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 |
|---|---|---|---|
| 4fhd | 0TT | Spore photoproduct lyase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4fhd | 0TT | Spore photoproduct lyase | / | 1.000 | |
| 4rh1 | 0TT | Spore photoproduct lyase | / | 0.711 | |
| 4fhf | 0TT | Spore photoproduct lyase | / | 0.651 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.496 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.485 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.475 | |
| 2bt4 | CA2 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.472 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.470 | |
| 4v2g | ITC | Tetracycline repressor protein class D | / | 0.468 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.467 | |
| 3imx | B84 | Glucokinase | 2.7.1.2 | 0.467 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.466 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.466 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.466 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.465 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 2uxh | QUE | HTH-type transcriptional regulator TtgR | / | 0.462 | |
| 3bi6 | 396 | Wee1-like protein kinase | 2.7.10.2 | 0.462 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.462 | |
| 4z63 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.462 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1pkf | EPD | Epothilone C/D epoxidase | 1.14 | 0.460 | |
| 1u1c | BAU | Uridine phosphorylase | 2.4.2.3 | 0.460 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.460 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.460 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.459 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.459 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.459 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.458 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.458 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.458 | |
| 4z5w | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.458 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.458 | |
| 1u1d | 181 | Uridine phosphorylase | 2.4.2.3 | 0.457 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.457 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4iar | ERM | 5-hydroxytryptamine receptor 1B | / | 0.457 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.457 | |
| 1r2j | FAD | FkbI | / | 0.456 | |
| 1xoq | ROF | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.456 | |
| 2a2d | ANP | N-acetylgalactosamine kinase | 2.7.1.157 | 0.456 | |
| 2c94 | TSF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.456 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.456 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.456 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.455 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.455 | |
| 2e0n | SAH | Precorrin-2 C20-methyltransferase | / | 0.454 | |
| 2in6 | 839 | Wee1-like protein kinase | 2.7.10.2 | 0.454 | |
| 2wo7 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 3f63 | GTX | Glutathione transferase GST1-4 | / | 0.454 | |
| 3ft8 | MOJ | Heat shock protein HSP 90-alpha | / | 0.454 | |
| 4ixd | 1HV | Integrin alpha-L | / | 0.454 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.454 | |
| 2c29 | NAP | Dihydroflavonol 4-reductase | / | 0.453 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.453 | |
| 3d5w | ADP | Serine/threonine-protein kinase PLK | / | 0.453 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.452 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.452 | |
| 3lfe | Z84 | Mitogen-activated protein kinase 14 | / | 0.452 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.452 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.452 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.451 | |
| 3c16 | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 3c16 | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.450 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.450 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2nnl | NAP | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.449 | |
| 2y65 | ADP | Kinesin heavy chain | / | 0.449 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 3gnc | QQQ | Glutaryl-CoA dehydrogenase | / | 0.449 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.449 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 2zcv | NDP | Quinone oxidoreductase 2 | 1.6.5.2 | 0.448 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.448 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.448 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.448 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.448 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.447 | |
| 2vrb | NAP | Triphenylmethane reductase | / | 0.447 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.447 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.447 | |
| 1nqu | RDL | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.446 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.446 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 3o56 | ZG1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.446 | |
| 3up0 | D7S | aceDAF-12 | / | 0.446 | |
| 3v2u | ATP | Protein GAL3 | / | 0.446 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.446 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 1syn | F89 | Thymidylate synthase | / | 0.445 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.445 | |
| 2vtd | LKM | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.445 | |
| 3p5p | A3C | Taxadiene synthase | 4.2.3.17 | 0.445 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.445 | |
| 4k39 | SAM | Anaerobic sulfatase-maturating enzyme | 1.8.98 | 0.445 | |
| 2iod | MYC | Dihydroflavonol 4-reductase | 1.1.1.219 | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 4cdm | FO1 | Deoxyribodipyrimidine photolyase | / | 0.444 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.444 | |
| 1ork | ATC | Tetracycline repressor protein class D | / | 0.443 | |
| 1qv1 | CZH | Obelin | / | 0.443 | |
| 1u1f | 183 | Uridine phosphorylase | 2.4.2.3 | 0.443 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 1ove | 358 | Mitogen-activated protein kinase 14 | / | 0.442 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.442 | |
| 2ivp | ATP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.442 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3itu | IBM | cGMP-dependent 3',5'-cyclic phosphodiesterase | 3.1.4.17 | 0.442 | |
| 3u8l | 09Q | Acetylcholine-binding protein | / | 0.442 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.442 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.442 | |
| 4kp6 | 1S1 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.442 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.442 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.442 | |
| 1bsv | NDP | GDP-L-fucose synthase | / | 0.441 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.441 | |
| 1xuo | LA1 | Integrin alpha-L | / | 0.441 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.441 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 2y05 | RAL | Prostaglandin reductase 1 | / | 0.441 | |
| 3gyu | DL7 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.441 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.441 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.441 | |
| 1cjt | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cjt | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.440 | |
| 1sd2 | MTH | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 1y2k | 7DE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.440 | |
| 1ygj | RMC | Pyridoxal kinase | 2.7.1.35 | 0.440 | |
| 1yqz | COA | Coenzyme A disulfide reductase | / | 0.440 | |
| 2hk9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.440 | |
| 3gmd | 2M3 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4a95 | 9MT | Glycylpeptide N-tetradecanoyltransferase | / | 0.440 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.440 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.440 | |
| 4s1i | PLP | Pyridoxal kinase, putative | / | 0.440 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA2 | 3.6.3 | 0.440 | |
| 4zir | ANP | Energy-coupling factor transporter ATP-binding protein EcfA1 | / | 0.440 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.440 |