 | 0.446 | |
| 2d4e | NAD | 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenaseiheyensis HTE831] | / | 0.446 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.446 | |
| 2obj | VRV | Serine/threonine-protein kinase pim-1 | 2.7.11.1 | 0.446 | |
| 2qi1 | MZ4 | Gag-Pol polyprotein | / | 0.446 | |
| 2xbj | XBJ | Serine/threonine-protein kinase Chk2 | 2.7.11.1 | 0.446 | |
| 3d1x | ROC | Gag-Pol polyprotein | 3.4.23.16 | 0.446 | |
| 3s0o | 50Z | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.446 | |
| 3s56 | ROC | Protease | / | 0.446 | |
| 1hwr | 216 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.445 | |
| 1zdw | FLV | Prenyltransferase | / | 0.445 | |
| 2idw | 017 | Protease | / | 0.445 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2p33 | J07 | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.445 | |
| 3cyl | VIT | Basic phospholipase A2 homolog piratoxin-2 | / | 0.445 | |
| 3eky | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 3mqe | 416 | Prostaglandin G/H synthase 2 | 1.14.99.1 | 0.445 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.444 | |
| 1sxj | ADP | Replication factor C subunit 5 | / | 0.444 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.444 | |
| 2bts | U32 | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.444 | |
| 2hc0 | AB2 | Protease | / | 0.444 | |
| 2i4z | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2v51 | LAB | Actin, alpha skeletal muscle | / | 0.444 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.444 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.444 | |
| 3nu3 | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.444 | |
| 4g6n | EK0 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.444 | |
| 4oj4 | DIF | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 4wq4 | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.444 | |
| 1bdq | IM1 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.443 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 1lwl | DSO | Camphor 5-monooxygenase | 1.14.15.1 | 0.443 | |
| 1odw | 0E8 | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 2o12 | FMN | Chorismate synthase | / | 0.443 | |
| 3i2l | 2NC | Protease | / | 0.443 | |
| 3nwq | 2NC | Gag-Pol polyprotein | 3.4.23.16 | 0.443 | |
| 4bb5 | HD2 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.443 | |
| 5iub | CLR | Adenosine receptor A2a | / | 0.443 | |
| 5iu8 | 6DZ | Adenosine receptor A2a | / | 0.443 | |
| 1bwb | 146 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1k6t | XN1 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 1meu | DMP | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 2gtk | 208 | Peroxisome proliferator-activated receptor gamma | / | 0.442 | |
| 2iw8 | 4SP | Cyclin-dependent kinase 2 | 2.7.11.22 | 0.442 | |
| 2pvh | P19 | Casein kinase II subunit alpha | 2.7.11.1 | 0.442 | |
| 3fhy | ATP | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 3frq | ERY | Erythromycin resistance repressor protein | / | 0.442 | |
| 3pjc | PJC | Tyrosine-protein kinase JAK3 | 2.7.10.2 | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 3w32 | W32 | Epidermal growth factor receptor | 2.7.10.1 | 0.442 | |
| 4e8w | IHA | D-beta-D-heptose 7-phosphate kinase | / | 0.442 | |
| 4jx1 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.441 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.441 | |
| 2r3t | G4G | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.441 | |
| 3gbu | ATP | Uncharacterized sugar kinase PH1459 | 2.7.1 | 0.441 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.441 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3lzv | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.441 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 4upj | U04 | Gag-Pol polyprotein | / | 0.441 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1ebk | 0Q4 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1ivq | 0PX | Gag-Pol polyprotein | / | 0.440 | |
| 1qbr | XV6 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1t3r | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1w5x | BE5 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2wou | ZZF | TGF-beta receptor type-1 | 2.7.11.30 | 0.440 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.440 | |
| 2zno | S44 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 3ekv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3f47 | I2C | 5,10-methenyltetrahydromethanopterin hydrogenase | 1.12.98.2 | 0.440 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.440 | |
| 3ttp | 017 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.440 | |
| 4fv1 | EK4 | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 4gt3 | ATP | Mitogen-activated protein kinase 1 | 2.7.11.24 | 0.440 | |
| 4h1m | 0YJ | Protein-tyrosine kinase 2-beta | 2.7.10.2 | 0.440 | |
| 4h50 | NAP | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.440 | |
| 4lch | 1WN | UDP-3-O-acyl-N-acetylglucosamine deacetylase | / | 0.440 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4o76 | 1M3 | Bromodomain-containing protein 4 | / | 0.440 | |
| 4xum | IMN | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 | |
| 5eyp | LOC | Tubulin beta chain | / | 0.440 | |
| 5iua | 6DX | Adenosine receptor A2a | / | 0.440 | |
| 4z35 | ON9 | Lysophosphatidic acid receptor 1 | / | 0.440 |