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 |
|---|---|---|---|
| 4nhk | PD2 | Prolyl 3,4-dihydroxylase TPA1 | 1.14.11 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4nhk | PD2 | Prolyl 3,4-dihydroxylase TPA1 | 1.14.11 | 1.000 | |
| 4nhm | UN9 | Prolyl 3,4-dihydroxylase TPA1 | 1.14.11 | 0.653 | |
| 2qw8 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.496 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.485 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.479 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.478 | |
| 2avi | BTN | Avidin | / | 0.477 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.476 | |
| 3gnv | XNZ | Genome polyprotein | 2.7.7.48 | 0.475 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.474 | |
| 4bbh | YBN | Glycylpeptide N-tetradecanoyltransferase | / | 0.474 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.474 | |
| 3dg8 | RJ6 | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.473 | |
| 4nhy | PD2 | Prolyl 3-hydroxylase OGFOD1 | 1.14.11 | 0.473 | |
| 4xg1 | LLP | Diaminopimelate decarboxylase | / | 0.471 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 1thn | ADP | Anti-sigma F factor | / | 0.469 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.468 | |
| 3g4l | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.467 | |
| 1lkd | BP6 | Biphenyl-2,3-diol 1,2-dioxygenase | 1.13.11.39 | 0.465 | |
| 2acl | L05 | Oxysterols receptor LXR-alpha | / | 0.465 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.465 | |
| 1w06 | W05 | Isopenicillin N synthase | 1.21.3.1 | 0.464 | |
| 2r6j | NDP | Eugenol synthase 1 | 1.1.1.318 | 0.464 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.464 | |
| 4loh | 1SY | Stimulator of interferon genes protein | / | 0.464 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.464 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.463 | |
| 1j3k | WRA | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.463 | |
| 1syn | F89 | Thymidylate synthase | / | 0.463 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.463 | |
| 3nl6 | TPS | Uncharacterized protein | / | 0.463 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.461 | |
| 1tbb | ROL | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.461 | |
| 1y2e | 5DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.459 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.457 | |
| 1nlm | UD1 | UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase | / | 0.456 | |
| 1sbr | VIB | Putative HMP/thiamine-binding protein YkoF | / | 0.456 | |
| 3ddw | 055 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.456 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.455 | |
| 2xy9 | 3ES | Angiotensin-converting enzyme | 3.2.1 | 0.455 | |
| 3c9r | ATP | Thiamine-monophosphate kinase | / | 0.455 | |
| 3ed1 | GA3 | Gibberellin receptor GID1 | / | 0.455 | |
| 3g0c | RUF | Dipeptidyl peptidase 4 | / | 0.455 | |
| 3q1k | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.455 | |
| 4fex | 0TO | Aminoglycoside 3'-phosphotransferase AphA1-IAB | / | 0.455 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.455 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.454 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.454 | |
| 3i12 | ADP | D-alanine--D-alanine ligase A | 6.3.2.4 | 0.454 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.454 | |
| 3uyk | 0CX | Probable NDP-rhamnosyltransferase | / | 0.454 | |
| 1pt5 | ACO | Formyl-CoA:oxalate CoA-transferase | / | 0.453 | |
| 2r2l | PB9 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.453 | |
| 3hxb | BD5 | Geranylgeranyl transferase type-2 subunit beta | 2.5.1.60 | 0.453 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.453 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.453 | |
| 5cb3 | APR | O-acetyl-ADP-ribose deacetylase | / | 0.453 | |
| 3biy | 01K | Histone acetyltransferase p300 | / | 0.452 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.452 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.452 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.452 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.451 | |
| 1dr2 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1tka | N3T | Transketolase 1 | 2.2.1.1 | 0.451 | |
| 2y99 | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | 1.3.1.56 | 0.451 | |
| 1cjk | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cjk | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.450 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 3qiy | QI1 | Botulinum neurotoxin type A | 3.4.24.69 | 0.450 | |
| 1g28 | FMN | PHY3 | / | 0.449 | |
| 1ni1 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.449 | |
| 3lbe | COA | Uncharacterized protein | / | 0.449 | |
| 3wi2 | P98 | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.449 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 4pzs | ACO | Histone acetyltransferase p300 | / | 0.449 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.449 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.448 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.448 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3tq9 | MTX | Dihydrofolate reductase | / | 0.448 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.447 | |
| 1rp7 | TZD | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.447 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.447 | |
| 2izh | BTN | Streptavidin | / | 0.447 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.447 | |
| 3dhc | CYK | N-acyl homoserine lactonase AiiA | 3.1.1.81 | 0.447 | |
| 3hgg | CHD | CmeR | / | 0.447 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.447 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.447 | |
| 4da6 | GA2 | Purine nucleoside phosphorylase DeoD-type | 2.4.2.1 | 0.447 | |
| 4ho8 | THM | Glucose-1-phosphate thymidylyltransferase | / | 0.447 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.446 | |
| 1nzy | BCA | 4-chlorobenzoyl coenzyme A dehalogenase | 3.8.1.7 | 0.446 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.446 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.446 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.446 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.446 | |
| 2ij7 | TPF | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.446 | |
| 3dd1 | 25D | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.446 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 4jq4 | IMN | Aldo-keto reductase family 1 member C2 | / | 0.446 | |
| 1odn | APV | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2z4s | ADP | Chromosomal replication initiator protein DnaA | / | 0.445 | |
| 3hdy | GDU | UDP-galactopyranose mutase | / | 0.445 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.445 | |
| 4zla | BES | Cytosol aminopeptidase | 3.4.11.1 | 0.445 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1eio | GCH | Gastrotropin | / | 0.444 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 1x8b | 824 | Wee1-like protein kinase | 2.7.10.2 | 0.444 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.444 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.444 | |
| 3s7a | 684 | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 3t1a | 5MA | Gag-Pol polyprotein | 2.7.7.49 | 0.444 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 2a2c | ADP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.443 | |
| 2jiz | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.443 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.443 | |
| 3iak | EV1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.443 | |
| 3jzd | NAD | Maleylacetate reductase | / | 0.443 | |
| 3mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.443 | |
| 3qg2 | CP6 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.443 | |
| 3t58 | FAD | Sulfhydryl oxidase 1 | 1.8.3.2 | 0.443 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.443 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.443 | |
| 1fml | RTL | Retinol dehydratase | / | 0.442 | |
| 1gqy | ACP | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.442 | |
| 1ndz | FR5 | Adenosine deaminase | 3.5.4.4 | 0.442 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.442 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.442 | |
| 2qx7 | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.442 | |
| 2z4y | 252 | Geranylgeranyl pyrophosphate synthase | / | 0.442 | |
| 3eej | 53R | Uncharacterized protein | / | 0.442 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.442 | |
| 4b1i | A8P | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.442 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.442 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.442 | |
| 1gve | NAP | Aflatoxin B1 aldehyde reductase member 3 | 1 | 0.441 | |
| 1l8q | ADP | Chromosomal replication initiator protein DnaA | / | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.441 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.441 | |
| 2rtd | BTN | Streptavidin | / | 0.441 | |
| 2vqq | TFG | Histone deacetylase 4 | 3.5.1.98 | 0.441 | |
| 3c6u | M22 | Gag-Pol polyprotein | 2.7.7.49 | 0.441 | |
| 3w0g | W07 | Vitamin D3 receptor | / | 0.441 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4j7g | TRH | PCZA361.3 | / | 0.441 | |
| 4qnu | GEK | tRNA U34 carboxymethyltransferase | / | 0.441 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.441 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.440 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit alpha | 1.2.4.4 | 0.440 | |
| 1umc | TDP | 2-oxoisovalerate dehydrogenase subunit beta | 1.2.4.4 | 0.440 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.440 | |
| 2w6p | OA4 | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 2xvv | 9DN | Serum albumin | / | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.440 | |
| 3v94 | WYQ | Phosphodiesterase | / | 0.440 | |
| 4efu | EFU | Heat shock protein HSP 90-alpha | / | 0.440 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4j7x | SAS | Sepiapterin reductase | 1.1.1.153 | 0.440 | |
| 4xd1 | T3Q | Qdtf | / | 0.440 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.440 | |
| 5ftf | ADP | TPR domain protein | / | 0.440 |